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Changes between Initial Version and Version 1 of Ticket #16079

Timestamp:: Oct 7, 2024, 2:16:58 PM (13 months ago)
Author:: Eric Pettersen
Comment:

Legend:

: Unmodified
: Added
: Removed
: Modified

Ticket #16079
- Property Component Unassigned → Window Toolkit
- Property Owner set to Tom Goddard
- Property Platform → all
- Property Project → ChimeraX
- Property Status new → assigned
- Property Summary ChimeraX bug report submission → Crash on Mac waking from sleep

Ticket #16079 – Description

-              initial
+              v1
  "threads" : 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+Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
+pixel 0.95, shown at level 0.274, step 1, values float32
+Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
+.95, shown at level 2.1, step 1, values float32
+Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
+level 0.32, step 1, values float32
+Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
+.255, step 1, values float32
+Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
+.78, step 1, values float32
+Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
+.78, step 1, values float32
+Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 7 copy as #7, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Log from Fri Sep 6 19:48:00 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_2.cxs
+Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
+.27, shown at level 2.79, step 1, values float32
+Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
+at level 0.155, step 1, values float32
+Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
+#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
+float32
+Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
+shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
+pixel 0.95, shown at level 0.27, step 1, values float32
+Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
+pixel 0.95, shown at level 0.274, step 1, values float32
+Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
+.95, shown at level 2.1, step 1, values float32
+Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
+level 0.32, step 1, values float32
+Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
+.255, step 1, values float32
+Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Log from Fri Sep 6 19:04:03 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
+,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
+,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
+Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
+size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc as #3, grid size
+,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc as #4, grid size
+,440,440, pixel 0.95, shown at level 0.00374, step 2, values float32
+Opened cryosparc_P17_J1207_map_sharp.mrc as #5, grid size 440,440,440, pixel
+.95, shown at level 2.63e-06, step 2, values float32
+Opened cryosparc_P17_J1210_map_sharp.mrc as #6, grid size 440,440,440, pixel
+.95, shown at level 0.000291, step 2, values float32
+Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #7, grid size
+,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
+Opened cryosparc_P17_J1163_006_volume_map.mrc as #8, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #9, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J959_008_volume_map_zflip.mrc as #10, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened Ref3D_job802_run_class001.mrc as #11, grid size 588,588,588, pixel
+.95, shown at level 0.00416, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip as #12, grid size
+,440,440, pixel 0.95, shown at level 2.11, step 1, values float32
+Opened cryosparc_P17_J1207_map_sharp.mrc z flip as #13, grid size 440,440,440,
+pixel 0.95, shown at level 0.02, step 1, values float32
+Opened cryosparc_P17_J1210_map_sharp.mrc z flip as #14, grid size 440,440,440,
+pixel 0.95, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #15, grid size
+,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
+Opened cryosparc_P17_J535_003_volume_map_zflip.mrc as #16, grid size
+,588,588, pixel 0.95, shown at level 0.232, step 1, values float32
+Opened cryosparc_P17_J655_005_volume_map_sharp.mrc as #17, grid size
+,588,588, pixel 0.95, shown at level 0.427, step 1, values float32
+Opened cryosparc_P17_J645_010_volume_map_sharp.mrc as #18, grid size
+,588,588, pixel 0.95, shown at level 0.442, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #19, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #20, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #21, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc copy as #42, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy as #44, grid
+size 440,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #45, grid size
+,588,588, pixel 0.95, shown at level 0.957, step 1, values float32
+Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
+pixel 0.95, shown at level 0.27, step 1, values float32
+Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
+pixel 0.95, shown at level 0.227, step 1, values float32
+Log from Fri Sep 6 16:21:36 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
+,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
+,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
+Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
+size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc as #3, grid size
+,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc as #4, grid size
+,440,440, pixel 0.95, shown at level 0.00374, step 2, values float32
+Opened cryosparc_P17_J1207_map_sharp.mrc as #5, grid size 440,440,440, pixel
+.95, shown at level 2.63e-06, step 2, values float32
+Opened cryosparc_P17_J1210_map_sharp.mrc as #6, grid size 440,440,440, pixel
+.95, shown at level 0.000291, step 2, values float32
+Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #7, grid size
+,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
+Opened cryosparc_P17_J1163_006_volume_map.mrc as #8, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #9, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J959_008_volume_map_zflip.mrc as #10, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened Ref3D_job802_run_class001.mrc as #11, grid size 588,588,588, pixel
+.95, shown at level 0.00416, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip as #12, grid size
+,440,440, pixel 0.95, shown at level 2.11, step 1, values float32
+Opened cryosparc_P17_J1207_map_sharp.mrc z flip as #13, grid size 440,440,440,
+pixel 0.95, shown at level 0.02, step 1, values float32
+Opened cryosparc_P17_J1210_map_sharp.mrc z flip as #14, grid size 440,440,440,
+pixel 0.95, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #15, grid size
+,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
+Opened cryosparc_P17_J535_003_volume_map_zflip.mrc as #16, grid size
+,588,588, pixel 0.95, shown at level 0.232, step 1, values float32
+Opened cryosparc_P17_J655_005_volume_map_sharp.mrc as #17, grid size
+,588,588, pixel 0.95, shown at level 0.427, step 1, values float32
+Opened cryosparc_P17_J645_010_volume_map_sharp.mrc as #18, grid size
+,588,588, pixel 0.95, shown at level 0.442, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #19, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #20, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #21, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc copy as #42, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy as #44, grid
+size 440,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #45, grid size
+,588,588, pixel 0.95, shown at level 0.957, step 1, values float32
+Log from Wed Sep 4 08:32:44 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
+,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
+,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
+Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
+size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc as #3, grid size
+,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc as #4, grid size
+,440,440, pixel 0.95, shown at level 0.00374, step 2, values float32
+Opened cryosparc_P17_J1207_map_sharp.mrc as #5, grid size 440,440,440, pixel
+.95, shown at level 2.63e-06, step 2, values float32
+Opened cryosparc_P17_J1210_map_sharp.mrc as #6, grid size 440,440,440, pixel
+.95, shown at level 0.000291, step 2, values float32
+Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #7, grid size
+,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
+Opened cryosparc_P17_J1163_006_volume_map.mrc as #8, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #9, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J959_008_volume_map_zflip.mrc as #10, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened Ref3D_job802_run_class001.mrc as #11, grid size 588,588,588, pixel
+.95, shown at level 0.00416, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip as #12, grid size
+,440,440, pixel 0.95, shown at level 2.11, step 1, values float32
+Opened cryosparc_P17_J1207_map_sharp.mrc z flip as #13, grid size 440,440,440,
+pixel 0.95, shown at level 0.02, step 1, values float32
+Opened cryosparc_P17_J1210_map_sharp.mrc z flip as #14, grid size 440,440,440,
+pixel 0.95, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #15, grid size
+,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
+Opened cryosparc_P17_J535_003_volume_map_zflip.mrc as #16, grid size
+,588,588, pixel 0.95, shown at level 0.232, step 1, values float32
+Opened cryosparc_P17_J655_005_volume_map_sharp.mrc as #17, grid size
+,588,588, pixel 0.95, shown at level 0.427, step 1, values float32
+Opened cryosparc_P17_J645_010_volume_map_sharp.mrc as #18, grid size
+,588,588, pixel 0.95, shown at level 0.442, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #19, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #20, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #21, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc copy as #42, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Log from Wed Sep 4 05:32:36 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
+,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
+,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
+Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
+size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc as #3, grid size
+,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc as #4, grid size
+,440,440, pixel 0.95, shown at level 0.00374, step 2, values float32
+Opened cryosparc_P17_J1207_map_sharp.mrc as #5, grid size 440,440,440, pixel
+.95, shown at level 2.63e-06, step 2, values float32
+Opened cryosparc_P17_J1210_map_sharp.mrc as #6, grid size 440,440,440, pixel
+.95, shown at level 0.000291, step 2, values float32
+Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #7, grid size
+,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
+Opened cryosparc_P17_J1163_006_volume_map.mrc as #8, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #9, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J959_008_volume_map_zflip.mrc as #10, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened Ref3D_job802_run_class001.mrc as #11, grid size 588,588,588, pixel
+.95, shown at level 0.00416, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip as #12, grid size
+,440,440, pixel 0.95, shown at level 2.11, step 1, values float32
+Opened cryosparc_P17_J1207_map_sharp.mrc z flip as #13, grid size 440,440,440,
+pixel 0.95, shown at level 0.02, step 1, values float32
+Opened cryosparc_P17_J1210_map_sharp.mrc z flip as #14, grid size 440,440,440,
+pixel 0.95, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #15, grid size
+,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
+Log from Tue Sep 3 13:30:10 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
+restore_snapshot for "Volume" returned None
+restore_snapshot for "VolumeSurface" returned None
+restore_snapshot for "Volume" returned None
+restore_snapshot for "VolumeSurface" returned None
+restore_snapshot for "Volume" returned None
+restore_snapshot for "VolumeSurface" returned None
+restore_snapshot for "Volume" returned None
+restore_snapshot for "VolumeSurface" returned None
+restore_snapshot for "Volume" returned None
+restore_snapshot for "VolumeSurface" returned None
+restore_snapshot for "Volume" returned None
+restore_snapshot for "VolumeSurface" returned None
+restore_snapshot for "Volume" returned None
+restore_snapshot for "VolumeSurface" returned None
+restore_snapshot for "Volume" returned None
+restore_snapshot for "VolumeSurface" returned None
+restore_snapshot for "Volume" returned None
+restore_snapshot for "VolumeSurface" returned None
+Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
+,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
+.9, shown at level 0.0185, step 1, values float32
+Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
+.9, shown at level 0.0198, step 1, values float32
+Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
+.9, shown at level 0.0163, step 1, values float32
+Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
+.9, shown at level 0.0136, step 1, values float32
+Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
+,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
+Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
+,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
+Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
+pixel 1.9, shown at level 0.45, step 1, values float32
+Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
+pixel 1.9, shown at level 0.45, step 1, values float32
+Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
+,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
+Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
+,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
+Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
+pixel 1.9, shown at level 0.32, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
+pixel 1.9, shown at level 0.35, step 1, values float32
+Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
+,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
+Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
+pixel 1.9, shown at level 0.32, step 1, values float32
+Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
+pixel 1.9, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
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+Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
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+Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j590_run_it025_class001.mrc as #122, grid size 294,294,294, pixel
+.9, shown at level 0.015, step 1, values float32
+Opened Cl3D_j590_run_it025_class002.mrc as #123, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j590_run_it025_class003.mrc as #124, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j590_run_it025_class004.mrc as #125, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j590_run_it025_class005.mrc as #126, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j590_run_it025_class006.mrc as #127, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
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+Opened Cl3D_j591_run_it025_class001.mrc as #129, grid size 294,294,294, pixel
+.9, shown at level 0.014, step 1, values float32
+Opened Cl3D_j591_run_it025_class002.mrc as #130, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j591_run_it025_class003.mrc as #131, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j591_run_it025_class004.mrc as #132, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j591_run_it025_class005.mrc as #133, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j591_run_it025_class006.mrc as #134, grid size 294,294,294, pixel
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+Opened Cl3D_j591_run_it025_class007.mrc as #135, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J681_volume_map.mrc as #139, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
+,192,192, pixel 2.91, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
+pixel 1.9, shown at level 0.365, step 1, values float32
+Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
+pixel 1.9, shown at level 0.365, step 1, values float32
+Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
+pixel 1.9, shown at level 0.365, step 1, values float32
+Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
+pixel 1.9, shown at level 0.366, step 1, values float32
+Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
+pixel 1.9, shown at level 0.2, step 1, values float32
+Opened cryosparc_P17_J688_007_volume_map.mrc z flip as #151, grid size
+,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
+,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
+Opened cryosparc_P17_J691_008_volume_map.mrc z flip as #153, grid size
+,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
+Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
+,294,294, pixel 1.9, shown at level 0.366, step 1, values float32
+Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
+,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
+,294,294, pixel 1.9, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
+pixel 1.9, shown at level 0.4, step 1, values float32
+Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
+pixel 1.9, shown at level 0.384, step 1, values float32
+Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
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+Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
+pixel 1.9, shown at level 0.351, step 1, values float32
+Opened cryosparc_P17_J709_007_volume_map_sharp.mrc as #158, grid size
+,294,294, pixel 1.9, shown at level 0.338, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
+,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
+,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
+Opened cryosparc_P17_J786_005_volume_map_sharp.mrc as #181, grid size
+,588,588, pixel 0.95, shown at level 0.4, step 1, values float32
+Opened cryosparc_P17_J787_005_volume_map_sharp.mrc as #182, grid size
+,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
+Opened cryosparc_P17_J792_volume_map_sharp.mrc as #183, grid size 520,520,520,
+pixel 0.95, shown at level 0.392, step 1, values float32
+Opened cryosparc_P17_J757_volume_map.mrc as #186, grid size 520,520,520, pixel
+.95, shown at level 0.226, step 1, values float32
+Opened cryosparc_P17_J792_volume_map.mrc as #187, grid size 520,520,520, pixel
+.95, shown at level 0.247, step 1, values float32
+Opened cryosparc_P17_J797_009_volume_map_sharp.mrc as #184, grid size
+,520,520, pixel 0.95, shown at level 0.716, step 1, values float32
+Opened cryosparc_P17_J797_009_volume_map.mrc as #185, grid size 520,520,520,
+pixel 0.95, shown at level 0.31, step 1, values float32
+Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
+.95, shown at level 0.998, step 1, values float32
+Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
+pixel 0.95, shown at level 0.31, step 1, values float32
+Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
+,520,520, pixel 0.95, shown at level 0.6, step 1, values float32
+Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
+pixel 0.95, shown at level 0.301, step 1, values float32
+Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
+,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
+Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
+.95, shown at level 0.1, step 1, values float32
+Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
+pixel 0.95, shown at level 0.348, step 1, values float32
+Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
+,336,336, pixel 1.47, shown at level 0.283, step 1, values float32
+Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
+,336,336, pixel 1.47, shown at level 0.289, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
+pixel 0.95, shown at level 0.196, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
+,588,588, pixel 0.95, shown at level 0.46, step 1, values float32
+Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
+.95, shown at level 0.15, step 1, values float32
+Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
+,588,588, pixel 0.95, shown at level 0.35, step 1, values float32
+Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
+.95, shown at level 0.0845, step 1, values float32
+Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
+,192,192, pixel 2.91, shown at level 0.5, step 1, values float32
+Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
+,588,588, pixel 0.95, shown at level 0.239, step 1, values float32
+Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
+,588,588, pixel 0.95, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
+,520,520, pixel 0.95, shown at level 0.65, step 1, values float32
+Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
+pixel 1.9, shown at level 0.333, step 1, values float32
+Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
+,588,588, pixel 0.95, shown at level 0.158, step 1, values float32
+Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
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+Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
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+Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
+pixel 0.95, shown at level 0.154, step 1, values float32
+Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
+,128,128, pixel 4.36, shown at level 0.9, step 1, values float32
+Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 1, values float32
+Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
+pixel 0.95, shown at level 0.151, step 1, values float32
+Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
+,192,192, pixel 2.91, shown at level 0.348, step 1, values float32
+Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
+,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
+Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
+,128,128, pixel 4.36, shown at level 1.25, step 1, values float32
+Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
+,128,128, pixel 4.36, shown at level 0.8, step 1, values float32
+Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
+.95, shown at level 0.0045, step 1, values float32
+Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
+.95, shown at level 0.0045, step 1, values float32
+Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
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+Opened Ref3D_job506_run_class001_bareNCP.mrc as #224, grid size 588,588,588,
+pixel 0.95, shown at level 0.0045, step 1, values float32
+Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
+pixel 1.9, shown at level 0.35, step 1, values float32
+Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
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+Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
+pixel 1.9, shown at level 0.356, step 1, values float32
+Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc as #225, grid size
+,128,128, pixel 3.27, shown at level 1.6, step 1, values float32
+Opened cryosparc_P17_J981_class_00_00062_volume_sharp.mrc as #228, grid size
+,128,128, pixel 3.27, shown at level 1.82, step 1, values float32
+Opened cryosparc_P17_J967_class_00_final_volume.mrc as #229, grid size
+,192,192, pixel 2.18, shown at level 0.8, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #226, grid size
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+Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #230, grid size
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+Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #231, grid size
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+Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
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+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
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+Opened cryosparc_P17_J864_007_volume_map.mrc as #239, grid size 588,588,588,
+pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
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+Opened cryosparc_P17_J368_007_volume_map.mrc as #244, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J685_007_volume_map.mrc as #245, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J690_006_volume_map.mrc as #246, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J697_006_volume_map.mrc as #247, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J362_007_volume_map.mrc as #248, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J1103_006_volume_map.mrc as #249, grid size 294,294,294,
+pixel 1.9, shown at level 0.358, step 2, values float32
+Opened cryosparc_P17_J1105_008_volume_map.mrc as #250, grid size 294,294,294,
+pixel 1.9, shown at level 0.362, step 2, values float32
+Opened cryosparc_P17_J1106_006_volume_map.mrc as #251, grid size 294,294,294,
+pixel 1.9, shown at level 0.333, step 1, values float32
+Opened cryosparc_P17_J1107_006_volume_map.mrc as #252, grid size 294,294,294,
+pixel 1.9, shown at level 0.34, step 1, values float32
+Log from Tue Jul 30 11:34:25 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
+Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
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+Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
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+Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
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+Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
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+Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
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+Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
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+Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
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+Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
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+Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
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+Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
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+Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
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+Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
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+Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
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+Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
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+Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
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+Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
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+Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
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+Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
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+Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
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+Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
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+Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
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+Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
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+Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
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+Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
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+Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
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+Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
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+Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
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+Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
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+Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 1, values float32
+Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
+pixel 0.95, shown at level 0.151, step 1, values float32
+Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
+,192,192, pixel 2.91, shown at level 0.348, step 1, values float32
+Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
+,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
+Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
+.9, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
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+Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
+,128,128, pixel 4.36, shown at level 0.8, step 1, values float32
+Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
+.95, shown at level 0.0045, step 1, values float32
+Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
+.95, shown at level 0.0045, step 1, values float32
+Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
+level 1, step 1, values float32
+Opened Ref3D_job506_run_class001_bareNCP.mrc as #224, grid size 588,588,588,
+pixel 0.95, shown at level 0.0045, step 1, values float32
+Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
+pixel 1.9, shown at level 0.426, step 2, values float32
+Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
+pixel 1.9, shown at level 0.347, step 1, values float32
+Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
+pixel 1.9, shown at level 0.356, step 1, values float32
+Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc as #225, grid size
+,128,128, pixel 3.27, shown at level 1.6, step 1, values float32
+Opened cryosparc_P17_J981_class_00_00062_volume_sharp.mrc as #228, grid size
+,128,128, pixel 3.27, shown at level 1.82, step 1, values float32
+Opened cryosparc_P17_J967_class_00_final_volume.mrc as #229, grid size
+,192,192, pixel 2.18, shown at level 0.8, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #226, grid size
+,588,588, pixel 0.95, shown at level 0.33, step 1, values float32
+Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #230, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #231, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
+size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map.mrc as #239, grid size 588,588,588,
+pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
+Log from Wed Jul 24 16:21:27 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
+Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
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+Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
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+Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
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+Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
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+Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
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+Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
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+Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
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+Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
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+Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
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+Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
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+Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
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+Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
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+Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
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+Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
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+Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
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+Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
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+Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
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+Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
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+Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
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+Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
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+Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
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+Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
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+Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
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+Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
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+Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
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+Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
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+Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
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+Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
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+Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
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+Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
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+Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
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+Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
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+Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
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+Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
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+Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
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+Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
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+Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
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+Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
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+Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
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+Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
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+Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
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+Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
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+Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
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+Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
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+Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
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+Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
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+Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
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+Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
+,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
+Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
+,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
+Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
+pixel 1.9, shown at level 0.45, step 1, values float32
+Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
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+Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
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+Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
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+Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
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+Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
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+Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
+pixel 1.9, shown at level 0.45, step 1, values float32
+Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
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+Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
+,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
+Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
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+Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
+pixel 1.9, shown at level 0.32, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
+pixel 1.9, shown at level 0.35, step 1, values float32
+Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
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+Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
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+Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
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+Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
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+Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
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+Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
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+Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
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+Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
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+Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
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+Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
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+Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
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+Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
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+Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
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+Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
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+Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
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+Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
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+Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
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+Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
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+Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
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+Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
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+Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
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+Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
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+Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
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+Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
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+Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
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+Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
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+Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
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+Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
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+Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
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+Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
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+Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
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+Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
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+Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
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+Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
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+Opened cryosparc_P17_J690_006_volume_map.mrc as #147, grid size 294,294,294,
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+Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
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+Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
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+Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
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+Opened cryosparc_P17_J688_007_volume_map.mrc z flip as #151, grid size
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+Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
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+Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
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+Opened cryosparc_P17_J697_006_volume_map.mrc as #157, grid size 294,294,294,
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+Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
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+Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
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+Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
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+Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
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+Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
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+Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
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+Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
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+Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
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+Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
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+Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
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+Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
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+Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
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+Opened cryosparc_P17_J712_007_volume_map.mrc as #174, grid size 294,294,294,
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+Opened cryosparc_P17_J709_007_volume_map_sharp.mrc as #158, grid size
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+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
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+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
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+Opened cryosparc_P17_J786_005_volume_map_sharp.mrc as #181, grid size
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+Opened cryosparc_P17_J787_005_volume_map_sharp.mrc as #182, grid size
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+Opened cryosparc_P17_J792_volume_map_sharp.mrc as #183, grid size 520,520,520,
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+Opened cryosparc_P17_J757_volume_map.mrc as #186, grid size 520,520,520, pixel
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+Opened cryosparc_P17_J792_volume_map.mrc as #187, grid size 520,520,520, pixel
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+Opened cryosparc_P17_J797_009_volume_map_sharp.mrc as #184, grid size
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+Opened cryosparc_P17_J797_009_volume_map.mrc as #185, grid size 520,520,520,
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+Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
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+Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
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+Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
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+Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
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+Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
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+Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
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+Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
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+Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
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+Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
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+Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
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+Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
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+Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
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+Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
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+Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
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+Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
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+Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
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+Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
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+Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
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+Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
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+Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
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+Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
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+Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
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+Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
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+Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
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+Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
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+Opened cryosparc_P17_J857_mask.mrc as #160, grid size 588,588,588, pixel 0.95,
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+Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
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+Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
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+Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
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+Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
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+Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
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+Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
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+Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
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+Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
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+Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
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+Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
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+Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
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+Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
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+Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
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+Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
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+Opened Ref3D_job506_run_class001_bareNCP.mrc as #224, grid size 588,588,588,
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+Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
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+Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
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+Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
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+Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc as #225, grid size
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+Opened cryosparc_P17_J981_class_00_00062_volume_sharp.mrc as #228, grid size
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+Opened cryosparc_P17_J967_class_00_final_volume.mrc as #229, grid size
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+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #226, grid size
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+Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #230, grid size
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+Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #231, grid size
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+Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
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+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
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+Opened cryosparc_P17_J864_007_volume_map.mrc as #239, grid size 588,588,588,
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+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
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+Log from Thu Jul 18 19:11:33 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
+© 2016-2023 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
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+Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
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+Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
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+Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
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+Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
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+Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
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+Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
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+Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
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+Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
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+Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
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+Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
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+Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
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+Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
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+Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
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+Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
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+Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
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+Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
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+Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
+pixel 0.95, shown at level 0.31, step 1, values float32
+Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
+,520,520, pixel 0.95, shown at level 0.6, step 1, values float32
+Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
+pixel 0.95, shown at level 0.301, step 1, values float32
+Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
+,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
+Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
+.95, shown at level 0.1, step 1, values float32
+Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
+pixel 0.95, shown at level 0.348, step 1, values float32
+Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
+,336,336, pixel 1.47, shown at level 0.283, step 1, values float32
+Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
+,336,336, pixel 1.47, shown at level 0.289, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
+pixel 0.95, shown at level 0.196, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
+,588,588, pixel 0.95, shown at level 0.46, step 1, values float32
+Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
+.95, shown at level 0.15, step 1, values float32
+Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
+,588,588, pixel 0.95, shown at level 0.35, step 1, values float32
+Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
+.95, shown at level 0.0845, step 1, values float32
+Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
+,192,192, pixel 2.91, shown at level 0.5, step 1, values float32
+Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
+,588,588, pixel 0.95, shown at level 0.239, step 1, values float32
+Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
+,588,588, pixel 0.95, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
+,520,520, pixel 0.95, shown at level 0.55, step 1, values float32
+Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
+pixel 1.9, shown at level 0.333, step 1, values float32
+Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
+,588,588, pixel 0.95, shown at level 0.158, step 1, values float32
+Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
+.95, shown at level 0.08, step 1, values float32
+Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
+.95, shown at level 0.15, step 1, values float32
+Opened cryosparc_P17_J857_mask.mrc as #160, grid size 588,588,588, pixel 0.95,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
+pixel 0.95, shown at level 0.154, step 1, values float32
+Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
+,128,128, pixel 4.36, shown at level 0.9, step 1, values float32
+Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 1, values float32
+Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
+pixel 0.95, shown at level 0.151, step 1, values float32
+Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
+,192,192, pixel 2.91, shown at level 0.348, step 1, values float32
+Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
+,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
+Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
+.9, shown at level 0.33, step 1, values float32
+Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
+.9, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
+,128,128, pixel 4.36, shown at level 1.25, step 1, values float32
+Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
+,128,128, pixel 4.36, shown at level 0.8, step 1, values float32
+Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
+.95, shown at level 0.0045, step 1, values float32
+Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
+.95, shown at level 0.0045, step 1, values float32
+Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
+level 1, step 1, values float32
+Opened Ref3D_job506_run_class001_bareNCP.mrc as #224, grid size 588,588,588,
+pixel 0.95, shown at level 0.0045, step 1, values float32
+Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
+pixel 1.9, shown at level 0.426, step 2, values float32
+Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
+pixel 1.9, shown at level 0.347, step 1, values float32
+Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
+pixel 1.9, shown at level 0.356, step 1, values float32
+Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc as #225, grid size
+,128,128, pixel 3.27, shown at level 1.6, step 1, values float32
+Opened cryosparc_P17_J981_class_00_00062_volume_sharp.mrc as #228, grid size
+,128,128, pixel 3.27, shown at level 1.82, step 1, values float32
+Opened cryosparc_P17_J967_class_00_final_volume.mrc as #229, grid size
+,192,192, pixel 2.18, shown at level 0.8, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #226, grid size
+,588,588, pixel 0.95, shown at level 0.33, step 1, values float32
+Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #230, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #231, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
+size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map.mrc as #239, grid size 588,588,588,
+pixel 0.95, shown at level 0.153, step 1, values float32
+Log from Thu Jul 18 17:16:17 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
+© 2016-2023 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
+Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
+,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
+.9, shown at level 0.0185, step 1, values float32
+Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
+.9, shown at level 0.0198, step 1, values float32
+Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
+.9, shown at level 0.0163, step 1, values float32
+Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
+.9, shown at level 0.0136, step 1, values float32
+Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
+,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
+Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
+,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
+Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
+pixel 1.9, shown at level 0.45, step 1, values float32
+Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
+pixel 1.9, shown at level 0.45, step 1, values float32
+Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
+,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
+Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
+,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
+Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
+pixel 1.9, shown at level 0.32, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
+pixel 1.9, shown at level 0.35, step 1, values float32
+Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
+,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
+Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
+pixel 1.9, shown at level 0.32, step 1, values float32
+Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
+pixel 1.9, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
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+Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
+.9, shown at level 0.0146, step 1, values float32
+Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j590_run_it025_class001.mrc as #122, grid size 294,294,294, pixel
+.9, shown at level 0.015, step 1, values float32
+Opened Cl3D_j590_run_it025_class002.mrc as #123, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j590_run_it025_class003.mrc as #124, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j590_run_it025_class004.mrc as #125, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j590_run_it025_class005.mrc as #126, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j590_run_it025_class006.mrc as #127, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
+.9, shown at level 0.014, step 1, values float32
+Opened Cl3D_j591_run_it025_class001.mrc as #129, grid size 294,294,294, pixel
+.9, shown at level 0.014, step 1, values float32
+Opened Cl3D_j591_run_it025_class002.mrc as #130, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j591_run_it025_class003.mrc as #131, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j591_run_it025_class004.mrc as #132, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j591_run_it025_class005.mrc as #133, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j591_run_it025_class006.mrc as #134, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j591_run_it025_class007.mrc as #135, grid size 294,294,294, pixel
+.9, shown at level 0.014, step 1, values float32
+Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
+.9, shown at level 0.314, step 1, values float32
+Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J681_volume_map.mrc as #139, grid size 294,294,294, pixel
+.9, shown at level 0.294, step 1, values float32
+Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J685_007_volume_map.mrc as #141, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
+,192,192, pixel 2.91, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
+pixel 1.9, shown at level 0.365, step 1, values float32
+Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
+pixel 1.9, shown at level 0.365, step 1, values float32
+Opened cryosparc_P17_J690_006_volume_map.mrc as #147, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
+pixel 1.9, shown at level 0.365, step 1, values float32
+Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
+pixel 1.9, shown at level 0.366, step 1, values float32
+Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
+pixel 1.9, shown at level 0.2, step 1, values float32
+Opened cryosparc_P17_J688_007_volume_map.mrc z flip as #151, grid size
+,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
+,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
+Opened cryosparc_P17_J691_008_volume_map.mrc z flip as #153, grid size
+,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
+Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
+,294,294, pixel 1.9, shown at level 0.366, step 1, values float32
+Opened cryosparc_P17_J697_006_volume_map.mrc as #157, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
+,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
+,294,294, pixel 1.9, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
+pixel 1.9, shown at level 0.4, step 1, values float32
+Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
+pixel 1.9, shown at level 0.384, step 1, values float32
+Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
+.91, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
+pixel 1.9, shown at level 0.351, step 1, values float32
+Opened cryosparc_P17_J712_007_volume_map.mrc as #174, grid size 294,294,294,
+pixel 1.9, shown at level 0.329, step 1, values float32
+Opened cryosparc_P17_J709_007_volume_map_sharp.mrc as #158, grid size
+,294,294, pixel 1.9, shown at level 0.338, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
+,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
+,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
+Opened cryosparc_P17_J786_005_volume_map_sharp.mrc as #181, grid size
+,588,588, pixel 0.95, shown at level 0.4, step 1, values float32
+Opened cryosparc_P17_J787_005_volume_map_sharp.mrc as #182, grid size
+,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
+Opened cryosparc_P17_J792_volume_map_sharp.mrc as #183, grid size 520,520,520,
+pixel 0.95, shown at level 0.392, step 1, values float32
+Opened cryosparc_P17_J757_volume_map.mrc as #186, grid size 520,520,520, pixel
+.95, shown at level 0.226, step 1, values float32
+Opened cryosparc_P17_J792_volume_map.mrc as #187, grid size 520,520,520, pixel
+.95, shown at level 0.247, step 1, values float32
+Opened cryosparc_P17_J797_009_volume_map_sharp.mrc as #184, grid size
+,520,520, pixel 0.95, shown at level 0.716, step 1, values float32
+Opened cryosparc_P17_J797_009_volume_map.mrc as #185, grid size 520,520,520,
+pixel 0.95, shown at level 0.31, step 1, values float32
+Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
+.95, shown at level 0.998, step 1, values float32
+Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
+pixel 0.95, shown at level 0.31, step 1, values float32
+Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
+,520,520, pixel 0.95, shown at level 0.6, step 1, values float32
+Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
+pixel 0.95, shown at level 0.301, step 1, values float32
+Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
+,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
+Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
+.95, shown at level 0.1, step 1, values float32
+Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
+pixel 0.95, shown at level 0.348, step 1, values float32
+Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
+,336,336, pixel 1.47, shown at level 0.283, step 1, values float32
+Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
+,336,336, pixel 1.47, shown at level 0.289, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
+pixel 0.95, shown at level 0.196, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
+,588,588, pixel 0.95, shown at level 0.46, step 1, values float32
+Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
+.95, shown at level 0.15, step 1, values float32
+Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
+,588,588, pixel 0.95, shown at level 0.35, step 1, values float32
+Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
+.95, shown at level 0.0845, step 1, values float32
+Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
+,192,192, pixel 2.91, shown at level 0.5, step 1, values float32
+Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
+,588,588, pixel 0.95, shown at level 0.239, step 1, values float32
+Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
+,588,588, pixel 0.95, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
+,520,520, pixel 0.95, shown at level 0.55, step 1, values float32
+Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
+pixel 1.9, shown at level 0.333, step 1, values float32
+Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
+,588,588, pixel 0.95, shown at level 0.158, step 1, values float32
+Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
+.95, shown at level 0.08, step 1, values float32
+Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
+.95, shown at level 0.15, step 1, values float32
+Opened cryosparc_P17_J857_mask.mrc as #160, grid size 588,588,588, pixel 0.95,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
+pixel 0.95, shown at level 0.154, step 1, values float32
+Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
+,128,128, pixel 4.36, shown at level 0.9, step 1, values float32
+Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 1, values float32
+Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
+pixel 0.95, shown at level 0.151, step 1, values float32
+Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
+,192,192, pixel 2.91, shown at level 0.348, step 1, values float32
+Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
+,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
+Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
+.9, shown at level 0.33, step 1, values float32
+Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
+.9, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
+,128,128, pixel 4.36, shown at level 1.25, step 1, values float32
+Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
+,128,128, pixel 4.36, shown at level 0.8, step 1, values float32
+Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
+.95, shown at level 0.0045, step 1, values float32
+Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
+.95, shown at level 0.0045, step 1, values float32
+Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
+level 1, step 1, values float32
+Opened Ref3D_job506_run_class001_bareNCP.mrc as #224, grid size 588,588,588,
+pixel 0.95, shown at level 0.0045, step 1, values float32
+Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
+pixel 1.9, shown at level 0.426, step 2, values float32
+Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
+pixel 1.9, shown at level 0.347, step 1, values float32
+Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
+pixel 1.9, shown at level 0.356, step 1, values float32
+Log from Thu Jul 11 13:31:37 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
+© 2016-2023 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes_ref.cxs
+restore_snapshot for "Volume" returned None
+restore_snapshot for "VolumeSurface" returned None
+Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
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+Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
+pixel 1.9, shown at level 0.359, step 1, values float32
+Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
+.91, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J710_008_volume_map.mrc as #173, grid size 294,294,294,
+pixel 1.9, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J712_007_volume_map.mrc as #174, grid size 294,294,294,
+pixel 1.9, shown at level 0.2, step 1, values float32
+Opened cryosparc_P17_J711_009_volume_map.mrc as #175, grid size 294,294,294,
+pixel 1.9, shown at level 0.2, step 1, values float32
+Opened cryosparc_P17_J716_mask.mrc as #176, grid size 294,294,294, pixel 1.9,
+shown at level 1, step 1, values float32
+Log from Fri Jun 21 11:35:11 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
+© 2016-2023 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
+Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
+,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
+.9, shown at level 0.0185, step 1, values float32
+Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
+.9, shown at level 0.0198, step 1, values float32
+Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
+.9, shown at level 0.0163, step 1, values float32
+Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
+.9, shown at level 0.0136, step 1, values float32
+Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
+,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
+Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
+,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
+Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
+pixel 1.9, shown at level 0.45, step 1, values float32
+Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
+pixel 1.9, shown at level 0.45, step 1, values float32
+Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
+,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
+Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
+,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
+Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
+pixel 1.9, shown at level 0.32, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
+pixel 1.9, shown at level 0.35, step 1, values float32
+Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
+,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
+Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
+pixel 1.9, shown at level 0.32, step 1, values float32
+Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
+pixel 1.9, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
+.9, shown at level 0.0146, step 1, values float32
+Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+Log from Tue Jun 11 16:35:40 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
+© 2016-2023 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
+Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
+,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
+.9, shown at level 0.0185, step 1, values float32
+Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
+.9, shown at level 0.0198, step 1, values float32
+Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
+.9, shown at level 0.0163, step 1, values float32
+Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
+.9, shown at level 0.0136, step 1, values float32
+Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
+,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
+Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
+,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
+Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
+pixel 1.9, shown at level 0.45, step 1, values float32
+Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
+pixel 1.9, shown at level 0.45, step 1, values float32
+Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
+,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
+Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
+,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
+Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
+pixel 1.9, shown at level 0.32, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
+pixel 1.9, shown at level 0.35, step 1, values float32
+Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
+,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
+Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
+pixel 1.9, shown at level 0.32, step 1, values float32
+Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
+pixel 1.9, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
+.9, shown at level 0.0146, step 1, values float32
+Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
+.9, shown at level 0.0156, step 2, values float32
+Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
+.9, shown at level 0.0158, step 2, values float32
+Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
+.9, shown at level 0.0195, step 2, values float32
+Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
+.9, shown at level 0.0161, step 2, values float32
+Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
+.9, shown at level 0.0197, step 2, values float32
+Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
+.9, shown at level 0.0161, step 2, values float32
+Log from Mon Jun 3 09:50:12 2024 Startup Messages
+---
+note | available bundle cache has not been initialized yet
+UCSF ChimeraX version: 1.7.1 (2024-01-23)
+© 2016-2023 Regents of the University of California. All rights reserved.
+How to cite UCSF ChimeraX
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class001.mrc
+Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
+.9, shown at level 0.0106, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class002.mrc
+Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class003.mrc
+Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
+.9, shown at level 0.0124, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class004.mrc
+Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
+.9, shown at level 0.0133, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class005.mrc
+Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class006.mrc
+Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+> volume all step 1
+> hide #!1 models
+> hide #!2 models
+> hide #!3 models
+> hide #!4 models
+> hide #!5 models
+> hide #!6 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class001.mrc
+Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
+.9, shown at level 0.0153, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class002.mrc
+Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
+.9, shown at level 0.0105, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class003.mrc
+Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
+.9, shown at level 0.0136, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class004.mrc
+Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
+.9, shown at level 0.0132, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class005.mrc
+Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
+.9, shown at level 0.0142, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class006.mrc
+Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
+.9, shown at level 0.0149, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class001.mrc
+Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
+.9, shown at level 0.0144, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class002.mrc
+Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
+.9, shown at level 0.014, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class003.mrc
+Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
+.9, shown at level 0.0161, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class004.mrc
+Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
+.9, shown at level 0.0153, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class005.mrc
+Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
+.9, shown at level 0.0143, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class006.mrc
+Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
+.9, shown at level 0.014, step 2, values float32
+> hide #!7 models
+> hide #!8 models
+> hide #!9 models
+> hide #!10 models
+> hide #!11 models
+> hide #!12 models
+> hide #!13 models
+> hide #!14 models
+> hide #!15 models
+> hide #!16 models
+> hide #!17 models
+> hide #!18 models
+> volume all step 1
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job417_run_class001.mrc
+Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
+shown at level 0.0163, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/postprocess_masked_job423.mrc
+Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
+shown at level 0.0162, step 2, values float32
+> hide #!19 models
+> volume #19 step 1
+> volume #20 step 1
+> hide #!20 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J368_007_volume_map_sharp.mrc
+Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
+,294,294, pixel 1.9, shown at level 0.362, step 2, values float32
+> volume #21 step 1
+> volume #21 level 0.4566
+> volume #21 level 0.421
+> volume #21 level 0.4151
+> show #!19 models
+> hide #!19 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
+> show #!13 models
+> hide #!13 models
+> show #!14 models
+> hide #!14 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!15 models
+> show #!3 models
+> hide #!3 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!4 models
+> hide #!4 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!13 models
+> hide #!13 models
+> show #!14 models
+> hide #!14 models
+> show #!15 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> hide #!15 models
+> show #!7 models
+> hide #!7 models
+> show #!8 models
+> show #!10 models
+> hide #!10 models
+> hide #!8 models
+> show #!7 models
+> show #!9 models
+> volume #7 level 0.01497
+> volume #9 level 0.01231
+> show #!10 models
+> hide #!10 models
+> show #!11 models
+> show #!12 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class001.mrc
+Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
+.9, shown at level 0.0146, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class002.mrc
+Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
+.9, shown at level 0.0139, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class003.mrc
+Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
+.9, shown at level 0.0161, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class004.mrc
+Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class005.mrc
+Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
+.9, shown at level 0.014, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class006.mrc
+Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
+.9, shown at level 0.0181, step 2, values float32
+> hide #!7 models
+> hide #!9 models
+> hide #!11 models
+> hide #!12 models
+> volume all step 1
+> hide #!23 models
+> hide #!24 models
+> hide #!25 models
+> hide #!26 models
+> hide #!27 models
+> volume #22 level 0.01345
+> volume #22 level 0.0119
+> volume #23 level 0.01121
+> volume #24 level 0.01399
+> volume #24 level 0.01119
+> volume #24 level 0.01287
+> volume #25 level 0.01349
+> hide #!25 models
+> show #!26 models
+> volume #26 level 0.01133
+> hide #!26 models
+> show #!27 models
+> volume #27 level 0.01296
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!2 models
+> hide #!3 models
+> show #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!4 models
+> hide #!2 models
+> volume #4 level 0.01157
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> hide #!4 models
+> hide #!2 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> show #!3 models
+> show #!4 models
+> show #!5 models
+> show #!6 models
+> hide #!2 models
+> hide #!3 models
+> hide #!4 models
+> hide #!5 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!5 models
+> hide #!5 models
+> show #!4 models
+> hide #!4 models
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> hide #!2 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job559/Cl3D_j559_run_it025_class001.mrc
+Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
+.9, shown at level 0.0155, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job559/Cl3D_j559_run_it025_class002.mrc
+Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
+.9, shown at level 0.0155, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job559/Cl3D_j559_run_it025_class003.mrc
+Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
+.9, shown at level 0.0194, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job559/Cl3D_j559_run_it025_class004.mrc
+Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
+.9, shown at level 0.0153, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job560/Cl3D_j560_run_it025_class001.mrc
+Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
+.9, shown at level 0.0156, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job560/Cl3D_j560_run_it025_class002.mrc
+Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
+.9, shown at level 0.0153, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job560/Cl3D_j560_run_it025_class003.mrc
+Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
+.9, shown at level 0.0161, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job560/Cl3D_j560_run_it025_class004.mrc
+Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
+.9, shown at level 0.0189, step 2, values float32
+> volume all step 1
+> hide #!29 models
+> hide #!30 models
+> hide #!31 models
+> hide #!32 models
+> hide #!33 models
+> hide #!34 models
+> hide #!35 models
+> volume #28 level 0.01275
+> volume #28 level 0.01205
+> volume #28 level 0.01231
+> volume #29 level 0.01315
+> volume #29 level 0.013
+> volume #30 level 0.01741
+> volume #31 level 0.01451
+> volume #31 level 0.01487
+> volume #32 level 0.01315
+> volume #33 level 0.01302
+> volume #34 level 0.01352
+> volume #35 level 0.01616
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job561/Cl3D_j561_run_it025_class001.mrc
+Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
+.9, shown at level 0.0153, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job561/Cl3D_j561_run_it025_class002.mrc
+Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
+.9, shown at level 0.0162, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job561/Cl3D_j561_run_it025_class003.mrc
+Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job569/Cl3D_j569_run_it025_class001.mrc
+Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
+.9, shown at level 0.0155, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job569/Cl3D_j569_run_it025_class002.mrc
+Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
+.9, shown at level 0.0162, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job569/Cl3D_j569_run_it025_class003.mrc
+Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
+.9, shown at level 0.0152, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job569/Cl3D_j569_run_it025_class004.mrc
+Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
+.9, shown at level 0.0168, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job569/Cl3D_j569_run_it025_class005.mrc
+Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
+.9, shown at level 0.0159, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class001.mrc
+Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
+.9, shown at level 0.0155, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class002.mrc
+Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
+.9, shown at level 0.0187, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class003.mrc
+Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
+.9, shown at level 0.0159, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class004.mrc
+Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
+.9, shown at level 0.016, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class005.mrc
+Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
+.9, shown at level 0.0153, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class006.mrc
+Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
+.9, shown at level 0.0158, step 2, values float32
+> volume all step 1
+> hide #!49 models
+> hide #!48 models
+> hide #!47 models
+> hide #!46 models
+> hide #!45 models
+> hide #!44 models
+> hide #!43 models
+> hide #!42 models
+> hide #!41 models
+> hide #!40 models
+> hide #!39 models
+> hide #!38 models
+> hide #!37 models
+> hide #!36 models
+> show #!36 models
+> hide #!36 models
+> show #!36 models
+> show #!37 models
+> show #!38 models
+> volume #36 level 0.013
+> volume #37 level 0.013
+> volume #38 level 0.013
+> volume #39 level 0.013
+> volume #40 level 0.013
+> hide #!40 models
+> show #!41 models
+> volume #41 level 0.013
+> show #!40 models
+> hide #!40 models
+> show #!39 models
+> hide #!39 models
+> show #!40 models
+> hide #!40 models
+> hide #!41 models
+> show #!41 models
+> hide #!41 models
+> show #!42 models
+> volume #42 level 0.013
+> hide #!42 models
+> show #!43 models
+> volume #43 level 0.013
+> volume #43 level 0.012
+> volume #44 level 0.013
+> volume #45 level 0.013
+> volume #46 level 0.013
+> volume #47 level 0.013
+> volume #48 level 0.013
+> volume #49 level 0.013
+> show #!44 models
+> hide #!49 models
+> show #!45 models
+> hide #!45 models
+> show #!46 models
+> hide #!46 models
+> show #!47 models
+> hide #!47 models
+> show #!48 models
+> hide #!48 models
+> show #!49 models
+> hide #!49 models
+> show #!48 models
+> hide #!48 models
+> hide #!44 models
+> show #!43 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!43 models
+> hide #!42 models
+> show #!40 models
+> hide #!40 models
+> show #!39 models
+> show #!38 models
+> hide #!38 models
+> hide #!39 models
+> show #!49 models
+> hide #!49 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job542/Cl3D_job542_run_it025_class001.mrc
+Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
+.9, shown at level 0.0156, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job542/Cl3D_job542_run_it025_class002.mrc
+Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job542/Cl3D_job542_run_it025_class003.mrc
+Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
+.9, shown at level 0.0189, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job545/Cl3D_job545_run_it025_class001.mrc
+Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
+.9, shown at level 0.0193, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job545/Cl3D_job545_run_it025_class002.mrc
+Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
+.9, shown at level 0.0155, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job545/Cl3D_job545_run_it025_class003.mrc
+Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+> volume all step 1
+> hide #!51 models
+> hide #!52 models
+> hide #!53 models
+> hide #!54 models
+> hide #!55 models
+> volume #50 level 0.013
+> show #!51 models
+> volume #51 level 0.013
+> volume all level 0.013
+> hide #!51 models
+> hide #!50 models
+> show #!52 models
+> hide #!52 models
+> show #!53 models
+> hide #!53 models
+> show #!50 models
+> show #!51 models
+> show #!52 models
+> hide #!52 models
+> show #!52 models
+> hide #!51 models
+> hide #!50 models
+> hide #!52 models
+> show #!51 models
+> show #!50 models
+> hide #!51 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> volume #50 level 0.012
+> show #!13 models
+> hide #!13 models
+> show #!14 models
+> hide #!14 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> ui tool show "Fit in Map"
+> fitmap #50 inMap #15
+Fit map Cl3D_job542_run_it025_class001.mrc in map
+Cl3D_job411_run_it025_class003.mrc using 342972 points
+correlation = 0.9888, correlation about mean = 0.813, overlap = 133.4
+steps = 68, shift = 1.95, angle = 0.993 degrees
+Position of Cl3D_job542_run_it025_class001.mrc (#50) relative to
+Cl3D_job411_run_it025_class003.mrc (#15) coordinates:
+Matrix rotation and translation
+.99987080 0.01439337 0.00715694 -5.19984751
+-0.01434662 0.99987569 -0.00654060 6.68005810
+-0.00725019 0.00643707 0.99995300 -1.28059948
+Axis 0.37432567 0.41555671 -0.82897100
+Axis point 407.25464445 414.10389399 0.00000000
+Rotation angle (degrees) 0.99325686
+Shift along axis 1.89108642
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> hide #!50 models
+> show #!53 models
+> hide #!53 models
+> show #!54 models
+> hide #!54 models
+> show #!55 models
+> hide #!55 models
+> show #!54 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> volume #54 level 0.012
+> hide #!54 models
+> show #!54 models
+> hide #!54 models
+> show #!54 models
+> fitmap #50 inMap #54
+Fit map Cl3D_job542_run_it025_class001.mrc in map
+Cl3D_job545_run_it025_class002.mrc using 342972 points
+correlation = 0.9989, correlation about mean = 0.9796, overlap = 133
+steps = 56, shift = 2.3, angle = 1.62 degrees
+Position of Cl3D_job542_run_it025_class001.mrc (#50) relative to
+Cl3D_job545_run_it025_class002.mrc (#54) coordinates:
+Matrix rotation and translation
+.99982077 -0.01310087 0.01366700 -0.20479433
+.01319269 0.99989086 -0.00664955 -1.77455886
+-0.01357839 0.00682866 0.99988449 1.74879695
+Axis 0.33535327 0.67789597 0.65421345
+Axis point 134.82260247 0.00000000 13.62266755
+Rotation angle (degrees) 1.15146770
+Shift along axis -0.12755828
+> hide #!54 models
+> show #!54 models
+> hide #!50 models
+> show #!50 models
+> hide #!54 models
+> show #!54 models
+> hide #!54 models
+> show #!54 models
+> hide #!54 models
+> show #!54 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!54 models
+> show #!54 models
+> hide #!54 models
+> show #!54 models
+> hide #!50 models
+> show #!50 models
+> hide #!54 models
+> hide #!50 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job563/Cl3D_j563_run_it025_class001.mrc
+Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
+.9, shown at level 0.0153, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job563/Cl3D_j563_run_it025_class002.mrc
+Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
+.9, shown at level 0.0159, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job563/Cl3D_j563_run_it025_class003.mrc
+Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
+.9, shown at level 0.0184, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job566/Cl3D_job566_run_it025_class001.mrc
+Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
+.9, shown at level 0.0155, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job566/Cl3D_job566_run_it025_class002.mrc
+Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
+.9, shown at level 0.0166, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job566/Cl3D_job566_run_it025_class003.mrc
+Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
+.9, shown at level 0.0195, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job566/Cl3D_job566_run_it025_class004.mrc
+Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+> volume all step 1
+> volume all level 0.013
+> hide #!57 models
+> hide #!58 models
+> hide #!59 models
+> hide #!60 models
+> hide #!61 models
+> hide #!62 models
+> show #!57 models
+> hide #!56 models
+> show #!58 models
+> hide #!57 models
+> volume #58 level 0.01852
+> hide #!58 models
+> show #!57 models
+> hide #!57 models
+> show #!56 models
+> volume #56 level 0.012
+> hide #!56 models
+> show #!59 models
+> volume #59 level 0.012
+> show #!56 models
+> hide #!56 models
+> show #!56 models
+> hide #!56 models
+> show #!56 models
+> hide #!56 models
+> show #!60 models
+> hide #!60 models
+> show #!60 models
+> hide #!59 models
+> hide #!60 models
+> show #!61 models
+> hide #!61 models
+> show #!62 models
+> show #!59 models
+> hide #!59 models
+> volume #62 level 0.012
+> hide #!62 models
+> show #!62 models
+> hide #!62 models
+> show #!61 models
+> hide #!61 models
+> show #!60 models
+> hide #!60 models
+> show #!59 models
+> show #!56 models
+> hide #!56 models
+> show #!56 models
+> hide #!56 models
+> show #!56 models
+> hide #!56 models
+> show #!56 models
+> hide #!59 models
+> show #!59 models
+> hide #!59 models
+> show #!59 models
+> hide #!56 models
+> hide #!59 models
+> show #!59 models
+> hide #!59 models
+> show #!60 models
+> hide #!60 models
+> show #!61 models
+> hide #!61 models
+> show #!62 models
+> hide #!62 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job567/Cl3D_j567_run_it025_class001.mrc
+Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job567/Cl3D_j567_run_it025_class002.mrc
+Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job567/Cl3D_j567_run_it025_class003.mrc
+Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
+.9, shown at level 0.0198, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job567/Cl3D_j567_run_it025_class004.mrc
+Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
+.9, shown at level 0.0163, step 2, values float32
+> volume all step 1
+> hide #!66 models
+> hide #!65 models
+> hide #!64 models
+> volume #63 level 0.013
+> volume #64 level 0.013
+> volume #63 level 0.012
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job568/Cl3D_j568_run_it025_class001.mrc
+Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
+.9, shown at level 0.0187, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job568/Cl3D_j568_run_it025_class002.mrc
+Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
+.9, shown at level 0.0155, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job568/Cl3D_j568_run_it025_class003.mrc
+Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> volume all step 1
+> hide #!68 models
+> hide #!69 models
+> show #!68 models
+> hide #!67 models
+> show #!69 models
+> hide #!68 models
+> volume #69 level 0.013
+> volume #68 level 0.013
+> volume #67 level 0.013
+> show #!67 models
+> hide #!67 models
+> show #!68 models
+> hide #!68 models
+> show #!69 models
+> hide #!69 models
+> show #!29 models
+> hide #!29 models
+> show #!30 models
+> hide #!30 models
+> show #!31 models
+> show #!29 models
+> hide #!29 models
+> hide #!31 models
+> show #!28 models
+> show #!29 models
+> hide #!29 models
+> hide #!28 models
+> show #!50 models
+> hide #!50 models
+> show #!51 models
+> hide #!51 models
+> show #!52 models
+> hide #!52 models
+> show #!50 models
+> show #!51 models
+> hide #!50 models
+> hide #!51 models
+> show #!53 models
+> hide #!53 models
+> show #!54 models
+> show #!55 models
+> hide #!55 models
+> hide #!54 models
+> show #!50 models
+> show #!51 models
+> hide #!51 models
+> show #!51 models
+> hide #!51 models
+> show #!51 models
+> hide #!51 models
+> show #!52 models
+> hide #!52 models
+> show #!53 models
+> hide #!53 models
+> show #!54 models
+> hide #!54 models
+> show #!54 models
+> hide #!54 models
+> hide #!50 models
+> show #!56 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class001.mrc
+Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
+.9, shown at level 0.0156, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class002.mrc
+Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
+.9, shown at level 0.0131, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class003.mrc
+Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
+.9, shown at level 0.014, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class004.mrc
+Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
+.9, shown at level 0.0132, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class005.mrc
+Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
+.9, shown at level 0.0165, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class006.mrc
+Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
+.9, shown at level 0.0159, step 2, values float32
+> hide #!56 models
+> volume all step 1
+> hide #!71 models
+> hide #!72 models
+> hide #!73 models
+> hide #!74 models
+> hide #!75 models
+> volume #70 level 0.013
+> volume #71 level 0.013
+> volume #71 level 0.01
+> volume #71 level 0.012
+> volume #72 level 0.013
+> volume #72 level 0.01
+> volume #72 level 0.012
+> volume #73 level 0.012
+> volume #74 level 0.013
+> volume #75 level 0.013
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class001.mrc
+Opened Cl3D_j577_run_it025_class001.mrc as #76, grid size 294,294,294, pixel
+.9, shown at level 0.0166, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class002.mrc
+Opened Cl3D_j577_run_it025_class002.mrc as #77, grid size 294,294,294, pixel
+.9, shown at level 0.0135, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class003.mrc
+Opened Cl3D_j577_run_it025_class003.mrc as #78, grid size 294,294,294, pixel
+.9, shown at level 0.0153, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class004.mrc
+Opened Cl3D_j577_run_it025_class004.mrc as #79, grid size 294,294,294, pixel
+.9, shown at level 0.015, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class005.mrc
+Opened Cl3D_j577_run_it025_class005.mrc as #80, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class006.mrc
+Opened Cl3D_j577_run_it025_class006.mrc as #81, grid size 294,294,294, pixel
+.9, shown at level 0.0136, step 2, values float32
+> volume all step 1
+> hide #!77 models
+> hide #!78 models
+> hide #!79 models
+> hide #!80 models
+> hide #!81 models
+> volume #76 level 0.013
+> volume #77 level 0.013
+> volume #78 level 0.013
+> volume #79 level 0.013
+> volume #80 level 0.007565
+> volume #80 level 0.02
+> volume #80 level 0.012
+> volume #81 level 0.012
+> volume #81 level 0.01
+> volume #81 level 0.008841
+> volume #81 level 0.012
+> volume #81 level 0.01
+> show #!80 models
+> hide #!80 models
+> show #!80 models
+> hide #!80 models
+> show #!79 models
+> hide #!79 models
+> show #!78 models
+> hide #!81 models
+> hide #!78 models
+> show #!77 models
+> hide #!77 models
+> show #!76 models
+> hide #!76 models
+> show #!81 models
+> hide #!81 models
+> show #!80 models
+> hide #!80 models
+> show #!79 models
+> hide #!79 models
+> show #!78 models
+> hide #!78 models
+> show #!77 models
+> hide #!77 models
+> show #!77 models
+> hide #!77 models
+> show #!76 models
+> hide #!76 models
+> show #!76 models
+> hide #!76 models
+> show #!77 models
+> hide #!77 models
+> show #!78 models
+> hide #!78 models
+> show #!78 models
+> hide #!78 models
+> show #!79 models
+> hide #!79 models
+> show #!80 models
+> hide #!80 models
+> show #!81 models
+> hide #!81 models
+> show #!75 models
+> hide #!75 models
+> show #!74 models
+> volume #74 level 0.01584
+> volume #74 level 0.01357
+> hide #!74 models
+> show #!73 models
+> hide #!73 models
+> show #!72 models
+> hide #!72 models
+> show #!71 models
+> hide #!71 models
+> show #!70 models
+> hide #!70 models
+> show #!70 models
+> hide #!70 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J577_class_02_00082_volume.mrc
+Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
+,128,128, pixel 4.36, shown at level 0.888, step 1, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J583_class_02_00082_volume.mrc
+Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
+,128,128, pixel 4.36, shown at level 0.827, step 1, values float32
+> hide #!83 models
+> volume #82 level 1.108
+> volume #82 level 1.632
+> volume #83 level 1.361
+> open /Users/cvetkom/Downloads/cryosparc_P17_J610_002_volume_map.mrc
+Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
+pixel 1.9, shown at level 0.289, step 2, values float32
+> volume #84 step 1
+> volume #84 level 0.3974
+> volume #84 level 0.3145
+> volume #84 level 0.3879
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class001.mrc
+Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
+.9, shown at level 0.0156, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class002.mrc
+Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
+.9, shown at level 0.0134, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class003.mrc
+Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
+.9, shown at level 0.0132, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class004.mrc
+Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
+.9, shown at level 0.0143, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class005.mrc
+Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
+.9, shown at level 0.0158, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class006.mrc
+Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
+.9, shown at level 0.0179, step 2, values float32
+> hide #!84 models
+> volume all step 1
+> hide #!86 models
+> hide #!87 models
+> hide #!88 models
+> hide #!89 models
+> hide #!90 models
+> volume #85 level 0.013
+> volume #86 level 0.013
+> volume #86 level 0.012
+> volume #87 level 0.012
+> show #!85 models
+> hide #!85 models
+> show #!85 models
+> hide #!85 models
+> volume #88 level 0.013
+> volume #88 level 0.012
+> show #!86 models
+> hide #!86 models
+> show #!85 models
+> hide #!85 models
+> hide #!88 models
+> show #!89 models
+> show #!88 models
+> hide #!88 models
+> volume #89 level 0.013
+> volume #90 level 0.013
+> hide #!90 models
+> show #!90 models
+> hide #!90 models
+> show #!89 models
+> show #!88 models
+> show #!87 models
+> hide #!87 models
+> show #!87 models
+> hide #!87 models
+> hide #!89 models
+> hide #!88 models
+> show #!87 models
+> hide #!87 models
+> show #!86 models
+> hide #!86 models
+> show #!85 models
+> hide #!85 models
+> show #!84 models
+> hide #!84 models
+> show #!85 models
+> show #!86 models
+> hide #!86 models
+> show #!86 models
+> hide #!86 models
+> show #!86 models
+> hide #!86 models
+> show #!87 models
+> hide #!87 models
+> show #!88 models
+> hide #!88 models
+> show #!88 models
+> show #!89 models
+> hide #!89 models
+> show #!90 models
+> hide #!90 models
+> hide #!88 models
+> show #!88 models
+> hide #!88 models
+> hide #!85 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class001.mrc
+Opened Cl3D_j575_run_it025_class001.mrc as #91, grid size 294,294,294, pixel
+.9, shown at level 0.0167, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class002.mrc
+Opened Cl3D_j575_run_it025_class002.mrc as #92, grid size 294,294,294, pixel
+.9, shown at level 0.014, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class003.mrc
+Opened Cl3D_j575_run_it025_class003.mrc as #93, grid size 294,294,294, pixel
+.9, shown at level 0.014, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class004.mrc
+Opened Cl3D_j575_run_it025_class004.mrc as #94, grid size 294,294,294, pixel
+.9, shown at level 0.0158, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class005.mrc
+Opened Cl3D_j575_run_it025_class005.mrc as #95, grid size 294,294,294, pixel
+.9, shown at level 0.0132, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class006.mrc
+Opened Cl3D_j575_run_it025_class006.mrc as #96, grid size 294,294,294, pixel
+.9, shown at level 0.0132, step 2, values float32
+> hide #!92 models
+> hide #!93 models
+> hide #!94 models
+> hide #!95 models
+> hide #!96 models
+> volume all step 1
+> volume #91 level 0.013
+> volume #92 level 0.012
+> volume #93 level 0.012
+> volume #94 level 0.013
+> volume #95 level 0.013
+> close #91-96
+> show #!85 models
+> show #!86 models
+> hide #!85 models
+> show #!85 models
+> hide #!85 models
+> show #!85 models
+> hide #!85 models
+> hide #!86 models
+> show #!87 models
+> hide #!87 models
+> show #!87 models
+> hide #!87 models
+> show #!88 models
+> show #!86 models
+> hide #!86 models
+> show #!85 models
+> hide #!85 models
+> hide #!88 models
+> show #!89 models
+> hide #!89 models
+> show #!90 models
+> hide #!90 models
+> show #!89 models
+> show #!88 models
+> hide #!88 models
+> show #!87 models
+> hide #!87 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
+> show #!14 models
+> hide #!14 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> hide #!89 models
+> show #!90 models
+> hide #!90 models
+> show #!89 models
+> hide #!89 models
+> show #!88 models
+> hide #!88 models
+> show #!88 models
+> show #!87 models
+> hide #!87 models
+> show #!87 models
+> hide #!87 models
+> show #!87 models
+> hide #!87 models
+> show #!86 models
+> hide #!86 models
+> hide #!88 models
+> show #!70 models
+> show #!71 models
+> hide #!71 models
+> show #!72 models
+> hide #!70 models
+> hide #!72 models
+> show #!73 models
+> hide #!73 models
+> show #!74 models
+> hide #!74 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> show #!86 models
+> hide #!86 models
+> show #!85 models
+> hide #!85 models
+> show #!87 models
+> hide #!87 models
+> show #!88 models
+> hide #!88 models
+> show #!89 models
+> hide #!89 models
+> show #!89 models
+> hide #!89 models
+> show #!89 models
+> hide #!89 models
+> show #!89 models
+> hide #!89 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!74 models
+> hide #!74 models
+> show #!73 models
+> hide #!73 models
+> show #!72 models
+> hide #!72 models
+> show #!71 models
+> hide #!71 models
+> show #!70 models
+> hide #!70 models
+> show #!70 models
+> hide #!70 models
+> show #!69 models
+> hide #!69 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> hide #!32 models
+> hide #!34 models
+> show #!34 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!35 models
+> hide #!32 models
+> hide #!35 models
+> show #!36 models
+> hide #!36 models
+> show #!36 models
+> hide #!36 models
+> show #!37 models
+> hide #!37 models
+> show #!38 models
+> show #!39 models
+> hide #!39 models
+> show #!40 models
+> hide #!40 models
+> show #!39 models
+> show #!40 models
+> hide #!40 models
+> hide #!39 models
+> show #!41 models
+> hide #!41 models
+> hide #!38 models
+> show #!82 models
+> show #!83 models
+> hide #!83 models
+> hide #!82 models
+> show #!84 models
+> hide #!84 models
+> show #!82 models
+> hide #!82 models
+> show #!83 models
+> hide #!83 models
+> show #!84 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J611_002_volume_map.mrc
+Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
+pixel 1.9, shown at level 0.273, step 2, values float32
+> hide #!84 models
+> show #!84 models
+> hide #!84 models
+> volume #91 step 1
+> show #!84 models
+> volume #84 level 0.4
+> volume #84 level 0.36
+> hide #!91 models
+> volume #91 level 0.36
+> hide #!84 models
+> show #!84 models
+> hide #!84 models
+> volume #91 level 0.4
+> volume #91 level 0.45
+> show #!84 models
+> volume #84 level 0.45
+> hide #!84 models
+> show #!84 models
+> hide #!84 models
+> show #!84 models
+> hide #!84 models
+> show #!84 models
+> hide #!91 models
+> show #!91 models
+> hide #!91 models
+> show #!91 models
+> hide #!91 models
+> show #!91 models
+> hide #!84 models
+> show #!84 models
+> hide #!84 models
+> show #!84 models
+> hide #!84 models
+> show #!84 models
+> hide #!84 models
+> hide #!91 models
+> show #!91 models
+> hide #!91 models
+> show #!91 models
+> hide #!91 models
+> show #!90 models
+> hide #!90 models
+> show #!85 models
+> show #!86 models
+> hide #!86 models
+> hide #!85 models
+> show #!85 models
+> show #!86 models
+> hide #!85 models
+> show #!85 models
+> hide #!85 models
+> show #!85 models
+> hide #!85 models
+> show #!85 models
+> hide #!85 models
+> show #!87 models
+> hide #!87 models
+> show #!88 models
+> hide #!88 models
+> show #!89 models
+> hide #!89 models
+> show #!90 models
+> hide #!90 models
+> hide #!86 models
+> show #!28 models
+> hide #!28 models
+> show #!29 models
+> show #!28 models
+> hide #!28 models
+> show #!28 models
+> hide #!28 models
+> hide #!29 models
+> show #!29 models
+> show #!28 models
+> hide #!28 models
+> hide #!29 models
+> show #!30 models
+> hide #!30 models
+> show #!31 models
+> show #!28 models
+> hide #!28 models
+> hide #!31 models
+> show #!32 models
+> show #!33 models
+> hide #!33 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> hide #!32 models
+> show #!28 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!28 models
+> hide #!34 models
+> show #!28 models
+> show #!29 models
+> hide #!29 models
+> show #!29 models
+> hide #!28 models
+> hide #!29 models
+> show #!30 models
+> hide #!30 models
+> show #!31 models
+> hide #!31 models
+> show #!32 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> hide #!34 models
+> show #!33 models
+> hide #!32 models
+> show #!31 models
+> hide #!31 models
+> show #!32 models
+> hide #!32 models
+> show #!34 models
+> hide #!33 models
+> hide #!34 models
+> show #!35 models
+> show #!32 models
+> hide #!35 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> hide #!32 models
+> hide #!34 models
+> show #!36 models
+> show #!37 models
+> hide #!36 models
+> show #!38 models
+> hide #!38 models
+> show #!38 models
+> hide #!37 models
+> show #!37 models
+> show #!36 models
+> hide #!36 models
+> show #!36 models
+> hide #!36 models
+> hide #!38 models
+> hide #!37 models
+> show #!39 models
+> show #!40 models
+> hide #!39 models
+> hide #!40 models
+> show #!41 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!41 models
+> show #!43 models
+> hide #!42 models
+> hide #!43 models
+> show #!44 models
+> show #!45 models
+> hide #!45 models
+> show #!46 models
+> hide #!44 models
+> hide #!46 models
+> show #!47 models
+> hide #!47 models
+> show #!48 models
+> hide #!48 models
+> show #!49 models
+> hide #!49 models
+> show #!50 models
+> show #!51 models
+> hide #!51 models
+> show #!52 models
+> hide #!52 models
+> hide #!50 models
+> show #!53 models
+> hide #!53 models
+> show #!54 models
+> hide #!54 models
+> show #!55 models
+> hide #!55 models
+> show #!56 models
+> hide #!56 models
+> show #!57 models
+> hide #!57 models
+> show #!58 models
+> hide #!58 models
+> show #!59 models
+> show #!60 models
+> hide #!60 models
+> show #!61 models
+> hide #!61 models
+> show #!62 models
+> hide #!62 models
+> hide #!59 models
+> show #!63 models
+> show #!64 models
+> show #!65 models
+> hide #!65 models
+> show #!66 models
+> hide #!64 models
+> hide #!63 models
+> hide #!66 models
+> show #!63 models
+> show #!64 models
+> hide #!63 models
+> hide #!64 models
+> show #!67 models
+> hide #!67 models
+> show #!68 models
+> show #!69 models
+> hide #!68 models
+> show #!68 models
+> hide #!69 models
+> show #!69 models
+> hide #!68 models
+> hide #!69 models
+> show #!70 models
+> show #!71 models
+> hide #!71 models
+> show #!72 models
+> hide #!72 models
+> show #!73 models
+> hide #!73 models
+> hide #!70 models
+> show #!75 models
+> show #!74 models
+> show #!73 models
+> hide #!73 models
+> hide #!74 models
+> hide #!75 models
+> show #!72 models
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+> show #!71 models
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+> show #!70 models
+> show #!71 models
+> hide #!71 models
+> hide #!70 models
+> show #!71 models
+> hide #!71 models
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+> hide #!72 models
+> show #!73 models
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+> show #!74 models
+> show #!75 models
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+> show #!74 models
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+> hide #!74 models
+> hide #!75 models
+> show #!76 models
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+> hide #!77 models
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+> hide #!78 models
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+> hide #!79 models
+> show #!80 models
+> hide #!80 models
+> show #!81 models
+> hide #!81 models
+> hide #!76 models
+> show #!85 models
+> show #!86 models
+> hide #!86 models
+> show #!87 models
+> hide #!87 models
+> show #!88 models
+> hide #!88 models
+> hide #!85 models
+> show #!86 models
+> hide #!86 models
+> show #!87 models
+> hide #!87 models
+> show #!88 models
+> hide #!88 models
+> show #!88 models
+> hide #!88 models
+> show #!89 models
+> hide #!89 models
+> show #!90 models
+> hide #!90 models
+> show #!89 models
+> show #!88 models
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+> show #!87 models
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+> show #!86 models
+> hide #!86 models
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+> hide #!85 models
+> show #!84 models
+> hide #!84 models
+> hide #!89 models
+> show #!33 models
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+> hide #!32 models
+> hide #!33 models
+> show #!33 models
+> hide #!33 models
+> show #!32 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> show #!35 models
+> hide #!35 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!33 models
+> hide #!33 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
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+> hide #!33 models
+> show #!35 models
+> hide #!35 models
+> show #!33 models
+> hide #!33 models
+> show #!35 models
+> hide #!35 models
+> show #!35 models
+> hide #!35 models
+> hide #!34 models
+> show #!34 models
+> hide #!32 models
+> hide #!34 models
+> show #!36 models
+> hide #!36 models
+> show #!37 models
+> hide #!37 models
+> show #!38 models
+> hide #!38 models
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+> hide #!39 models
+> show #!40 models
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+> show #!41 models
+> hide #!41 models
+> show #!41 models
+> hide #!41 models
+> show #!42 models
+> hide #!42 models
+> show #!70 models
+> show #!71 models
+> hide #!71 models
+> show #!72 models
+> hide #!70 models
+> hide #!72 models
+> show #!73 models
+> hide #!73 models
+> show #!74 models
+> show #!75 models
+> hide #!74 models
+> hide #!75 models
+> show #!76 models
+> show #!75 models
+> hide #!75 models
+> show #!77 models
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+> show #!78 models
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+> show #!79 models
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+> hide #!76 models
+> show #!85 models
+> hide #!85 models
+> show #!86 models
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+> show #!87 models
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+> show #!88 models
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+> show #!89 models
+> hide #!89 models
+> show #!89 models
+> show #!90 models
+> hide #!90 models
+> show #!32 models
+> show #!34 models
+> hide #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
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+> hide #!32 models
+> show #!32 models
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+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> show #!32 models
+> hide #!34 models
+> show #!34 models
+> hide #!32 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> show #!13 models
+> hide #!13 models
+> show #!14 models
+> hide #!14 models
+> show #!15 models
+> hide #!15 models
+> show #!16 models
+> hide #!16 models
+> show #!17 models
+> hide #!17 models
+> show #!15 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> hide #!15 models
+> show #!50 models
+> show #!51 models
+> show #!52 models
+> hide #!51 models
+> show #!51 models
+> hide #!51 models
+> hide #!50 models
+> hide #!52 models
+> show #!51 models
+> hide #!51 models
+> show #!50 models
+> hide #!50 models
+> show #!53 models
+> hide #!53 models
+> show #!54 models
+> hide #!54 models
+> show #!55 models
+> hide #!55 models
+> show #!55 models
+> hide #!55 models
+> show #!50 models
+> hide #!50 models
+> show #!51 models
+> show #!56 models
+> hide #!56 models
+> show #!57 models
+> hide #!57 models
+> show #!57 models
+> hide #!51 models
+> show #!51 models
+> hide #!57 models
+> show #!55 models
+> hide #!55 models
+> show #!55 models
+> hide #!51 models
+> show #!51 models
+> hide #!51 models
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+> hide #!55 models
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+> hide #!55 models
+> show #!55 models
+> hide #!55 models
+> hide #!51 models
+> show #!50 models
+> show #!52 models
+> hide #!52 models
+> show #!54 models
+> hide #!54 models
+> show #!54 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!54 models
+> show #!54 models
+> hide #!54 models
+> show #!54 models
+> hide #!54 models
+> show #!54 models
+> hide #!54 models
+> show #!54 models
+> hide #!54 models
+> show #!54 models
+> hide #!54 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
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+> hide #!50 models
+> hide #!51 models
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+> hide #!52 models
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+> hide #!53 models
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+> show #!50 models
+> show #!14 models
+> hide #!14 models
+> show #!13 models
+> hide #!13 models
+> show #!15 models
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+> show #!15 models
+> hide #!15 models
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+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
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+> hide #!15 models
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+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!16 models
+> hide #!16 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!56 models
+> hide #!56 models
+> show #!57 models
+> hide #!57 models
+> show #!58 models
+> hide #!58 models
+> show #!57 models
+> hide #!57 models
+> show #!56 models
+> hide #!56 models
+> show #!56 models
+> volume #56 level 0.013
+> volume #56 level 0.012
+> show #!57 models
+> hide #!57 models
+> show #!57 models
+> hide #!56 models
+> hide #!57 models
+> show #!58 models
+> hide #!58 models
+> show #!56 models
+> hide #!56 models
+> show #!59 models
+> hide #!59 models
+> show #!56 models
+> show #!50 models
+> hide #!56 models
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+> hide #!56 models
+> show #!56 models
+> hide #!50 models
+> show #!57 models
+> hide #!57 models
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+> hide #!58 models
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+> hide #!58 models
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+> hide #!58 models
+> show #!14 models
+> hide #!14 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> hide #!56 models
+> show #!56 models
+> hide #!56 models
+> show #!59 models
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+> hide #!59 models
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+> hide #!61 models
+> show #!61 models
+> hide #!61 models
+> show #!62 models
+> hide #!62 models
+> show #!59 models
+> show #!56 models
+> hide #!56 models
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+> show #!34 models
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+> show #!34 models
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+> show #!32 models
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+> hide #!34 models
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+> hide #!34 models
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+> hide #!38 models
+> hide #!32 models
+> show #!39 models
+> hide #!39 models
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+> show #!40 models
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+> show #!40 models
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+> hide #!42 models
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+> hide #!39 models
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+> hide #!40 models
+> show #!40 models
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+> hide #!40 models
+> show #!44 models
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+> hide #!44 models
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+> hide #!45 models
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+> hide #!46 models
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+> show #!39 models
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+> show #!35 models
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+> hide #!45 models
+> show #!45 models
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+> show #!70 models
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+> hide #!70 models
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+> hide #!72 models
+> show #!71 models
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+> hide #!73 models
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+> show #!71 models
+> hide #!71 models
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+> hide #!70 models
+> show #!70 models
+> hide #!70 models
+> show #!70 models
+> hide #!74 models
+> show #!74 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> hide #!74 models
+> hide #!70 models
+> show #!76 models
+> hide #!76 models
+> show #!75 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
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+> hide #!15 models
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+> hide #!15 models
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+> hide #!15 models
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+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> hide #!75 models
+> show #!76 models
+> show #!77 models
+> hide #!76 models
+> show #!78 models
+> hide #!78 models
+> show #!79 models
+> hide #!79 models
+> show #!80 models
+> hide #!80 models
+> show #!81 models
+> hide #!81 models
+> close #76-81
+> show #!85 models
+> show #!86 models
+> hide #!86 models
+> hide #!85 models
+> show #!85 models
+> show #!86 models
+> hide #!85 models
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+> hide #!87 models
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+> hide #!86 models
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+> show #!88 models
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+> show #!85 models
+> hide #!85 models
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+> show #!90 models
+> hide #!90 models
+> show #!90 models
+> hide #!90 models
+> hide #!85 models
+> show #!85 models
+> hide #!88 models
+> show #!88 models
+> hide #!88 models
+> show #!88 models
+> hide #!88 models
+> show #!88 models
+> hide #!88 models
+> hide #!89 models
+> hide #!85 models
+> show #!85 models
+> hide #!85 models
+> show #!86 models
+> hide #!86 models
+> show #!87 models
+> hide #!87 models
+> show #!88 models
+> hide #!88 models
+> show #!88 models
+> hide #!88 models
+> show #!89 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!90 models
+> hide #!89 models
+> hide #!90 models
+> show #!89 models
+> hide #!89 models
+> show #!88 models
+> hide #!88 models
+> show #!87 models
+> hide #!87 models
+> show #!86 models
+> hide #!86 models
+> show #!56 models
+> show #!57 models
+> hide #!57 models
+> show #!57 models
+> hide #!57 models
+> show #!58 models
+> hide #!58 models
+> show #!59 models
+> hide #!56 models
+> show #!60 models
+> hide #!60 models
+> show #!61 models
+> hide #!61 models
+> show #!62 models
+> hide #!62 models
+> show #!62 models
+> hide #!62 models
+> hide #!59 models
+> show #!59 models
+> hide #!59 models
+> show #!32 models
+> show #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!34 models
+> show #!34 models
+> hide #!32 models
+> hide #!34 models
+> show #!56 models
+> show #!59 models
+> hide #!59 models
+> hide #!56 models
+> show #!32 models
+> show #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> hide #!34 models
+> show #!33 models
+> hide #!33 models
+> show #!35 models
+> hide #!35 models
+> show #!35 models
+> show #!90 models
+> hide #!90 models
+> show #!90 models
+> hide #!90 models
+> show #!89 models
+> hide #!89 models
+> show #!90 models
+> hide #!90 models
+> show #!90 models
+> hide #!90 models
+> show #!90 models
+> hide #!90 models
+> hide #!35 models
+> show #!85 models
+> show #!86 models
+> hide #!86 models
+> show #!87 models
+> hide #!87 models
+> show #!88 models
+> hide #!88 models
+> hide #!85 models
+> show #!86 models
+> show #!87 models
+> hide #!87 models
+> show #!87 models
+> hide #!87 models
+> show #!87 models
+> hide #!86 models
+> show #!86 models
+> hide #!86 models
+> show #!86 models
+> hide #!86 models
+> hide #!87 models
+> show #!89 models
+> hide #!89 models
+> show #!90 models
+> hide #!90 models
+> show #!85 models
+> hide #!85 models
+> show #!86 models
+> show #!87 models
+> show #!88 models
+> hide #!88 models
+> show #!88 models
+> hide #!88 models
+> hide #!87 models
+> hide #!86 models
+> show #!86 models
+> hide #!86 models
+> show #!86 models
+> show #!87 models
+> hide #!86 models
+> show #!86 models
+> hide #!87 models
+> show #!87 models
+> hide #!87 models
+> show #!87 models
+> show #!89 models
+> hide #!89 models
+> show #!89 models
+> hide #!89 models
+> hide #!87 models
+> show #!87 models
+> hide #!87 models
+> hide #!86 models
+> show #!86 models
+> show #!87 models
+> hide #!87 models
+> show #!87 models
+> hide #!87 models
+> hide #!86 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> show #!40 models
+> hide #!39 models
+> hide #!40 models
+> show #!41 models
+> hide #!41 models
+> show #!42 models
+> hide #!42 models
+> show #!43 models
+> hide #!43 models
+> show #!42 models
+> hide #!42 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> show #!40 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> hide #!40 models
+> show #!39 models
+> show #!40 models
+> hide #!40 models
+> hide #!39 models
+> show #!41 models
+> show #!42 models
+> hide #!42 models
+> hide #!41 models
+> show #!43 models
+> show #!41 models
+> show #!42 models
+> hide #!42 models
+> hide #!41 models
+> show #!42 models
+> hide #!42 models
+> hide #!43 models
+> show #!41 models
+> show #!42 models
+> hide #!41 models
+> hide #!42 models
+> show #!43 models
+> show #!41 models
+> show #!42 models
+> hide #!41 models
+> hide #!42 models
+> hide #!43 models
+> show #!41 models
+> show #!42 models
+> hide #!41 models
+> hide #!42 models
+> show #!43 models
+> hide #!43 models
+> show #!41 models
+> show #!42 models
+> show #!43 models
+> hide #!43 models
+> hide #!42 models
+> hide #!41 models
+> show #!32 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> hide #!32 models
+> hide #!34 models
+> show #!35 models
+> hide #!35 models
+> show #!35 models
+> hide #!35 models
+> show #!36 models
+> hide #!36 models
+> show #!35 models
+> show #!34 models
+> hide #!35 models
+> show #!35 models
+> hide #!34 models
+> show #!39 models
+> hide #!39 models
+> show #!40 models
+> hide #!40 models
+> show #!34 models
+> hide #!34 models
+> hide #!35 models
+> show #!34 models
+> hide #!34 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> hide #!34 models
+> show #!35 models
+> hide #!35 models
+> show #!91 models
+> hide #!91 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J615_class_00_final_volume.mrc
+Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
+,192,192, pixel 2.91, shown at level 0.526, step 1, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J616_class_00_final_volume.mrc
+Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
+,192,192, pixel 2.91, shown at level 0.499, step 1, values float32
+> volume #76 level 0.4164
+> volume #77 level 0.4158
+> volume #76 level 0.4
+> volume #76 level 0.3
+> volume #76 level 0.35
+> volume #76 level 0.3
+> open /Users/cvetkom/Downloads/cryosparc_P17_J621_mask.mrc
+Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+> volume #78 level 1
+> volume #78 color #cccc9980
+> open /Users/cvetkom/Downloads/cryosparc_P17_J617_class_00_final_volume.mrc
+Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
+,192,192, pixel 2.91, shown at level 0.517, step 1, values float32
+> hide #!78 models
+> hide #!79 models
+> show #!79 models
+> hide #!79 models
+> show #!79 models
+> hide #!76 models
+> volume #79 level 0.3
+> volume #79 level 0.4
+> volume #79 level 0.35
+> volume #79 level 0.3
+> open /Users/cvetkom/Downloads/cryosparc_P17_J620_007_volume_map.mrc
+Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
+pixel 1.9, shown at level 0.339, step 2, values float32
+> hide #!79 models
+> volume #80 step 1
+> volume #80 level 0.3095
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J368_007_volume_map.mrc
+Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
+pixel 1.9, shown at level 0.37, step 2, values float32
+> hide #!81 models
+> show #!81 models
+> hide #!80 models
+> volume #81 step 1
+> show #!80 models
+> hide #!80 models
+> volume #81 level 0.35
+> hide #!81 models
+> show #!80 models
+> volume #80 level 0.35
+> volume #80 level 0.32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J619_class_00_final_volume.mrc
+Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
+,192,192, pixel 2.91, shown at level 0.517, step 1, values float32
+> hide #!80 models
+> show #!79 models
+> hide #!79 models
+> volume #92 level 0.35
+> volume #92 level 0.4
+> volume #92 level 0.4136
+> show #!79 models
+> hide #!92 models
+> volume #79 level 0.3729
+> show #!76 models
+> hide #!79 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J623_007_volume_map.mrc
+Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
+pixel 1.9, shown at level 0.341, step 2, values float32
+> hide #!76 models
+> volume #93 step 1
+> volume #93 level 0.32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J626_class_01_00400_volume.mrc
+Opened cryosparc_P17_J626_class_01_00400_volume.mrc as #94, grid size
+,128,128, pixel 4.36, shown at level 1.11, step 1, values float32
+> hide #!93 models
+> volume #94 level 0.8311
+> close #94
+> open /Users/cvetkom/Downloads/cryosparc_P17_J625_007_volume_map.mrc
+Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
+pixel 1.9, shown at level 0.341, step 2, values float32
+> volume #94 step 1
+> volume #94 level 0.3
+> volume #94 level 0.25
+> open /Users/cvetkom/Downloads/cryosparc_P17_J631_class_01_00042_volume.mrc
+Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
+,128,128, pixel 4.36, shown at level 1.32, step 1, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J629_class_01_00042_volume.mrc
+Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
+,128,128, pixel 4.36, shown at level 1.32, step 1, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J628_class_01_00042_volume.mrc
+Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
+,128,128, pixel 4.36, shown at level 1.32, step 1, values float32
+> hide #!94 models
+> hide #!95 models
+> hide #!96 models
+> volume #97 level 1.082
+> volume #97 level 1
+> volume #96 level 1
+> volume #95 level 1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J620_007_volume_map.mrc
+Opened cryosparc_P17_J620_007_volume_map.mrc as #98, grid size 294,294,294,
+pixel 1.9, shown at level 0.339, step 2, values float32
+> close #98
+> show #!80 models
+> show #!93 models
+Drag select of 80 cryosparc_P17_J620_007_volume_map.mrc , 93
+cryosparc_P17_J623_007_volume_map.mrc
+> select clear
+> hide #!93 models
+> show #!93 models
+> hide #!80 models
+> show #!80 models
+> hide #!80 models
+> show #!80 models
+> hide #!80 models
+> show #!80 models
+> hide #!80 models
+> show #!80 models
+> lighting soft
+> hide #!80 models
+> show #!80 models
+> hide #!80 models
+> show #!80 models
+> hide #!80 models
+> show #!80 models
+> hide #!80 models
+> show #!82 models
+> hide #!82 models
+> show #!80 models
+> hide #!80 models
+> show #!80 models
+> hide #!80 models
+> show #!80 models
+> hide #!80 models
+> hide #!93 models
+> show #!81 models
+> show #!80 models
+> hide #!80 models
+> volume #81 level 0.32
+> volume #81 level 0.35
+> show #!80 models
+> select add #81
+models selected
+> ui mousemode right "rotate selected models"
+> select subtract #81
+Nothing selected
+> hide #!81 models
+> open /Volumes/lab-
+> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job581/run_it025_class006.mrc
+Opened run_it025_class006.mrc as #98, grid size 294,294,294, pixel 1.9, shown
+at level 0.0154, step 2, values float32
+> open /Volumes/lab-
+> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job581/run_it025_class003.mrc
+Opened run_it025_class003.mrc as #99, grid size 294,294,294, pixel 1.9, shown
+at level 0.0157, step 2, values float32
+> hide #!80 models
+> hide #!98 models
+> hide #!99 models
+> show #!99 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> hide #!99 models
+> open /Volumes/lab-
+> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job581/run_it025_class001.mrc
+Opened run_it025_class001.mrc as #100, grid size 294,294,294, pixel 1.9, shown
+at level 0.0158, step 2, values float32
+> open /Volumes/lab-
+> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job581/run_it025_class002.mrc
+Opened run_it025_class002.mrc as #101, grid size 294,294,294, pixel 1.9, shown
+at level 0.0166, step 2, values float32
+> hide #!101 models
+> volume #98 step 1
+> volume #99 step 1
+> volume #100 step 1
+> volume #101 step 1
+> volume #100 level 0.01165
+> volume #101 level 0.01425
+> volume #101 level 0.01268
+> show #!98 models
+> show #!99 models
+> hide #!99 models
+> hide #!98 models
+> show #!100 models
+> hide #!100 models
+> show #!100 models
+> show #!32 models
+> volume #100 level 0.02
+> hide #!32 models
+> show #!32 models
+> volume #100 level 0.015
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> volume #100 level 0.014
+> volume #100 level 0.013
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> volume #101 level 0.014
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> hide #!101 models
+> show #!99 models
+> show #!98 models
+> show #!85 models
+> hide #!85 models
+> show #!85 models
+> hide #!85 models
+> show #!85 models
+> hide #!85 models
+> show #!88 models
+> hide #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!88 models
+> show #!88 models
+> hide #!88 models
+> show #!88 models
+> hide #!88 models
+> show #!88 models
+> hide #!88 models
+> show #!39 models
+> hide #!39 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> hide #!40 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!40 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> show #!40 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> hide #!40 models
+> show #!40 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!40 models
+> show #!40 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> hide #!40 models
+> close #98-101
+> show #!97 models
+> hide #!97 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class001.mrc
+Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
+.9, shown at level 0.0158, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class002.mrc
+Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
+.9, shown at level 0.0166, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class003.mrc
+Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class004.mrc
+Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
+.9, shown at level 0.0131, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class005.mrc
+Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class006.mrc
+Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class007.mrc
+Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
+.9, shown at level 0.018, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class001.mrc
+Opened Cl3D_j585_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
+.9, shown at level 0.0155, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class002.mrc
+Opened Cl3D_j585_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
+.9, shown at level 0.0159, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class003.mrc
+Opened Cl3D_j585_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
+.9, shown at level 0.0197, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class004.mrc
+Opened Cl3D_j585_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class005.mrc
+Opened Cl3D_j585_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
+.9, shown at level 0.016, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class006.mrc
+Opened Cl3D_j585_run_it025_class006.mrc as #110, grid size 294,294,294, pixel
+.9, shown at level 0.0002, step 2, values float32
+> volume all step 1
+> hide #!99 models
+> hide #!100 models
+> hide #!101 models
+> hide #!102 models
+> hide #!103 models
+> hide #!104 models
+> hide #!105 models
+> hide #!106 models
+> hide #!107 models
+> hide #!108 models
+> hide #!109 models
+> hide #!110 models
+> volume #98 level 0.013
+> volume #98 level 0.012
+> volume #99 level 0.012
+> volume #100 level 0.013
+> volume #101 level 0.012
+> volume #102 level 0.012
+> volume #103 level 0.013
+> ui mousemode right zoom
+> lighting simple
+> show #!98 models
+> hide #!98 models
+> show #!100 models
+> hide #!100 models
+> show #!100 models
+> hide #!100 models
+> hide #!103 models
+> show #!104 models
+> show #!103 models
+> hide #!104 models
+> show #!104 models
+> volume #104 level 0.013
+> show #!103 models
+> hide #!103 models
+> volume #105 level 0.013
+> volume #106 level 0.013
+> volume #106 level 0.012
+> volume #105 level 0.012
+> volume #107 level 0.013
+> volume #108 level 0.013
+> volume #109 level 0.013
+> volume #110 level -0.02134
+> close #110
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class001.mrc
+Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
+.9, shown at level 0.0159, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class002.mrc
+Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
+.9, shown at level 0.017, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class003.mrc
+Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
+.9, shown at level 0.0158, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class004.mrc
+Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
+.9, shown at level 0.0134, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class005.mrc
+Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
+.9, shown at level 0.0127, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class006.mrc
+Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class007.mrc
+Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
+.9, shown at level 0.0179, step 2, values float32
+> close #105-109
+> hide #!111 models
+> hide #!112 models
+> hide #!113 models
+> hide #!114 models
+> hide #!115 models
+> hide #!116 models
+> volume #110 level 0.012
+> volume #111 level 0.012
+> volume #111 level 0.013
+> volume #110 step 1
+> volume #111 step 1
+> volume #112 step 1
+> volume #112 level 0.013
+> volume #113 step 1
+> volume #113 level 0.012
+> volume #114 step 1
+> volume #114 level 0.012
+> volume #115 step 1
+> volume #115 level 0.013
+> show #!112 models
+> hide #!112 models
+> show #!112 models
+> hide #!112 models
+> show #!112 models
+> hide #!112 models
+> show #!112 models
+> hide #!112 models
+> show #!112 models
+> hide #!112 models
+> volume #116 step 1
+> volume #116 level 0.013
+> show #!110 models
+> show #!111 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> volume #111 level 0.01556
+> volume #111 level 0.01455
+> show #!110 models
+> hide #!110 models
+> hide #!111 models
+> show #!111 models
+> show #!99 models
+> hide #!111 models
+> show #!98 models
+> hide #!99 models
+> show #!110 models
+> hide #!110 models
+> hide #!98 models
+> show #!110 models
+> hide #!110 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job583/Cl3D_j583_run_it025_class001.mrc
+Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
+.9, shown at level 0.0156, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job583/Cl3D_j583_run_it025_class002.mrc
+Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
+.9, shown at level 0.0158, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job583/Cl3D_j583_run_it025_class003.mrc
+Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
+.9, shown at level 0.0195, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job583/Cl3D_j583_run_it025_class004.mrc
+Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job583/Cl3D_j583_run_it025_class005.mrc
+Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
+.9, shown at level 0.0161, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job587/Cl3D_j587_run_it025_class001.mrc
+Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job587/Cl3D_j587_run_it025_class002.mrc
+Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job587/Cl3D_j587_run_it025_class003.mrc
+Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
+.9, shown at level 0.0197, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job587/Cl3D_j587_run_it025_class004.mrc
+Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job587/Cl3D_j587_run_it025_class005.mrc
+Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
+.9, shown at level 0.0161, step 2, values float32
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
+\u2014\u2014\u2014 End of log from Mon Jun 3 09:50:12 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> hide #!105 models
+> show #!105 models
+> show #!111 models
+> hide #!111 models
+> hide #!105 models
+> show #!105 models
+> hide #!105 models
+> show #!105 models
+> volume #105,106,107,108,109,117,118,119,120,121 level 0.013
+> hide #!106 models
+> show #!106 models
+> hide #!109 models
+> hide #!121 models
+> hide #!120 models
+> hide #!119 models
+> hide #!118 models
+> hide #!117 models
+> hide #!108 models
+> hide #!107 models
+> hide #!106 models
+> show #!106 models
+> hide #!106 models
+> hide #!105 models
+> show #!105 models
+> show #!106 models
+> hide #!106 models
+> hide #!105 models
+> show #!107 models
+> hide #!107 models
+> show #!108 models
+> hide #!108 models
+> show #!109 models
+> hide #!109 models
+> show #!108 models
+> show #!109 models
+> hide #!109 models
+> show #!109 models
+> hide #!109 models
+> hide #!108 models
+> show #!121 models
+> hide #!121 models
+> show #!1 models
+> show #!2 models
+> hide #!1 models
+> hide #!2 models
+> show #!2 models
+> show #!1 models
+> hide #!1 models
+> hide #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!4 models
+> hide #!4 models
+> show #!5 models
+> hide #!5 models
+> show #!6 models
+> hide #!6 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job325_0p95apix.mrc
+Opened Ref3D_job325_0p95apix.mrc as #122, grid size 588,588,588, pixel 0.95,
+shown at level 0.0107, step 4, values float32
+> close #122
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
+> show #!2 models
+> volume #2 level 0.003218
+> volume #2 level 0.006199
+> volume #2 level 0.013
+> hide #!2 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
+\u2014\u2014\u2014 End of log from Tue Jun 11 16:35:40 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> show #!119 models
+> hide #!119 models
+> show #!120 models
+> hide #!120 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class001.mrc
+Opened Cl3D_j590_run_it025_class001.mrc as #122, grid size 294,294,294, pixel
+.9, shown at level 0.0174, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class002.mrc
+Opened Cl3D_j590_run_it025_class002.mrc as #123, grid size 294,294,294, pixel
+.9, shown at level 0.0159, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class003.mrc
+Opened Cl3D_j590_run_it025_class003.mrc as #124, grid size 294,294,294, pixel
+.9, shown at level 0.0127, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class004.mrc
+Opened Cl3D_j590_run_it025_class004.mrc as #125, grid size 294,294,294, pixel
+.9, shown at level 0.0134, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class005.mrc
+Opened Cl3D_j590_run_it025_class005.mrc as #126, grid size 294,294,294, pixel
+.9, shown at level 0.0158, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class006.mrc
+Opened Cl3D_j590_run_it025_class006.mrc as #127, grid size 294,294,294, pixel
+.9, shown at level 0.0155, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class007.mrc
+Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
+.9, shown at level 0.0175, step 2, values float32
+> volume all step 1
+> hide #!123 models
+> hide #!124 models
+> hide #!125 models
+> hide #!126 models
+> hide #!127 models
+> hide #!128 models
+> volume #122 level 0.01525
+> volume #122 level 0.013
+> volume #123 level 0.013
+> show #!74 models
+> volume #122 level 0.014
+> volume #122 level 0.015
+> hide #!74 models
+> volume #124 level 0.013
+> volume #125 level 0.013
+> volume #126 level 0.013
+> volume #127 level 0.013
+> volume #128 level 0.014
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/run_it025_class001.mrc
+Opened run_it025_class001.mrc as #129, grid size 294,294,294, pixel 1.9, shown
+at level 0.0173, step 2, values float32
+> close #129
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class001.mrc
+Opened Cl3D_j591_run_it025_class001.mrc as #129, grid size 294,294,294, pixel
+.9, shown at level 0.0173, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class002.mrc
+Opened Cl3D_j591_run_it025_class002.mrc as #130, grid size 294,294,294, pixel
+.9, shown at level 0.0159, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class003.mrc
+Opened Cl3D_j591_run_it025_class003.mrc as #131, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class004.mrc
+Opened Cl3D_j591_run_it025_class004.mrc as #132, grid size 294,294,294, pixel
+.9, shown at level 0.0132, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class005.mrc
+Opened Cl3D_j591_run_it025_class005.mrc as #133, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class006.mrc
+Opened Cl3D_j591_run_it025_class006.mrc as #134, grid size 294,294,294, pixel
+.9, shown at level 0.0156, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class007.mrc
+Opened Cl3D_j591_run_it025_class007.mrc as #135, grid size 294,294,294, pixel
+.9, shown at level 0.0169, step 2, values float32
+> volume all step 1
+> hide #!130 models
+> hide #!131 models
+> hide #!132 models
+> hide #!133 models
+> hide #!134 models
+> hide #!135 models
+> volume #129 level 0.015
+> volume #129 level 0.014
+> show #!130 models
+> hide #!129 models
+> volume #130 level 0.013
+> volume #132 level 0.013
+> volume #133 level 0.013
+> volume #134 level 0.014
+> volume #134 level 0.013
+> volume #135 level 0.014
+> show #!134 models
+> hide #!134 models
+> show #!134 models
+> hide #!134 models
+> show #!133 models
+> hide #!133 models
+> hide #!135 models
+> show #!134 models
+> show #!133 models
+> hide #!133 models
+> show #!133 models
+> hide #!133 models
+> hide #!134 models
+> show #!132 models
+> hide #!132 models
+> show #!131 models
+> hide #!131 models
+> show #!130 models
+> hide #!130 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!135 models
+> hide #!135 models
+> show #!134 models
+> hide #!134 models
+> show #!133 models
+> hide #!133 models
+> show #!134 models
+> show #!133 models
+> hide #!133 models
+> show #!133 models
+> hide #!133 models
+> hide #!134 models
+> show #!132 models
+> hide #!132 models
+> show #!131 models
+> hide #!131 models
+> show #!130 models
+> hide #!130 models
+> show #!129 models
+> hide #!129 models
+> show #!130 models
+> hide #!130 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class001.mrc
+Opened Cl3D_j619_run_it025_class001.mrc as #136, grid size 320,320,320, pixel
+.9, shown at level 0.0108, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class002.mrc
+Opened Cl3D_j619_run_it025_class002.mrc as #137, grid size 320,320,320, pixel
+.9, shown at level 0.00682, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class003.mrc
+Opened Cl3D_j619_run_it025_class003.mrc as #138, grid size 320,320,320, pixel
+.9, shown at level 0.0091, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class004.mrc
+Opened Cl3D_j619_run_it025_class004.mrc as #139, grid size 320,320,320, pixel
+.9, shown at level 0.0104, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class005.mrc
+Opened Cl3D_j619_run_it025_class005.mrc as #140, grid size 320,320,320, pixel
+.9, shown at level 0.0128, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class006.mrc
+Opened Cl3D_j619_run_it025_class006.mrc as #141, grid size 320,320,320, pixel
+.9, shown at level 0.013, step 2, values float32
+> volume all step 1
+> hide #!137 models
+> hide #!138 models
+> hide #!139 models
+> hide #!140 models
+> hide #!141 models
+> hide #!136 models
+> show #!136 models
+> hide #!136 models
+> show #!136 models
+> hide #!136 models
+> show #!137 models
+> hide #!137 models
+> show #!136 models
+> hide #!136 models
+> show #!136 models
+> hide #!136 models
+> show #!137 models
+> show #!138 models
+> hide #!138 models
+> show #!138 models
+> hide #!137 models
+> hide #!138 models
+> show #!139 models
+> hide #!139 models
+> show #!140 models
+> show #!141 models
+> hide #!140 models
+> hide #!141 models
+> close #136-141
+> show #!130 models
+> show #!123 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!123 models
+> show #!123 models
+> hide #!130 models
+> show #!130 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!123 models
+> hide #!130 models
+> show #!117 models
+> show #!118 models
+> hide #!118 models
+> show #!118 models
+> hide #!118 models
+> show #!118 models
+> hide #!117 models
+> show #!117 models
+> hide #!118 models
+> show #!118 models
+> hide #!117 models
+> hide #!118 models
+> show #!110 models
+> show #!111 models
+> hide #!110 models
+> show #!110 models
+> hide #!111 models
+> hide #!110 models
+> show #!105 models
+> show #!106 models
+> hide #!106 models
+> show #!106 models
+> hide #!106 models
+> show #!106 models
+> hide #!106 models
+> hide #!105 models
+> show #!105 models
+> show #!106 models
+> hide #!105 models
+> hide #!106 models
+> show #!110 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> show #!122 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!122 models
+> hide #!123 models
+> show #!123 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!129 models
+> hide #!129 models
+> show #!130 models
+> hide #!110 models
+> show #!99 models
+> hide #!99 models
+> show #!98 models
+> volume #98 level 0.013
+> hide #!130 models
+> show #!130 models
+> volume #99 level 0.013
+> hide #!130 models
+> show #!110 models
+> hide #!98 models
+> show #!99 models
+> hide #!99 models
+> show #!98 models
+> volume #110 level 0.013
+> hide #!98 models
+> show #!98 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!110 models
+> show #!110 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!98 models
+> show #!111 models
+> hide #!110 models
+> show #!110 models
+> hide #!111 models
+> hide #!110 models
+> show #!32 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!34 models
+> hide #!32 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!129 models
+> hide #!129 models
+> show #!130 models
+> show #!129 models
+> hide #!129 models
+> show #!123 models
+> hide #!130 models
+> show #!130 models
+> hide #!123 models
+> show #!123 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!123 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J680_volume_map.mrc
+Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
+.9, shown at level 0.413, step 2, values float32
+> hide #!130 models
+> volume #136 step 1
+> volume #136 level 0.314
+> open /Users/cvetkom/Downloads/cryosparc_P17_J676_class_00_final_volume.mrc
+Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
+,192,192, pixel 2.91, shown at level 0.536, step 1, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J678_class_00_final_volume.mrc
+Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
+,192,192, pixel 2.91, shown at level 0.529, step 1, values float32
+> hide #!136 models
+> hide #!138 models
+> volume #137 level 0.5
+> volume #137 level 0.4
+> volume #137 level 0.3
+> volume #138 level 0.3
+> hide #!138 models
+> show #!137 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J681_volume_map.mrc
+Opened cryosparc_P17_J681_volume_map.mrc as #139, grid size 294,294,294, pixel
+.9, shown at level 0.411, step 2, values float32
+> hide #!137 models
+> volume #139 step 1
+> volume #139 level 0.2939
+> open /Users/cvetkom/Downloads/cryosparc_P17_J684_010_volume_map.mrc
+Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
+pixel 1.9, shown at level 0.365, step 2, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J685_007_volume_map.mrc
+Opened cryosparc_P17_J685_007_volume_map.mrc as #141, grid size 294,294,294,
+pixel 1.9, shown at level 0.361, step 2, values float32
+> hide #!139 models
+> hide #!141 models
+> volume #140 step 1
+> volume #141 step 1
+> volume #141 level 0.35
+> volume #140 level 0.36
+> volume #141 level 0.36
+> open /Users/cvetkom/Downloads/cryosparc_P17_J677_class_00_final_volume.mrc
+Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
+,192,192, pixel 2.91, shown at level 0.561, step 1, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J679_class_00_final_volume.mrc
+Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
+,192,192, pixel 2.91, shown at level 0.55, step 1, values float32
+> hide #!141 models
+> hide #!143 models
+> volume #142 level 0.3
+> hide #!142 models
+> show #!143 models
+> volume #143 level 0.3
+> volume #143 level 0.25
+> volume #142 level 0.25
+> open /Users/cvetkom/Downloads/cryosparc_P17_J686_mask.mrc
+Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+> volume #144 level 1
+> transparency #142.1#144.1 50
+> transparency #142.1#144.1 0
+> volume #144 color #cccc9980
+> volume #142 level 0.3
+> open /Users/cvetkom/Downloads/cryosparc_P17_J688_007_volume_map.mrc
+Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
+pixel 1.9, shown at level 0.365, step 2, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J689_008_volume_map.mrc
+Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
+pixel 1.9, shown at level 0.365, step 2, values float32
+> hide #!142 models
+> hide #!144 models
+> hide #!146 models
+> volume #145 step 1
+> show #!146 models
+> hide #!145 models
+> volume #146 step 1
+> show #!145 models
+> hide #!145 models
+> show #!145 models
+> hide #!146 models
+> show #!146 models
+> hide #!145 models
+> show #!145 models
+> hide #!146 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J690_006_volume_map.mrc
+Opened cryosparc_P17_J690_006_volume_map.mrc as #147, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 2, values float32
+> hide #!145 models
+> volume #147 step 1
+> lighting soft
+> show #!145 models
+> hide #!147 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J691_008_volume_map.mrc
+Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
+pixel 1.9, shown at level 0.365, step 2, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J692_009_volume_map.mrc
+Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
+pixel 1.9, shown at level 0.366, step 2, values float32
+> hide #!145 models
+> hide #!149 models
+> volume #148 step 1
+> volume #149 step 1
+> lighting soft
+> lighting simple
+> lighting soft
+> show #!145 models
+> hide #!149 models
+> show #!146 models
+> hide #!145 models
+> hide #!146 models
+> show #!145 models
+> show #!148 models
+> hide #!148 models
+> show #!148 models
+> show #!149 models
+> hide #!149 models
+> hide #!148 models
+> show #!147 models
+> hide #!147 models
+> hide #!145 models
+> show #!147 models
+> hide #!147 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J693_006_volume_map.mrc
+Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
+pixel 1.9, shown at level 0.37, step 2, values float32
+> volume #150 step 1
+> show #!149 models
+> hide #!149 models
+> show #!149 models
+> hide #!149 models
+> show #!145 models
+> hide #!150 models
+> hide #!145 models
+> show #!146 models
+> hide #!146 models
+> volume flip #145,146,148,149
+Opened cryosparc_P17_J688_007_volume_map.mrc z flip as #151, grid size
+,294,294, pixel 1.9, shown at step 1, values float32
+Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
+,294,294, pixel 1.9, shown at step 1, values float32
+Opened cryosparc_P17_J691_008_volume_map.mrc z flip as #153, grid size
+,294,294, pixel 1.9, shown at step 1, values float32
+Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
+,294,294, pixel 1.9, shown at step 1, values float32
+> hide #!154 models
+> hide #!153 models
+> hide #!152 models
+> show #!150 models
+> show #!152 models
+> show #!153 models
+> show #!154 models
+> select add #150
+models selected
+> select add #151
+models selected
+> select add #152
+models selected
+> select add #153
+models selected
+> select add #154
+models selected
+> lighting simple
+> select subtract #150
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #151,-0.054748,0.92128,0.38502,-64.171,0.99522,0.081557,-0.053637,-1.6415,-0.080816,0.38024,-0.92135,386.87,#152,-0.054748,0.92128,0.38502,-64.171,0.99522,0.081557,-0.053637,-1.6415,-0.080816,0.38024,-0.92135,386.87,#153,-0.054748,0.92128,0.38502,-64.171,0.99522,0.081557,-0.053637,-1.6415,-0.080816,0.38024,-0.92135,386.87,#154,-0.054748,0.92128,0.38502,-64.171,0.99522,0.081557,-0.053637,-1.6415,-0.080816,0.38024,-0.92135,386.87
+> view matrix models
+> #151,-0.99227,0.014424,0.12328,522.63,0.06591,0.90285,0.42487,-95.335,-0.10517,0.42971,-0.89682,373.38,#152,-0.99227,0.014424,0.12328,522.63,0.06591,0.90285,0.42487,-95.335,-0.10517,0.42971,-0.89682,373.38,#153,-0.99227,0.014424,0.12328,522.63,0.06591,0.90285,0.42487,-95.335,-0.10517,0.42971,-0.89682,373.38,#154,-0.99227,0.014424,0.12328,522.63,0.06591,0.90285,0.42487,-95.335,-0.10517,0.42971,-0.89682,373.38
+> view matrix models
+> #151,-0.97431,0.0085096,0.22505,494.23,0.077208,0.95135,0.29828,-81.204,-0.21157,0.30799,-0.92757,445.58,#152,-0.97431,0.0085096,0.22505,494.23,0.077208,0.95135,0.29828,-81.204,-0.21157,0.30799,-0.92757,445.58,#153,-0.97431,0.0085096,0.22505,494.23,0.077208,0.95135,0.29828,-81.204,-0.21157,0.30799,-0.92757,445.58,#154,-0.97431,0.0085096,0.22505,494.23,0.077208,0.95135,0.29828,-81.204,-0.21157,0.30799,-0.92757,445.58
+> view matrix models
+> #151,-0.99088,0.024916,0.13239,517,0.052496,0.97647,0.20914,-59.535,-0.12406,0.21419,-0.96888,458.2,#152,-0.99088,0.024916,0.13239,517,0.052496,0.97647,0.20914,-59.535,-0.12406,0.21419,-0.96888,458.2,#153,-0.99088,0.024916,0.13239,517,0.052496,0.97647,0.20914,-59.535,-0.12406,0.21419,-0.96888,458.2,#154,-0.99088,0.024916,0.13239,517,0.052496,0.97647,0.20914,-59.535,-0.12406,0.21419,-0.96888,458.2
+> ui mousemode right "translate selected models"
+> view matrix models
+> #151,-0.99088,0.024916,0.13239,510.53,0.052496,0.97647,0.20914,-71.716,-0.12406,0.21419,-0.96888,519.84,#152,-0.99088,0.024916,0.13239,510.53,0.052496,0.97647,0.20914,-71.716,-0.12406,0.21419,-0.96888,519.84,#153,-0.99088,0.024916,0.13239,510.53,0.052496,0.97647,0.20914,-71.716,-0.12406,0.21419,-0.96888,519.84,#154,-0.99088,0.024916,0.13239,510.53,0.052496,0.97647,0.20914,-71.716,-0.12406,0.21419,-0.96888,519.84
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #151,-0.9994,0.032362,0.012172,540.39,0.033337,0.99529,0.091041,-42.658,-0.0091686,0.091392,-0.99577,529.57,#152,-0.9994,0.032362,0.012172,540.39,0.033337,0.99529,0.091041,-42.658,-0.0091686,0.091392,-0.99577,529.57,#153,-0.9994,0.032362,0.012172,540.39,0.033337,0.99529,0.091041,-42.658,-0.0091686,0.091392,-0.99577,529.57,#154,-0.9994,0.032362,0.012172,540.39,0.033337,0.99529,0.091041,-42.658,-0.0091686,0.091392,-0.99577,529.57
+> ui mousemode right "translate selected models"
+> view matrix models
+> #151,-0.9994,0.032362,0.012172,544.8,0.033337,0.99529,0.091041,-38.35,-0.0091686,0.091392,-0.99577,530.75,#152,-0.9994,0.032362,0.012172,544.8,0.033337,0.99529,0.091041,-38.35,-0.0091686,0.091392,-0.99577,530.75,#153,-0.9994,0.032362,0.012172,544.8,0.033337,0.99529,0.091041,-38.35,-0.0091686,0.091392,-0.99577,530.75,#154,-0.9994,0.032362,0.012172,544.8,0.033337,0.99529,0.091041,-38.35,-0.0091686,0.091392,-0.99577,530.75
+> select subtract #151
+models selected
+> select subtract #152
+models selected
+> select add #152
+models selected
+> select add #151
+models selected
+> select subtract #151
+models selected
+> select subtract #152
+models selected
+> select subtract #153
+models selected
+> select subtract #154
+Nothing selected
+> ui tool show "Fit in Map"
+> fitmap #151 inMap #150
+Fit map cryosparc_P17_J688_007_volume_map.mrc z flip in map
+cryosparc_P17_J693_006_volume_map.mrc using 254273 points
+correlation = 0.995, correlation about mean = 0.9397, overlap = 9.223e+04
+steps = 100, shift = 5.99, angle = 2.29 degrees
+Position of cryosparc_P17_J688_007_volume_map.mrc z flip (#151) relative to
+cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
+Matrix rotation and translation
+-0.99999140 -0.00359338 0.00207026 559.46992299
+-0.00342330 0.99702499 0.07700290 -19.07074818
+-0.00234080 0.07699515 -0.99702872 534.50211369
+Axis -0.00175550 0.99925597 0.03852822
+Axis point 280.01335285 0.00000000 267.30976851
+Rotation angle (degrees) 179.87353804
+Shift along axis 0.55470700
+> fitmap #152 inMap #150
+Fit map cryosparc_P17_J689_008_volume_map.mrc z flip in map
+cryosparc_P17_J693_006_volume_map.mrc using 253853 points
+correlation = 0.995, correlation about mean = 0.939, overlap = 9.217e+04
+steps = 80, shift = 5.92, angle = 2.24 degrees
+Position of cryosparc_P17_J689_008_volume_map.mrc z flip (#152) relative to
+cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
+Matrix rotation and translation
+-0.99999493 -0.00290598 0.00130357 559.46976174
+-0.00279515 0.99693412 0.07819562 -19.59657377
+-0.00152681 0.07819157 -0.99693718 533.82278737
+Axis -0.00142641 0.99923323 0.03912681
+Axis point 279.91004169 0.00000000 267.09682063
+Rotation angle (degrees) 179.91885345
+Shift along axis 0.50720275
+> fitmap #153 inMap #150
+Fit map cryosparc_P17_J691_008_volume_map.mrc z flip in map
+cryosparc_P17_J693_006_volume_map.mrc using 254067 points
+correlation = 0.9949, correlation about mean = 0.9379, overlap = 9.218e+04
+steps = 100, shift = 5.99, angle = 2.29 degrees
+Position of cryosparc_P17_J691_008_volume_map.mrc z flip (#153) relative to
+cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
+Matrix rotation and translation
+-0.99999153 -0.00354328 0.00209321 559.43919323
+-0.00337135 0.99701735 0.07710412 -19.11074723
+-0.00236017 0.07709641 -0.99702085 534.50415261
+Axis -0.00172997 0.99925406 0.03857895
+Axis point 280.00103027 0.00000000 267.30909738
+Rotation angle (degrees) 179.87232473
+Shift along axis 0.55630498
+> fitmap #154 inMap #150
+Fit map cryosparc_P17_J692_009_volume_map.mrc z flip in map
+cryosparc_P17_J693_006_volume_map.mrc using 253930 points
+correlation = 0.9949, correlation about mean = 0.9381, overlap = 9.218e+04
+steps = 76, shift = 5.97, angle = 2.31 degrees
+Position of cryosparc_P17_J692_009_volume_map.mrc z flip (#154) relative to
+cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
+Matrix rotation and translation
+-0.99999289 -0.00347463 0.00146599 559.52836319
+-0.00335259 0.99707669 0.07633372 -18.91952628
+-0.00172694 0.07632826 -0.99708125 534.48491699
+Axis -0.00170809 0.99926890 0.03819344
+Axis point 279.96163715 0.00000000 267.38037953
+Rotation angle (degrees) 179.90846237
+Shift along axis 0.55239822
+> hide #!152 models
+> hide #!153 models
+> hide #!154 models
+> volume #151 level 0.37
+> ui mousemode right zoom
+> lighting soft
+> hide #!153 models
+> show #!153 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!153 models
+> show #!153 models
+> hide #!153 models
+> show #!153 models
+> hide #!153 models
+> show #!154 models
+> hide #!154 models
+> show #!153 models
+> show #!154 models
+> hide #!153 models
+> show #!153 models
+> hide #!154 models
+> show #!154 models
+> hide #!154 models
+> show #!154 models
+> hide #!153 models
+> show #!153 models
+> hide #!153 models
+> hide #!154 models
+> show #!154 models
+> hide #!154 models
+> show #!154 models
+> hide #!154 models
+> show #!154 models
+> hide #!150 models
+> hide #!154 models
+> show #!32 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!74 models
+> hide #!74 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> show #!74 models
+> hide #!74 models
+> hide #!32 models
+> show #!32 models
+> hide #!75 models
+> show #!75 models
+> show #!74 models
+> hide #!75 models
+> show #!75 models
+> hide #!74 models
+> hide #!32 models
+> show #!32 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!32 models
+> show #!130 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J699_class_00_00042_volume.mrc
+Opened cryosparc_P17_J699_class_00_00042_volume.mrc as #155, grid size
+,128,128, pixel 4.36, shown at level 1.37, step 1, values float32
+> hide #!75 models
+> hide #!130 models
+> volume #155 level 1.1
+> volume #155 level 0.5
+> volume #155 level 0.6
+> volume #155 level 0.55
+> open /Users/cvetkom/Downloads/cryosparc_P17_J700_mask.mrc
+Opened cryosparc_P17_J700_mask.mrc as #156, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+> volume #156 level 1
+> volume #156 color #ffffb27e
+> volume #156 color #ffffb27d
+> open /Users/cvetkom/Downloads/cryosparc_P17_J697_006_volume_map.mrc
+Opened cryosparc_P17_J697_006_volume_map.mrc as #157, grid size 294,294,294,
+pixel 1.9, shown at level 0.358, step 2, values float32
+> hide #!155 models
+> hide #!156 models
+> volume #157 step 1
+> volume #157 level 0.3
+> volume #157 level 0.32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J700_mask(1).mrc
+Opened cryosparc_P17_J700_mask(1).mrc as #158, grid size 128,128,128, pixel
+.36, shown at level 1, step 1, values float32
+> hide #!157 models
+> show #!155 models
+> show #!156 models
+> hide #!156 models
+> volume #158 color #b2b2ff7e
+> volume #158 color #b2b2ff7d
+> volume #158 level 1
+> volume #155 level 0.8
+> open /Users/cvetkom/Downloads/cryosparc_P17_J701_006_volume_map.mrc
+Opened cryosparc_P17_J701_006_volume_map.mrc as #159, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 2, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J703_007_volume_map.mrc
+Opened cryosparc_P17_J703_007_volume_map.mrc as #160, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 2, values float32
+> hide #!155 models
+> hide #!158 models
+> volume #159 step 1
+> volume #160 step 1
+> show #!159 models
+> show #!160 models
+> hide #!159 models
+> show #!159 models
+> hide #!159 models
+> show #!159 models
+> hide #!160 models
+> show #!157 models
+> hide #!159 models
+> show #!149 models
+> hide #!149 models
+> show #!149 models
+> hide #!149 models
+> show #!159 models
+> show #!160 models
+> select add #159
+models selected
+> select add #160
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #159,0.97634,0.21152,-0.044828,-40.291,0.16623,-0.86687,-0.47,584,-0.13828,0.45143,-0.88153,384.73,#160,0.97634,0.21152,-0.044828,-40.291,0.16623,-0.86687,-0.47,584,-0.13828,0.45143,-0.88153,384.73
+> view matrix models
+> #159,0.89639,-0.43386,0.09079,125.71,-0.43377,-0.90076,-0.021732,649.03,0.091209,-0.019902,-0.99563,478.69,#160,0.89639,-0.43386,0.09079,125.71,-0.43377,-0.90076,-0.021732,649.03,0.091209,-0.019902,-0.99563,478.69
+> select subtract #159
+models selected
+> select subtract #160
+Nothing selected
+> hide #!159 models
+> hide #!160 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!154 models
+> hide #!154 models
+> show #!159 models
+> hide #!159 models
+> hide #!157 models
+> show #!159 models
+> show #!160 models
+> hide #!159 models
+> hide #!160 models
+> show #!157 models
+> volume #157 level 0.36
+> show #!159 models
+> hide #!159 models
+> show #!159 models
+> hide #!157 models
+> volume flip #157
+Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
+,294,294, pixel 1.9, shown at step 1, values float32
+> hide #!159 models
+> show #!159 models
+> hide #!161 models
+> show #!161 models
+> select add #161
+models selected
+> view matrix models
+> #161,0.76891,-0.22832,0.5972,-18.442,0.24486,-0.75768,-0.60494,582.05,0.59061,0.61138,-0.52668,39.302
+> view matrix models
+> #161,0.67534,0.22196,0.70331,-146.74,0.10898,-0.9732,0.20249,480.95,0.72941,-0.060102,-0.68143,229.96
+> view matrix models
+> #161,-0.93098,0.36002,0.06057,425.2,0.36288,0.89435,0.26166,-136.94,0.040032,0.26557,-0.96326,401.04
+> view matrix models
+> #161,-0.89701,0.43896,0.051772,395.36,0.44113,0.89642,0.042718,-105.12,-0.027658,0.061157,-0.99774,486.85
+> select subtract #161
+Nothing selected
+> fitmap #161 inMap #159
+Fit map cryosparc_P17_J697_006_volume_map.mrc z flip in map
+cryosparc_P17_J701_006_volume_map.mrc using 252025 points
+correlation = 0.9982, correlation about mean = 0.9798, overlap = 9.355e+04
+steps = 112, shift = 10, angle = 4.47 degrees
+Position of cryosparc_P17_J697_006_volume_map.mrc z flip (#161) relative to
+cryosparc_P17_J701_006_volume_map.mrc (#159) coordinates:
+Matrix rotation and translation
+-0.99987255 -0.01520153 -0.00487783 564.75986128
+.01517723 -0.99987242 0.00497921 552.56953504
+-0.00495290 0.00490455 0.99997571 0.88182116
+Axis -0.00245783 0.00247107 0.99999393
+Axis point 280.28257868 278.42842383 0.00000000
+Rotation angle (degrees) 179.12967387
+Shift along axis 0.85917190
+> hide #!161 models
+> show #!161 models
+> hide #!159 models
+> show #!159 models
+> hide #!161 models
+> show #!161 models
+> hide #!159 models
+> show #!159 models
+> hide #!161 models
+> hide #!159 models
+> show #!155 models
+> hide #!155 models
+> show #!151 models
+> volume #151 level 0.36
+> ui mousemode right zoom
+> show #!153 models
+> show #!154 models
+> hide #!153 models
+> hide #!154 models
+> hide #!151 models
+> show #!151 models
+> show #!81 models
+> hide #!81 models
+> show #!81 models
+> hide #!151 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> volume #150 level 0.36
+> hide #!81 models
+> show #!81 models
+> hide #!81 models
+> show #!81 models
+> hide #!81 models
+> show #!81 models
+> hide #!81 models
+> hide #!150 models
+> show #!150 models
+> show #!157 models
+> hide #!157 models
+> show #!159 models
+> hide #!159 models
+> show #!159 models
+> hide #!159 models
+> show #!159 models
+> show #!160 models
+> select add #159
+models selected
+> select add #160
+models selected
+> ui mousemode right "translate selected models"
+> view matrix models
+> #159,0.89639,-0.43386,0.09079,116.59,-0.43377,-0.90076,-0.021732,665.59,0.091209,-0.019902,-0.99563,541.66,#160,0.89639,-0.43386,0.09079,116.59,-0.43377,-0.90076,-0.021732,665.59,0.091209,-0.019902,-0.99563,541.66
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #159,0.99562,-0.092981,0.009532,15.384,-0.093433,-0.98726,0.12878,556.58,-0.0025637,-0.12911,-0.99163,596.92,#160,0.99562,-0.092981,0.009532,15.384,-0.093433,-0.98726,0.12878,556.58,-0.0025637,-0.12911,-0.99163,596.92
+> select subtract #160
+models selected
+> select subtract #159
+Nothing selected
+> fitmap #159 inMap #150
+Fit map cryosparc_P17_J701_006_volume_map.mrc in map
+cryosparc_P17_J693_006_volume_map.mrc using 253555 points
+correlation = 0.995, correlation about mean = 0.9467, overlap = 9.384e+04
+steps = 92, shift = 15.9, angle = 4.91 degrees
+Position of cryosparc_P17_J701_006_volume_map.mrc (#159) relative to
+cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
+Matrix rotation and translation
+.99990377 -0.01280700 0.00533263 1.75411257
+-0.01349030 -0.98727395 0.15845557 514.15896836
+.00323543 -0.15851226 -0.98735171 596.92132464
+Axis -0.99997579 0.00661630 -0.00215569
+Axis point 0.00000000 280.88748875 277.95683594
+Rotation angle (degrees) 170.88086929
+Shift along axis 0.36097960
+> fitmap #160 inMap #150
+Fit map cryosparc_P17_J703_007_volume_map.mrc in map
+cryosparc_P17_J693_006_volume_map.mrc using 254051 points
+correlation = 0.9949, correlation about mean = 0.946, overlap = 9.382e+04
+steps = 140, shift = 15.9, angle = 4.85 degrees
+Position of cryosparc_P17_J703_007_volume_map.mrc (#160) relative to
+cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
+Matrix rotation and translation
+.99989095 -0.01388197 0.00503895 2.09422029
+-0.01450557 -0.98723491 0.15860902 514.34229109
+.00277282 -0.15866482 -0.98732861 597.00803822
+Axis -0.99997256 0.00714230 -0.00196544
+Axis point 0.00000000 281.00771740 277.97254777
+Rotation angle (degrees) 170.87196021
+Shift along axis 0.40604025
+> hide #!160 models
+> hide #!159 models
+> show #!159 models
+> hide #!150 models
+> show #!157 models
+> hide #!157 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> hide #!159 models
+> show #!159 models
+> hide #!159 models
+> show #!160 models
+> hide #!160 models
+> show #!161 models
+> hide #!161 models
+> show #!159 models
+> show #!161 models
+> hide #!161 models
+> show #!160 models
+> hide #!159 models
+> show #!159 models
+> hide #!160 models
+> show #!160 models
+> hide #!159 models
+> show #!159 models
+> hide #!160 models
+> show #!160 models
+> hide #!160 models
+> hide #!159 models
+> show #!159 models
+> show #!160 models
+> hide #!159 models
+> show #!159 models
+> hide #!159 models
+> show #!159 models
+> hide #!160 models
+> show #!160 models
+> hide #!159 models
+> show #!159 models
+> hide #!159 models
+> hide #!160 models
+> show #!159 models
+> hide #!159 models
+> show #!157 models
+> show #!159 models
+> hide #!159 models
+> hide #!157 models
+> show #!150 models
+> show #!159 models
+> hide #!159 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> show #!159 models
+> hide #!150 models
+> show #!150 models
+> hide #!159 models
+> hide #!150 models
+> show #!151 models
+> show #!150 models
+> hide #!151 models
+> show #!151 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> hide #!151 models
+> show #!150 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J693_006_volume_mask_refine.mrc
+Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
+,294,294, pixel 1.9, shown at level 1, step 2, values float32
+> volume #162 step 1
+> volume #162 color #e5bf9980
+> volume #162 level 1
+> volume #162 color #e5bf9967
+> volume #162 color #e5bf9966
+> volume #150 level 0.3
+> volume #150 level 0.2
+> hide #!162 models
+> show #!162 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J704_mask.mrc
+Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
+shown at level 1, step 2, values float32
+> hide #!162 models
+> volume #163 step 1
+> volume #163 color #99bfe565
+> volume #163 color #99bfe566
+> volume #163 level 1
+> show #!162 models
+> hide #!163 models
+> show #!163 models
+> hide #!163 models
+> show #!163 models
+> hide #!163 models
+> show #!163 models
+> hide #!163 models
+> show #!163 models
+> hide #!162 models
+> show #!162 models
+> hide #!162 models
+> show #!162 models
+> hide #!162 models
+> volume #163 level 0.5
+> volume #163 level 1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J707_009_volume_map.mrc
+Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
+pixel 1.9, shown at level 0.358, step 2, values float32
+> hide #!163 models
+> hide #!150 models
+> volume #164 step 1
+> volume #164 level 0.384
+> volume #164 level 0.35
+> volume #164 level 0.3
+> volume #164 level 0.2
+> open /Users/cvetkom/Downloads/cryosparc_P17_J708_mask.mrc
+Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
+shown at level 1, step 2, values float32
+> hide #!164 models
+> show #!164 models
+> hide #!165 models
+> show #!165 models
+> volume #165 step 1
+> volume #165 level 1
+> volume #165 color #b2b2b27c
+> volume #165 color #b2b2b26b
+> volume #165 color #b2b2b263
+> volume #165 color #b2b2b265
+> volume #165 color #b2b2b266
+> hide #!165 models
+> volume #164 level 0.5
+> volume #164 level 0.4
+> open /Users/cvetkom/Downloads/cryosparc_P17_J705_006_volume_map.mrc
+Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
+pixel 1.9, shown at level 0.359, step 2, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J706_004_volume_map.mrc
+Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 2, values float32
+> hide #!164 models
+> volume #166 step 1
+> volume #167 step 1
+> show #!164 models
+> hide #!167 models
+> show #!165 models
+> hide #!165 models
+> hide #!164 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J695_class_00_final_volume.mrc
+Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
+,192,192, pixel 2.91, shown at level 0.544, step 1, values float32
+> volume #168 level 0.3
+> volume #168 level 0.25
+> volume #168 level 0.3
+> open /Users/cvetkom/Downloads/cryosparc_P17_J714_mask.mrc
+Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+> volume #169 color #ffb2ff7d
+> volume #169 color #ffb2ff67
+> volume #169 color #ffb2ff66
+> volume #169 level 1
+> hide #!168 models
+> show #!168 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J715_mask.mrc
+Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+> volume #170 color #ffb2b266
+> volume #170 level 1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J715_mask(1).mrc
+Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
+.91, shown at level 1, step 1, values float32
+> volume #171 color #b2ffb266
+> volume #171 level 1
+> show #!169 models
+> hide #!171 models
+> show #!171 models
+> hide #!169 models
+> show #!169 models
+> hide #!169 models
+> show #!169 models
+> hide #!169 models
+> show #!169 models
+> hide #!169 models
+> show #!169 models
+> hide #!169 models
+> show #!169 models
+> hide #!169 models
+> show #!170 models
+> hide #!171 models
+> show #!171 models
+> hide #!171 models
+> show #!171 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J709_007_volume_map.mrc
+Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
+pixel 1.9, shown at level 0.354, step 2, values float32
+> hide #!168 models
+> hide #!170 models
+> hide #!171 models
+> volume #172 step 1
+> show #!168 models
+> hide #!168 models
+> show #!168 models
+> hide #!168 models
+> show #!164 models
+> hide #!164 models
+> show #!164 models
+> hide #!172 models
+> show #!172 models
+> hide #!164 models
+> volume #172 level 0.4
+> volume #172 level 0.38
+> volume #172 level 0.36
+> open /Users/cvetkom/Downloads/cryosparc_P17_J710_008_volume_map.mrc
+Opened cryosparc_P17_J710_008_volume_map.mrc as #173, grid size 294,294,294,
+pixel 1.9, shown at level 0.354, step 2, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J712_007_volume_map.mrc
+Opened cryosparc_P17_J712_007_volume_map.mrc as #174, grid size 294,294,294,
+pixel 1.9, shown at level 0.349, step 2, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J711_009_volume_map.mrc
+Opened cryosparc_P17_J711_009_volume_map.mrc as #175, grid size 294,294,294,
+pixel 1.9, shown at level 0.353, step 2, values float32
+> hide #!172 models
+> hide #!174 models
+> hide #!173 models
+> show #!173 models
+> hide #!175 models
+> volume #173 step 1
+> volume #174 step 1
+> volume #175 step 1
+> volume #173 level 0.3
+> volume #173 level 0.2
+> show #!164 models
+> hide #!164 models
+> show #!175 models
+> volume #175 level 0.2
+> hide #!175 models
+> show #!175 models
+> hide #!173 models
+> show #!173 models
+> hide #!175 models
+> show #!175 models
+> hide #!175 models
+> volume #173 level 0.25
+> volume #173 level 0.2
+> volume #173 level 0.25
+> open /Users/cvetkom/Downloads/cryosparc_P17_J716_mask.mrc
+Opened cryosparc_P17_J716_mask.mrc as #176, grid size 294,294,294, pixel 1.9,
+shown at level 1, step 2, values float32
+> volume #176 step 1
+> volume #176 color #ffffb266
+> volume #176 level 1
+> close #176
+> open /Users/cvetkom/Downloads/cryosparc_P17_J716_mask.mrc
+Opened cryosparc_P17_J716_mask.mrc as #176, grid size 294,294,294, pixel 1.9,
+shown at level 1, step 2, values float32
+> volume #176 step 1
+> volume #176 color #b2ffff66
+> volume #176 level 1
+> show #!174 models
+> hide #!173 models
+> hide #!176 models
+> volume #174 level 0.2
+> volume #174 level 0.25
+> volume #174 level 0.2
+> show #!173 models
+> hide #!174 models
+> show #!174 models
+> hide #!173 models
+> hide #!174 models
+> show #!151 models
+> show #!152 models
+> show #!153 models
+> show #!154 models
+> hide #!154 models
+> hide #!153 models
+> hide #!152 models
+> show #!152 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!152 models
+> show #!152 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!152 models
+> show #!152 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!152 models
+> show #!153 models
+> hide #!151 models
+> show #!154 models
+> hide #!153 models
+> show #!153 models
+> hide #!153 models
+> show #!153 models
+> hide #!154 models
+> show #!154 models
+> hide #!154 models
+> show #!154 models
+> hide #!153 models
+> show #!153 models
+> hide #!154 models
+> show #!154 models
+> hide #!153 models
+> show #!153 models
+> hide #!153 models
+> show #!153 models
+> hide #!154 models
+> show #!152 models
+> hide #!152 models
+> hide #!153 models
+> show #!152 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!152 models
+> show #!152 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!152 models
+> show #!153 models
+> hide #!153 models
+> show #!147 models
+> hide #!151 models
+> hide #!147 models
+> show #!147 models
+> show #!145 models
+> hide #!145 models
+> hide #!147 models
+> show #!145 models
+> hide #!145 models
+> show #!175 models
+> show #!174 models
+> hide #!175 models
+> hide #!174 models
+> show #!167 models
+> hide #!167 models
+> show #!168 models
+> hide #!168 models
+> show #!167 models
+> hide #!167 models
+> show #!168 models
+> hide #!168 models
+> show #!166 models
+> hide #!166 models
+> show #!173 models
+> show #!174 models
+> hide #!174 models
+> hide #!173 models
+> show #!161 models
+> hide #!161 models
+> show #!160 models
+> hide #!160 models
+> show #!154 models
+> show #!153 models
+> hide #!154 models
+> show #!154 models
+> hide #!154 models
+> hide #!153 models
+> show #!152 models
+> show #!153 models
+> hide #!153 models
+> hide #!152 models
+> show #!151 models
+> hide #!151 models
+> show #!150 models
+> hide #!150 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes_ref.cxs
+> ui mousemode right zoom
+[Repeated 1 time(s)]
+> show #!176 models
+> hide #!176 models
+> show #!175 models
+> hide #!175 models
+> show #!175 models
+> hide #!175 models
+> show #!174 models
+> hide #!174 models
+> show #!173 models
+> hide #!173 models
+> show #!172 models
+> hide #!172 models
+> show #!171 models
+> hide #!171 models
+> open 6SKL fromDatabase pdb format mmcif
+skl title:
+Cryo-EM structure of the CMG Fork Protection Complex at a replication fork -
+Conformation 1 [more info...]
+Chain information for 6skl #177
+---
+Chain | Description | UniProt
+| DNA replication licensing factor MCM2 | MCM2_YEAST 1-868
+| DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
+| DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
+| Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
+| DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
+| DNA replication licensing factor MCM7 | MCM7_YEAST 1-845
+A | DNA replication complex GINS protein PSF1 | PSF1_YEAST 1-208
+B | DNA replication complex GINS protein PSF2 | PSF2_YEAST 1-213
+C | DNA replication complex GINS protein PSF3 | PSF3_YEAST 1-194
+D | DNA replication complex GINS protein SLD5 | SLD5_YEAST 1-294
+E | Cell division control protein 45 | CDC45_YEAST 1-650
+F G H | DNA polymerase alpha-binding protein | CTF4_YEAST 1-927
+I | DNA fork, leading-strand template |
+J | DNA fork, lagging-strand template |
+X | Topoisomerase 1-associated factor 1 | TOF1_YEAST 1-1238
+Y | Chromosome segregation in meiosis protein 3 | CSM3_YEAST 1-317
+Non-standard residues in 6skl #177
+---
+ANP \u2014 phosphoaminophosphonic acid-adenylate ester
+MG \u2014 magnesium ion
+ZN \u2014 zinc ion
+> lighting simple
+> select /2
+atoms, 10708 bonds, 8 pseudobonds, 672 residues, 3 models selected
+> select /6
+atoms, 10126 bonds, 9 pseudobonds, 638 residues, 3 models selected
+> select /4
+atoms, 10952 bonds, 11 pseudobonds, 680 residues, 3 models selected
+> select /5
+atoms, 9789 bonds, 11 pseudobonds, 614 residues, 3 models selected
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes_ref.cxs
+\u2014\u2014\u2014 End of log from Fri Jun 21 11:35:11 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> select add #177
+atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
+> select subtract #177
+Nothing selected
+> hide #!177 models
+> show #!174 models
+> hide #!174 models
+> show #!166 models
+> show #!167 models
+> hide #!166 models
+> show #!166 models
+> hide #!167 models
+> show #!167 models
+> hide #!166 models
+> show #!166 models
+> hide #!167 models
+> hide #!166 models
+> show #!166 models
+> show #!172 models
+> hide #!166 models
+> show #!166 models
+> hide #!166 models
+> show #!166 models
+> hide #!166 models
+> show #!166 models
+> hide #!166 models
+> show #!166 models
+> hide #!166 models
+> show #!166 models
+> hide #!166 models
+> show #!166 models
+> hide #!172 models
+> hide #!166 models
+> show #!172 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J721_006_volume_map.mrc
+Opened cryosparc_P17_J721_006_volume_map.mrc as #158, grid size 294,294,294,
+pixel 1.9, shown at level 0.346, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J719_007_volume_map.mrc
+Opened cryosparc_P17_J719_007_volume_map.mrc as #178, grid size 294,294,294,
+pixel 1.9, shown at level 0.35, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J717_007_volume_map.mrc
+Opened cryosparc_P17_J717_007_volume_map.mrc as #179, grid size 294,294,294,
+pixel 1.9, shown at level 0.35, step 2, values float32
+> hide #!172 models
+> show #!172 models
+> hide #!172 models
+> volume #179 step 1
+> volume #178 step 1
+> volume #178 level 0.4299
+> volume #158 step 1
+> close #158
+> close #179
+> close #178
+> open /Users/cvetkom/Downloads/cryosparc_P17_J709_007_volume_map_sharp.mrc
+Opened cryosparc_P17_J709_007_volume_map_sharp.mrc as #158, grid size
+,294,294, pixel 1.9, shown at level 0.35, step 2, values float32
+> volume #158 step 1
+> volume #158 level 0.4035
+> volume #158 level 0.3381
+> show #!172 models
+> show #!166 models
+> hide #!172 models
+> hide #!166 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J645_010_volume_map_sharp.mrc
+Opened cryosparc_P17_J645_010_volume_map_sharp.mrc as #178, grid size
+,588,588, pixel 0.95, shown at level 0.158, step 4, values float32
+> volume #178 step 1
+> volume #178 level 0.5544
+> volume #178 level 0.3502
+> close #178
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc
+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
+,588,588, pixel 0.95, shown at level 0.957, step 4, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J544_007_volume_map_zflip.mrc
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
+,588,588, pixel 0.95, shown at level 0.158, step 4, values float32
+> volume #178 step 1
+> volume #178 level 0.9947
+> volume #179 step 1
+> volume #179 level 0.1617
+> volume #179 level 0.152
+> show #!172 models
+> hide #!172 models
+> lighting soft
+> volume #179 level 0.1695
+> hide #!179 models
+> show #!172 models
+> volume #172 level 0.3737
+> show #!166 models
+> hide #!166 models
+> show #!166 models
+> hide #!166 models
+> show #!166 models
+> hide #!172 models
+> volume #166 level 0.3843
+> show #!172 models
+> hide #!172 models
+> show #!172 models
+> hide #!172 models
+> show #!172 models
+> hide #!166 models
+> hide #!172 models
+> show #!178 models
+> hide #!178 models
+> show #!172 models
+> volume #172 level 0.3509
+> show #!171 models
+> hide #!171 models
+> hide #!172 models
+> show #!179 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J709_007_volume_map.mrc
+Opened cryosparc_P17_J709_007_volume_map.mrc as #180, grid size 294,294,294,
+pixel 1.9, shown at level 0.354, step 2, values float32
+> hide #!179 models
+> hide #!180 models
+> close #180
+> open /Users/cvetkom/Downloads/cryosparc_P17_J787_004_volume_map_sharp.mrc
+Opened cryosparc_P17_J787_004_volume_map_sharp.mrc as #180, grid size
+,588,588, pixel 0.95, shown at level 0.196, step 4, values float32
+> volume #180 level 0.3198
+> volume #180 step 1
+> volume #180 level 0.4233
+> volume #180 level 0.4003
+> open /Users/cvetkom/Downloads/cryosparc_P17_J786_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J786_005_volume_map_sharp.mrc as #181, grid size
+,588,588, pixel 0.95, shown at level 0.204, step 4, values float32
+> volume #181 step 1
+> volume #181 level 0.3442
+> volume #181 level 0.4
+> open /Users/cvetkom/Downloads/cryosparc_P17_J787_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J787_005_volume_map_sharp.mrc as #182, grid size
+,588,588, pixel 0.95, shown at level 0.21, step 4, values float32
+> hide #!181 models
+> volume #182 step 1
+> volume #182 level 0.3526
+> volume #182 level 0.4
+> show #!181 models
+> hide #!181 models
+> show #!181 models
+> hide #!181 models
+> show #!181 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!181 models
+> open /Volumes/lab-
+> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/MaskCreate/job690/mask.mrc
+Opened mask.mrc as #183, grid size 588,588,588, pixel 0.95, shown at level 1,
+step 4, values float32
+> close #183
+> open /Users/cvetkom/Downloads/cryosparc_P17_J792_volume_map_sharp.mrc
+Opened cryosparc_P17_J792_volume_map_sharp.mrc as #183, grid size 520,520,520,
+pixel 0.95, shown at level 0.153, step 4, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J792_volume_mask_fsc.mrc
+Opened cryosparc_P17_J792_volume_mask_fsc.mrc as #184, grid size 520,520,520,
+pixel 0.95, shown at level 5e-05, step 4, values float32
+> hide #!182 models
+> volume #183 step 1
+> volume #183 level 0.3916
+> lighting soft
+> lighting full
+> volume #184 step 1
+> volume #184 level 1
+> volume #184 color #b2b2ff80
+> volume #184 level 0
+> volume #184 level 0.03512
+> open /Users/cvetkom/Downloads/cryosparc_P17_J760_mask(1).mrc
+Opened cryosparc_P17_J760_mask(1).mrc as #185, grid size 520,520,520, pixel
+.95, shown at level 5e-05, step 4, values float32
+> volume #185 step 1
+> volume #185 color #ffb2ff7f
+> volume #185 level 1
+[Repeated 1 time(s)]
+> open /Users/cvetkom/Downloads/cryosparc_P17_J757_volume_map.mrc
+Opened cryosparc_P17_J757_volume_map.mrc as #186, grid size 520,520,520, pixel
+.95, shown at level 0.0189, step 4, values float32
+> volume #186 level 0.07565
+> volume #186 step 1
+> hide #!183 models
+> hide #!185 models
+> volume #186 level 0.1989
+> volume #186 level 0.1509
+> open /Users/cvetkom/Downloads/cryosparc_P17_J792_volume_map.mrc
+Opened cryosparc_P17_J792_volume_map.mrc as #187, grid size 520,520,520, pixel
+.95, shown at level 0.0388, step 4, values float32
+> hide #!183 models
+> hide #!186 models
+> volume #187 level 0.0929
+> volume #187 step 1
+> volume #187 level 0.2473
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!186 models
+> volume #186 level 0.1781
+> hide #!186 models
+> show #!186 models
+> hide #!186 models
+> show #!186 models
+> volume #186 level 0.2261
+> hide #!186 models
+> show #!186 models
+> hide #!186 models
+> show #!184 models
+> show #!185 models
+> volume #184 level 1
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!183 models
+> hide #!183 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J795_007_volume_map.mrc
+Opened cryosparc_P17_J795_007_volume_map.mrc as #188, grid size 520,520,520,
+pixel 0.95, shown at level 0.0131, step 4, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J795_007_volume_map_sharp.mrc
+Opened cryosparc_P17_J795_007_volume_map_sharp.mrc as #189, grid size
+,520,520, pixel 0.95, shown at level 0.0597, step 4, values float32
+> hide #!184 models
+> hide #!187 models
+> volume #188 level 0.1056
+> volume #188 step 1
+> volume #188 level 0.2671
+> volume #188 level 0.2362
+> volume #189 level 0.3385
+> volume #189 step 1
+> close #188-189
+> close #185
+> close #184
+> open /Users/cvetkom/Downloads/cryosparc_P17_J797_009_volume_map_sharp.mrc
+Opened cryosparc_P17_J797_009_volume_map_sharp.mrc as #184, grid size
+,520,520, pixel 0.95, shown at level 0.213, step 4, values float32
+> volume #184 level 0.4718
+> volume #184 step 1
+> volume #184 level 0.7484
+> volume #184 level 0.846
+> show #!183 models
+> hide #!183 models
+> show #!183 models
+> hide #!183 models
+> show #!183 models
+> hide #!183 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J797_009_volume_map.mrc
+Opened cryosparc_P17_J797_009_volume_map.mrc as #185, grid size 520,520,520,
+pixel 0.95, shown at level 0.0436, step 4, values float32
+> hide #!185 models
+> show #!185 models
+> hide #!184 models
+> volume #185 level 0.2092
+> volume #185 step 1
+> volume #185 level 0.2795
+> lighting soft
+> volume #185 level 0.2092
+> volume #185 level 0.08268
+> volume #185 level 0.1858
+> volume #185 level 0.1904
+> volume #185 level 0.2279
+> open /Users/cvetkom/Downloads/cryosparc_P17_J760_mask(1).mrc
+Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
+.95, shown at level 5e-05, step 4, values float32
+> volume #188 step 1
+> volume #188 level 0.9982
+> volume #188 color #ffffb280
+> volume #188 color #ffffb266
+> volume #185 level 0.2607
+> show #!183 models
+> hide #!183 models
+> show #!183 models
+> show #!182 models
+> hide #!182 models
+> show #!181 models
+> hide #!181 models
+> show #!181 models
+> hide #!181 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!183 models
+> volume #185 level 0.256
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!180 models
+> hide #!180 models
+> show #!177 models
+> hide #!177 models
+> show #!178 models
+> hide #!178 models
+> show #!179 models
+> hide #!179 models
+> show #!180 models
+> show #!182 models
+> hide #!182 models
+> close #180
+> show #!181 models
+> hide #!181 models
+> show #!179 models
+> hide #!179 models
+> show #!181 models
+> hide #!181 models
+> show #!182 models
+> show #!181 models
+> hide #!181 models
+> show #!181 models
+> hide #!181 models
+> show #!181 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!181 models
+> show #!181 models
+> hide #!181 models
+> show #!181 models
+> hide #!182 models
+> show #!179 models
+> hide #!179 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!181 models
+> show #!183 models
+> hide #!183 models
+> show #!184 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!184 models
+> volume #185 level 0.2841
+> show #!184 models
+> volume #184 level 0.7159
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!185 models
+> show #!185 models
+> hide #!182 models
+> volume #185 level 0.3076
+> open /Users/cvetkom/Downloads/cryosparc_P17_J802_009_volume_map.mrc
+Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
+pixel 0.95, shown at level 0.0442, step 4, values float32
+> hide #!185 models
+> volume #180 level 0.09552
+> volume #180 step 1
+> volume #180 level 0.2625
+> show #!182 models
+> hide #!182 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!180 models
+> show #!180 models
+> hide #!185 models
+> volume #180 level 0.2996
+> open /Users/cvetkom/Downloads/cryosparc_P17_J802_009_volume_map_sharp.mrc
+Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
+,520,520, pixel 0.95, shown at level 0.217, step 4, values float32
+> volume #189 step 1
+> volume #189 level 0.3
+> volume #189 level 0.7605
+> hide #!189 models
+> show #!185 models
+> volume #185 level 0.31
+> volume #180 level 0.31
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> select add #180
+models selected
+> color #180.1 cornflower blue
+> select subtract #180
+Nothing selected
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> hide #!180 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J803_005_volume_map.mrc
+Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
+pixel 0.95, shown at level 0.109, step 4, values float32
+> volume #190 level 0.1683
+> volume #190 step 1
+> volume #190 level 0.1911
+> volume #190 level 0.3013
+> open /Users/cvetkom/Downloads/cryosparc_P17_J803_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
+,588,588, pixel 0.95, shown at level 0.211, step 4, values float32
+> volume #191 level 0.2508
+> volume #191 step 1
+> volume #191 level 0.4399
+> volume #191 color #005493
+> volume #191 color #009193
+> select add #191
+models selected
+> ui tool show "Color Actions"
+> color sel medium blue
+> color sel light sea green
+> select subtract #191
+Nothing selected
+> volume #191 level 0.3926
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> show #!181 models
+> hide #!181 models
+> hide #!191 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> volume #191 level 0.39
+> hide #!182 models
+> show #!182 models
+> hide #!191 models
+> show #!191 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> volume #182 level 0.39
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J811_volume_map.mrc
+Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
+.95, shown at level 0.00828, step 4, values float32
+> hide #!191 models
+> volume #192 level 0.03286
+> volume #192 step 1
+> volume #192 color #4f8f00
+> volume #192 color #009051
+> volume #192 level 0.07832
+> volume #192 level 0.1052
+> volume #192 level 0.1
+> volume #192 level 0.3
+> volume #192 level 0.15
+> volume #192 level 0.12
+> volume #192 level 0.1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J813_mask.mrc
+Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
+shown at level 5e-05, step 4, values float32
+> volume #193 step 1
+> volume #193 color #e5bf9980
+> volume #193 color #e5bf9967
+> volume #193 color #e5bf9966
+> volume #193 level 1
+> volume #192 level 0.1186
+> volume #193 level 0.5009
+> volume #193 level 1
+> volume #192 level 0.1434
+> volume #192 level 0.1217
+> close #193
+> open /Users/cvetkom/Downloads/cryosparc_P17_J813_mask.mrc
+Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
+shown at level 5e-05, step 4, values float32
+> volume #193 level 1
+> volume #193 step 1
+> volume #193 color #99bfe574
+> volume #193 color #99bfe567
+> volume #193 color #99bfe566
+> volume #192 level 0.1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J812_volume_map.mrc
+Opened cryosparc_P17_J812_volume_map.mrc as #194, grid size 520,520,520, pixel
+.95, shown at level 0.0198, step 4, values float32
+> volume #194 level 0.05264
+> volume #194 step 1
+> volume #194 level 0.09845
+> volume #194 level 0.1
+> volume #194 level 0.12
+> close #194
+> show #!189 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J805_008_volume_map.mrc
+Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
+pixel 0.95, shown at level 0.0442, step 4, values float32
+> hide #!189 models
+> volume #194 level 0.2318
+> volume #194 step 1
+> volume #194 level 0.1158
+> volume #194 level 0.3478
+> open /Users/cvetkom/Downloads/cryosparc_P17_J817_class_00_00116_volume.mrc
+Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
+,336,336, pixel 1.47, shown at level 0.0447, step 2, values float32
+> hide #!194 models
+> volume #195 level 0.2559
+> volume #195 step 1
+> volume #195 level 0.2828
+> open /Users/cvetkom/Downloads/cryosparc_P17_J817_class_04_00116_volume.mrc
+Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
+,336,336, pixel 1.47, shown at level 0.0135, step 2, values float32
+> volume #196 step 1
+> volume #196 level 0.1881
+> volume #196 level 0.2658
+> volume #196 level 0.2887
+> open /Users/cvetkom/Downloads/cryosparc_P17_J819_005_volume_map.mrc
+Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
+pixel 0.95, shown at level 0.108, step 4, values float32
+> hide #!195 models
+> hide #!196 models
+> volume #197 level 0.1961
+> volume #197 step 1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J819_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
+,588,588, pixel 0.95, shown at level 0.207, step 4, values float32
+> volume #198 level 0.3147
+> volume #198 step 1
+> volume #198 level 0.4907
+> volume #198 level 0.46
+> volume #198 level 0.4
+> volume #198 level 0.36
+> volume #198 level 0.46
+> open /Users/cvetkom/Downloads/cryosparc_P17_J822_volume_map.mrc
+Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
+.95, shown at level 0.121, step 4, values float32
+> hide #!199 models
+> show #!199 models
+> hide #!198 models
+> volume #199 step 1
+> volume #199 level 0.12
+> volume #199 level 0.15
+> volume #199 level 0.16
+> volume #199 level 0.15
+> open /Users/cvetkom/Downloads/cryosparc_P17_J823_mask.mrc
+Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
+shown at level 1, step 4, values float32
+> volume #200 step 1
+> volume #200 color #b2ffb283
+> volume #200 color #b2ffb26c
+> volume #200 color #b2ffb26b
+> volume #200 level 1
+> close #200
+> open /Users/cvetkom/Downloads/cryosparc_P17_J823_mask.mrc
+Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
+shown at level 1, step 4, values float32
+> color #200 #e5bf996b models
+> color #200 #e5bf9968 models
+> color #200 #e5bf9967 models
+> color #200 #e5bf9966 models
+> volume #200 step 1
+> volume #200 level 1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J824_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
+,588,588, pixel 0.95, shown at level 0.191, step 4, values float32
+> hide #!200 models
+> hide #!199 models
+> volume #201 level 0.4868
+> volume #201 step 1
+> volume #201 level 0.46
+> volume #201 level 0.4
+> volume #201 level 0.38
+> volume #201 level 0.3
+> volume #201 level 0.32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class001.mrc
+Opened Cl3D_j718_run_it025_class001.mrc as #202, grid size 520,520,520, pixel
+.95, shown at level 7.31e-07, step 4, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class002.mrc
+Opened Cl3D_j718_run_it025_class002.mrc as #203, grid size 520,520,520, pixel
+.95, shown at level 6.19e-07, step 4, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class003.mrc
+Opened Cl3D_j718_run_it025_class003.mrc as #204, grid size 520,520,520, pixel
+.95, shown at level 5.74e-07, step 4, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class004.mrc
+Opened Cl3D_j718_run_it025_class004.mrc as #205, grid size 520,520,520, pixel
+.95, shown at level 1.81e-06, step 4, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class005.mrc
+Opened Cl3D_j718_run_it025_class005.mrc as #206, grid size 520,520,520, pixel
+.95, shown at level 5.25e-07, step 4, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class006.mrc
+Opened Cl3D_j718_run_it025_class006.mrc as #207, grid size 520,520,520, pixel
+.95, shown at level 2.64e-07, step 4, values float32
+> hide #!201 models
+> hide #!203 models
+> hide #!204 models
+> hide #!205 models
+> hide #!206 models
+> hide #!207 models
+> volume #202 step 1
+> volume #202 level 0.001537
+> volume #203 step 1
+> volume #203 level 0.00429
+> hide #!203 models
+> show #!205 models
+> volume #205 step 1
+> volume #205 level 0.006238
+> volume #205 level 0.007973
+> hide #!205 models
+> show #!205 models
+> hide #!205 models
+> volume #206 step 1
+> volume #206 level 0.003432
+> volume #206 level 0.004328
+> volume #202 level 0.001682
+> show #!205 models
+> hide #!205 models
+> show #!205 models
+> hide #!205 models
+> volume #202 level 0.001267
+> volume #203 level 0.004002
+> volume #204 step 1
+> volume #204 level 0.004153
+> volume #204 level 0.003947
+> volume #206 level 0.004481
+> volume #207 step 1
+> volume #207 level 0.00211
+> hide #!207 models
+> show #!205 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J828_volume_map.mrc
+Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
+.95, shown at level 0.14, step 4, values float32
+> hide #!205 models
+> volume #208 step 1
+> volume #208 level 0.1685
+> volume #208 level 0.1611
+> volume #208 level 0.08448
+> open /Users/cvetkom/Downloads/cryosparc_P17_J829_class_00_final_volume.mrc
+Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
+,192,192, pixel 2.91, shown at level 0.585, step 1, values float32
+> hide #!208 models
+> volume #209 level 0.5
+> volume #209 level 0.4
+> volume #209 level 0.45
+> volume #209 level 0.5
+> open /Users/cvetkom/Downloads/cryosparc_P17_J830_mask.mrc
+Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+> volume #210 color #e5bf9975
+> volume #210 color #e5bf9967
+> volume #210 color #e5bf9966
+> volume #210 level 1
+[Repeated 1 time(s)]
+> hide #!210 models
+> hide #!209 models
+> show #!201 models
+> hide #!201 models
+> show #!201 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J825_006_volume_map_sharp.mrc
+Opened cryosparc_P17_J825_006_volume_map_sharp.mrc as #211, grid size
+,588,588, pixel 0.95, shown at level 0.189, step 4, values float32
+> volume #211 step 1
+> volume #211 level 0.3194
+> volume #211 level 0.32
+> hide #!201 models
+> show #!201 models
+> hide #!201 models
+> show #!201 models
+> hide #!211 models
+> show #!211 models
+> hide #!211 models
+> show #!211 models
+> color #211 #ff40ffff models
+> color #211 #7a81ffff models
+> hide #!201 models
+> show #!201 models
+> hide #!211 models
+> show #!211 models
+> hide #!211 models
+> show #!211 models
+> show #!202 models
+> hide #!201 models
+> hide #!202 models
+> volume #211 level 0.35
+> show #!201 models
+> hide #!211 models
+> volume #201 level 0.35
+> open /Users/cvetkom/Downloads/cryosparc_P17_J831_007_volume_map_sharp.mrc
+Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
+,588,588, pixel 0.95, shown at level 0.148, step 4, values float32
+> hide #!201 models
+> volume #212 level 0.4011
+> volume #212 step 1
+> show #!201 models
+> hide #!201 models
+> show #!211 models
+> hide #!211 models
+> show #!211 models
+> select add #211
+models selected
+> ui mousemode right "rotate selected models"
+Drag select of 211 cryosparc_P17_J825_006_volume_map_sharp.mrc , 212
+cryosparc_P17_J831_007_volume_map_sharp.mrc
+> select subtract #212
+models selected
+> view matrix models
+> #211,0.99974,0.0073342,0.021665,-7.9265,-0.0059368,0.99794,-0.063871,19.839,-0.022089,0.063726,0.99772,-10.804
+> view matrix models
+> #211,-0.83053,-0.50843,-0.22743,701.17,-0.55206,0.80558,0.21509,144.3,0.073856,0.30419,-0.94974,435.51
+> select subtract #211
+Nothing selected
+> ui tool show "Fit in Map"
+> fitmap #211 inMap #212
+Fit map cryosparc_P17_J825_006_volume_map_sharp.mrc in map
+cryosparc_P17_J831_007_volume_map_sharp.mrc using 491366 points
+correlation = 0.5456, correlation about mean = 0.05943, overlap = 5.974e+04
+steps = 436, shift = 6.8, angle = 10.9 degrees
+Position of cryosparc_P17_J825_006_volume_map_sharp.mrc (#211) relative to
+cryosparc_P17_J831_007_volume_map_sharp.mrc (#212) coordinates:
+Matrix rotation and translation
+-0.89957058 -0.40667531 -0.15933603 680.38831906
+-0.42615436 0.89716922 0.11610278 108.46539449
+.09573525 0.17234438 -0.98037349 475.76940193
+Axis 0.21472534 -0.97383892 -0.07436926
+Axis point 336.07482386 0.00000000 256.67979639
+Rotation angle (degrees) 172.47482888
+Shift along axis 5.08617368
+Correlation = 0.5456, Correlation about mean = 0.05943, Overlap = 5.974e+04
+> fitmap #211 inMap #212
+Fit map cryosparc_P17_J825_006_volume_map_sharp.mrc in map
+cryosparc_P17_J831_007_volume_map_sharp.mrc using 491366 points
+correlation = 0.5457, correlation about mean = 0.0594, overlap = 5.974e+04
+steps = 44, shift = 0.0378, angle = 0.0389 degrees
+Position of cryosparc_P17_J825_006_volume_map_sharp.mrc (#211) relative to
+cryosparc_P17_J831_007_volume_map_sharp.mrc (#212) coordinates:
+Matrix rotation and translation
+-0.89980651 -0.40634880 -0.15883608 680.25943553
+-0.42572683 0.89739120 0.11595559 108.32590029
+.09541969 0.17195838 -0.98047203 475.96728322
+Axis 0.21451210 -0.97389690 -0.07422527
+Axis point 336.02953423 0.00000000 256.71123961
+Rotation angle (degrees) 172.49947586
+Shift along axis 5.09681985
+> select add #211
+models selected
+> view matrix models
+> #211,-0.90089,-0.40799,-0.14811,678.04,-0.41938,0.90616,0.054752,121.11,0.11187,0.11144,-0.98745,489.99
+> volume #211 level 0.4
+> select subtract #211
+Nothing selected
+> fitmap #211 inMap #212
+Fit map cryosparc_P17_J825_006_volume_map_sharp.mrc in map
+cryosparc_P17_J831_007_volume_map_sharp.mrc using 381853 points
+correlation = 0.9767, correlation about mean = 0.8803, overlap = 1.862e+05
+steps = 388, shift = 8.54, angle = 19 degrees
+Position of cryosparc_P17_J825_006_volume_map_sharp.mrc (#211) relative to
+cryosparc_P17_J831_007_volume_map_sharp.mrc (#212) coordinates:
+Matrix rotation and translation
+-0.97678811 -0.20990860 -0.04270100 623.15903654
+-0.20103231 0.96714269 -0.15563105 99.70859450
+.07396625 -0.14343428 -0.98689189 576.21341964
+Axis 0.10368016 -0.99174448 0.07545400
+Axis point 308.25071118 0.00000000 301.13328663
+Rotation angle (degrees) 176.62796126
+Shift along axis 9.20139044
+> hide #!212 models
+> show #!212 models
+> hide #!212 models
+> show #!212 models
+> hide #!212 models
+> show #!212 models
+> hide #!212 models
+> show #!212 models
+> hide #!212 models
+> show #!212 models
+> hide #!212 models
+> show #!212 models
+> hide #!212 models
+> show #!212 models
+> hide #!212 models
+> show #!212 models
+> hide #!212 models
+> show #!212 models
+> hide #!212 models
+> show #!212 models
+> hide #!212 models
+> show #!212 models
+> hide #!211 models
+> volume #212 level 0.4
+> volume #212 level 0.38
+> volume #212 level 0.35
+> open /Users/cvetkom/Downloads/cryosparc_P17_J831_007_volume_mask_refine.mrc
+Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
+,588,588, pixel 0.95, shown at level 1, step 4, values float32
+> volume #213 color #b2b2b259
+> volume #213 step 1
+> volume #213 level 1
+> volume #212 level 0.2391
+> close #211
+> open /Users/cvetkom/Downloads/cryosparc_P17_J843_008_volume_map_sharp.mrc
+Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
+,520,520, pixel 0.95, shown at level 0.249, step 4, values float32
+> hide #!211 models
+> hide #!212 models
+> hide #!213 models
+> show #!211 models
+> volume #211 level 0.7129
+> volume #211 step 1
+> volume #211 level 0.5829
+> volume #211 level 0.56
+> volume #211 level 0.55
+> volume #211 level 0.5
+> show #!194 models
+> hide #!194 models
+> show #!189 models
+> hide #!189 models
+> show #!189 models
+> hide #!189 models
+> show #!189 models
+> hide #!189 models
+> volume #211 level 0.55
+> show #!189 models
+> hide #!189 models
+> show #!189 models
+> volume #189 level 0.6
+> hide #!189 models
+> show #!189 models
+> hide #!189 models
+> ui mousemode right zoom
+> hide #!211 models
+> show #!210 models
+> hide #!210 models
+> show #!202 models
+> hide #!202 models
+> show #!203 models
+> hide #!203 models
+> show #!204 models
+> hide #!204 models
+> show #!205 models
+> hide #!205 models
+> show #!206 models
+> hide #!206 models
+> show #!207 models
+> close #202-207
+> show #!176 models
+> hide #!176 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> show #!130 models
+> hide #!129 models
+> hide #!130 models
+> show #!131 models
+> hide #!131 models
+> show #!132 models
+> hide #!132 models
+> show #!133 models
+> show #!134 models
+> show #!135 models
+> hide #!134 models
+> hide #!133 models
+> show #!133 models
+> hide #!135 models
+> show #!134 models
+> hide #!134 models
+> show #!134 models
+> hide #!134 models
+> show #!134 models
+> hide #!134 models
+> hide #!133 models
+> show #!133 models
+> show #!134 models
+> hide #!134 models
+> hide #!133 models
+> show #!129 models
+> show #!130 models
+> hide #!129 models
+> hide #!130 models
+> show #!131 models
+> hide #!131 models
+> show #!131 models
+> hide #!131 models
+> show #!132 models
+> hide #!132 models
+> show #!133 models
+> show #!134 models
+> hide #!133 models
+> show #!133 models
+> hide #!133 models
+> hide #!134 models
+> show #!110 models
+> show #!111 models
+> hide #!110 models
+> show #!110 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> hide #!110 models
+> show #!110 models
+> show #!111 models
+> hide #!110 models
+> hide #!111 models
+> show #!112 models
+> show #!120 models
+> hide #!120 models
+> show #!133 models
+> hide #!133 models
+> show #!133 models
+> hide #!112 models
+> show #!112 models
+> hide #!133 models
+> show #!134 models
+> hide #!112 models
+> show #!113 models
+> hide #!113 models
+> show #!113 models
+> hide #!113 models
+> show #!110 models
+> hide #!110 models
+> show #!111 models
+> hide #!111 models
+> show #!112 models
+> hide #!112 models
+> show #!113 models
+> hide #!113 models
+> show #!114 models
+> hide #!114 models
+> show #!115 models
+> hide #!115 models
+> show #!115 models
+> hide #!115 models
+> show #!115 models
+> hide #!115 models
+> hide #!134 models
+> show #!110 models
+> show #!111 models
+> hide #!110 models
+> show #!110 models
+> hide #!111 models
+> show #!71 models
+> hide #!71 models
+> show #!130 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> hide #!130 models
+> show #!110 models
+> show #!98 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!98 models
+> show #!98 models
+> hide #!110 models
+> hide #!98 models
+> show #!105 models
+> show #!106 models
+> hide #!105 models
+> hide #!106 models
+> show #!117 models
+> show #!118 models
+> hide #!117 models
+> hide #!118 models
+> show #!74 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!74 models
+> show #!74 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!74 models
+> hide #!75 models
+> show #!70 models
+> show #!71 models
+> hide #!70 models
+> show #!70 models
+> hide #!70 models
+> show #!70 models
+> hide #!71 models
+> show #!72 models
+> hide #!72 models
+> show #!73 models
+> hide #!73 models
+> show #!73 models
+> hide #!73 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!70 models
+> show #!75 models
+> hide #!74 models
+> hide #!75 models
+> show #!75 models
+> show #!74 models
+> hide #!74 models
+> hide #!75 models
+> show #!74 models
+> hide #!74 models
+> show #!75 models
+> hide #!75 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> show #!98 models
+> hide #!98 models
+> hide #!130 models
+> show #!130 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!130 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> show #!129 models
+> show #!130 models
+> hide #!98 models
+> hide #!99 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!129 models
+> show #!129 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!129 models
+> show #!139 models
+> hide #!139 models
+> show #!139 models
+> hide #!139 models
+> show #!139 models
+> hide #!130 models
+> show #!138 models
+> hide #!139 models
+> show #!143 models
+> hide #!143 models
+> show #!143 models
+> hide #!138 models
+> hide #!143 models
+> show #!141 models
+> show #!147 models
+> hide #!147 models
+> show #!147 models
+> hide #!141 models
+> show #!141 models
+> hide #!141 models
+> hide #!147 models
+> show #!140 models
+> hide #!140 models
+> show #!145 models
+> show #!146 models
+> hide #!146 models
+> show #!146 models
+> hide #!145 models
+> hide #!146 models
+> show #!148 models
+> hide #!148 models
+> show #!157 models
+> hide #!157 models
+> show #!161 models
+> hide #!161 models
+> show #!174 models
+> hide #!174 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J721_006_volume_map.mrc
+Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
+pixel 1.9, shown at level 0.346, step 2, values float32
+> volume #202 step 1
+> volume #202 level 0.3331
+> show #!157 models
+> hide #!157 models
+> show #!157 models
+> hide #!157 models
+> show #!161 models
+> volume #161 level 0.32
+> volume #161 level 0.34
+> hide #!161 models
+> show #!160 models
+> hide #!160 models
+> show #!159 models
+> show #!161 models
+> hide #!161 models
+> show #!161 models
+> hide #!161 models
+> hide #!159 models
+> show #!159 models
+> hide #!159 models
+> show #!160 models
+> show #!173 models
+> show #!175 models
+> show #!157 models
+> hide #!157 models
+> hide #!160 models
+> volume #173 level 0.3031
+> volume #173 level 0.3465
+> show #!175 models
+> hide #!173 models
+> volume #175 level 0.3281
+> hide #!175 models
+> show #!172 models
+> hide #!172 models
+> close #155-156,159-160,173,175-176
+> show #!157 models
+> show #!174 models
+> hide #!174 models
+> show #!174 models
+> volume #174 level 0.3294
+> hide #!174 models
+> show #!174 models
+> hide #!174 models
+> show #!174 models
+> hide #!174 models
+> show #!174 models
+> hide #!174 models
+> show #!174 models
+> hide #!174 models
+> hide #!157 models
+> show #!161 models
+> show #!141 models
+> hide #!141 models
+> show #!141 models
+> hide #!161 models
+> show #!161 models
+> hide #!161 models
+> show #!161 models
+> select add #161
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #161,-0.80087,-0.4765,-0.3627,729.62,0.10949,-0.71198,0.69361,276.28,-0.58874,0.51578,0.62238,115.15
+> view matrix models
+> #161,-0.84255,0.43705,-0.31481,469.51,-0.49419,-0.85972,0.12908,627.85,-0.21423,0.26433,0.94034,2.6659
+> view matrix models
+> #161,-0.91542,-0.17496,-0.36248,675.94,0.17298,-0.98418,0.038186,498.42,-0.36343,-0.027746,0.93121,129.94
+> view matrix models
+> #161,-0.95897,-0.26467,-0.1016,649.01,0.27072,-0.9613,-0.051053,486.58,-0.084153,-0.076463,0.99351,49.911
+> view matrix models
+> #161,-0.99187,0.12321,0.03177,514.81,-0.12543,-0.98874,-0.081553,613.22,0.021365,-0.084875,0.99616,22.011
+> ui mousemode right zoom
+> select clear
+> hide #!161 models
+> show #!161 models
+> fitmap #161 inMap #141
+Fit map cryosparc_P17_J697_006_volume_map.mrc z flip in map
+cryosparc_P17_J685_007_volume_map.mrc using 269413 points
+correlation = 0.9961, correlation about mean = 0.9593, overlap = 9.415e+04
+steps = 112, shift = 3.83, angle = 9.13 degrees
+Position of cryosparc_P17_J697_006_volume_map.mrc z flip (#161) relative to
+cryosparc_P17_J685_007_volume_map.mrc (#141) coordinates:
+Matrix rotation and translation
+-0.99974072 -0.02276472 -0.00050563 565.44941758
+.02276965 -0.99929232 -0.02994005 559.04447071
+.00017631 -0.02994380 0.99955157 8.32772983
+Axis -0.00008235 -0.01497460 0.99988787
+Axis point 279.54196619 282.80415641 0.00000000
+Rotation angle (degrees) 178.69527744
+Shift along axis -0.09123841
+> hide #!141 models
+> show #!141 models
+> volume #161 level 0.36
+> hide #!141 models
+> show #!141 models
+> hide #!141 models
+> show #!141 models
+> hide #!141 models
+> show #!141 models
+> hide #!141 models
+> show #!141 models
+> hide #!141 models
+> show #!141 models
+> hide #!141 models
+> show #!141 models
+> hide #!141 models
+> show #!141 models
+> hide #!141 models
+> show #!141 models
+> show #!147 models
+> hide #!141 models
+> show #!141 models
+> hide #!141 models
+> show #!147 models
+> hide #!147 models
+> show #!147 models
+> hide #!161 models
+> show #!161 models
+> hide #!161 models
+> show #!141 models
+> select add #147
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #147,0.75391,-0.62474,-0.20327,302.4,-0.65039,-0.66601,-0.36528,749.91,0.092824,0.40759,-0.90843,455.15
+> view matrix models
+> #147,-0.31245,-0.67282,-0.67059,759.97,-0.54055,0.70643,-0.45691,373.58,0.78114,0.21972,-0.58441,212.49
+> view matrix models
+> #147,-0.90083,-0.32948,-0.28274,711.29,-0.41209,0.85388,0.3179,56.872,0.13669,0.40289,-0.90498,443.04
+> view matrix models
+> #147,-0.99864,0.030742,-0.042093,565.93,0.029267,0.99895,0.035202,-18.858,0.043131,0.033922,-0.99849,598.86
+> ui mousemode right "translate selected models"
+> view matrix models
+> #147,-0.99864,0.030742,-0.042093,560.75,0.029267,0.99895,0.035202,-44.757,0.043131,0.033922,-0.99849,550.76
+> view matrix models
+> #147,-0.99864,0.030742,-0.042093,571.25,0.029267,0.99895,0.035202,-21.366,0.043131,0.033922,-0.99849,539.43
+> select subtract #147
+Nothing selected
+> fitmap #147 inMap #141
+Fit map cryosparc_P17_J690_006_volume_map.mrc in map
+cryosparc_P17_J685_007_volume_map.mrc using 254434 points
+correlation = 0.9983, correlation about mean = 0.9814, overlap = 9.297e+04
+steps = 84, shift = 10.7, angle = 2.98 degrees
+Position of cryosparc_P17_J690_006_volume_map.mrc (#147) relative to
+cryosparc_P17_J685_007_volume_map.mrc (#141) coordinates:
+Matrix rotation and translation
+-0.99966375 0.02590789 -0.00108426 552.09827323
+.02590403 0.99965851 0.00344015 -9.28972053
+.00117301 0.00341091 -0.99999349 555.06217083
+Axis -0.01295398 -0.99991463 -0.00171281
+Axis point 275.95266832 0.00000000 277.69485205
+Rotation angle (degrees) 179.93532851
+Shift along axis 1.18634199
+> hide #!147 models
+> show #!147 models
+> hide #!147 models
+> show #!147 models
+> hide #!147 models
+> show #!147 models
+> hide #!141 models
+> show #!157 models
+> hide #!157 models
+> show #!161 models
+> hide #!161 models
+> show #!161 models
+> color #161 #00fa92ff models
+> hide #!161 models
+> show #!161 models
+> hide #!147 models
+> show #!147 models
+> hide #!147 models
+> show #!147 models
+> hide #!161 models
+> hide #!147 models
+> show #!32 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!34 models
+> show #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!34 models
+> show #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!34 models
+> hide #!32 models
+> show #!32 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> ui mousemode right zoom
+> lighting full
+> lighting soft
+> lighting simple
+> lighting full
+> hide #!32 models
+> show #!32 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!95 models
+> hide #!95 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J517_006_volume_map_zflip.mrc
+Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
+,588,588, pixel 0.95, shown at level 0.158, step 4, values float32
+> volume #155 step 1
+> lighting soft
+> show #!179 models
+> hide #!179 models
+> show #!179 models
+> hide #!179 models
+> show #!179 models
+> select add #155
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #155,-0.98089,0.19377,-0.017464,502.92,0.10481,0.60192,0.79165,-107.18,0.16391,0.77469,-0.61072,122.66
+> view matrix models
+> #155,-0.25052,0.96798,-0.015979,76.052,0.96671,0.24923,-0.057953,-41.024,-0.052115,-0.029966,-0.99819,507.99
+> view matrix models
+> #155,0.96775,0.17696,-0.17931,1.7558,0.20922,-0.96102,0.18073,460.27,-0.14034,-0.21242,-0.96705,577.47
+> view matrix models
+> #155,0.96767,0.091902,-0.2349,39.67,0.12427,-0.9841,0.12691,503.72,-0.2195,-0.152,-0.9637,581.47
+> view matrix models
+> #155,0.91176,0.40771,0.049574,-104.32,0.37999,-0.79159,-0.47852,523.82,-0.15586,0.45514,-0.87667,368.35
+> lighting simple
+> view matrix models
+> #155,0.92481,0.37946,0.027133,-94.419,0.34082,-0.79474,-0.50223,541.44,-0.16901,0.47372,-0.86431,363.7
+> view matrix models
+> #155,0.94675,0.28168,0.15598,-103.76,0.32196,-0.82268,-0.46855,546.56,-0.0036582,0.49382,-0.86956,312.94
+> view matrix models
+> #155,0.9947,0.045724,-0.092058,10.698,0.043566,-0.99873,-0.02532,567.43,-0.093098,0.021175,-0.99543,504.12
+> ui mousemode right "translate selected models"
+> view matrix models
+> #155,0.9947,0.045724,-0.092058,46.226,0.043566,-0.99873,-0.02532,564.24,-0.093098,0.021175,-0.99543,557.75
+> view matrix models
+> #155,0.9947,0.045724,-0.092058,13.547,0.043566,-0.99873,-0.02532,566.45,-0.093098,0.021175,-0.99543,563.81
+> select subtract #155
+Nothing selected
+> fitmap #155 inMap #179
+Fit map cryosparc_P17_J517_006_volume_map_zflip.mrc in map
+cryosparc_P17_J544_007_volume_map_zflip.mrc using 2026669 points
+correlation = 0.9972, correlation about mean = 0.9729, overlap = 1.474e+05
+steps = 220, shift = 19.3, angle = 6.44 degrees
+Position of cryosparc_P17_J517_006_volume_map_zflip.mrc (#155) relative to
+cryosparc_P17_J544_007_volume_map_zflip.mrc (#179) coordinates:
+Matrix rotation and translation
+.99982429 0.01272017 0.01376969 -7.71473943
+.01281628 -0.99989397 -0.00691402 556.62008375
+.01368028 0.00708928 -0.99988130 552.40010778
+Axis 0.99995607 0.00638455 0.00686279
+Axis point 0.00000000 277.36764127 277.20094376
+Rotation angle (degrees) 179.59881412
+Shift along axis -0.36962502
+> ui mousemode right zoom
+> lighting soft
+> hide #!179 models
+> show #!179 models
+> hide #!179 models
+> show #!179 models
+> show #!178 models
+> hide #!179 models
+> show #!179 models
+> hide #!178 models
+> volume #179 level 0.16
+> hide #!179 models
+> show #!179 models
+> hide #!179 models
+> open /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J851_volume_map.mrc
+Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
+.95, shown at level 0.179, step 4, values float32
+> open /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J854_volume_map.mrc
+Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
+.95, shown at level 0.178, step 4, values float32
+> hide #!156 models
+> show #!156 models
+> hide #!156 models
+> hide #!159 models
+> show #!159 models
+> show #!156 models
+> volume #156 step 1
+> volume #159 step 1
+> volume #156 level 0.15
+> volume #159 level 0.15
+> volume #156 level 0.12
+> volume #156 level 0.1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J857_mask.mrc
+Opened cryosparc_P17_J857_mask.mrc as #160, grid size 588,588,588, pixel 0.95,
+shown at level 1, step 4, values float32
+> volume #160 step 1
+> volume #160 color #b2ffb260
+> volume #160 color #b2ffb261
+> volume #160 level 1
+> volume #160 color #b2ffb270
+> volume #160 level 1
+> volume #156 level 0.08
+> volume #156 level 0.1
+> volume #156 level 0.9
+> volume #156 level 0.09
+> volume #156 level 0.08
+> open /Users/cvetkom/Downloads/cryosparc_P17_J858_007_volume_map.mrc
+Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
+pixel 0.95, shown at level 0.154, step 4, values float32
+> volume #173 step 1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J866_class_00_00042_volume.mrc
+Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
+,128,128, pixel 4.36, shown at level 1.71, step 1, values float32
+> volume #175 level 1.364
+> volume #175 level 1
+> volume #175 level 0.9
+> volume #175 level 0.8
+> volume #175 level 0.9
+> open /Users/cvetkom/Downloads/cryosparc_P17_J869_mask.mrc
+Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+> volume #176 color #cccc9964
+> volume #176 color #cccc9963
+> volume #176 level 1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J870_mask.mrc
+Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+> volume #203 color #b2b2b267
+> volume #203 color #b2b2b266
+> volume #203 level 1
+[Repeated 1 time(s)]
+> show #!213 models
+> hide #!213 models
+> show #!213 models
+> hide #!213 models
+> hide #!203 models
+> show #!203 models
+> hide #!203 models
+> show #!211 models
+> hide #!211 models
+> show #!212 models
+> hide #!212 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J867_007_volume_map.mrc
+Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 4, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J871_007_volume_map.mrc
+Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 4, values float32
+> volume #204 step 1
+> volume #205 step 1
+> volume #205 level 0.2369
+> volume #205 level 0.1513
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> show #!74 models
+> hide #!75 models
+> show #!75 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> hide #!75 models
+> volume #129 level 0.01525
+> volume #129 level 0.02295
+> volume #129 level 0.02195
+> volume #129 level 0.02859
+> volume #129 level 0.01548
+> volume #129 level 0.01394
+> volume #129 level 0.02201
+> volume #129 level 0.02491
+> volume #129 level 0.02207
+> volume #129 level 0.01258
+> volume #129 level 0.01323
+> show #!74 models
+> volume #129 level 0.014
+> hide #!74 models
+> show #!74 models
+> show #!75 models
+> hide #!74 models
+> show #!74 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!74 models
+> show #!74 models
+> hide #!75 models
+> show #!75 models
+> hide #!74 models
+> hide #!75 models
+> show #!98 models
+> show #!99 models
+> hide #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!99 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!99 models
+> hide #!99 models
+> show #!98 models
+> hide #!98 models
+> show #!99 models
+> hide #!99 models
+> show #!98 models
+> hide #!98 models
+> show #!99 models
+> hide #!99 models
+> show #!98 models
+> hide #!98 models
+> show #!99 models
+> hide #!99 models
+> show #!100 models
+> hide #!100 models
+> show #!100 models
+> hide #!100 models
+> show #!122 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!130 models
+> hide #!122 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!130 models
+> show #!130 models
+> hide #!123 models
+> show #!123 models
+> hide #!130 models
+> hide #!123 models
+> show #!122 models
+> show #!123 models
+> hide #!122 models
+> show #!122 models
+> show #!124 models
+> hide #!123 models
+> hide #!122 models
+> hide #!124 models
+> show #!124 models
+> show #!123 models
+> hide #!123 models
+> show #!122 models
+> hide #!122 models
+> hide #!124 models
+> show #!124 models
+> hide #!124 models
+> show #!125 models
+> hide #!125 models
+> show #!125 models
+> hide #!125 models
+> show #!126 models
+> show #!127 models
+> show #!134 models
+> show #!135 models
+> hide #!135 models
+> show #!128 models
+> hide #!128 models
+> show #!135 models
+> hide #!135 models
+> show #!133 models
+> hide #!127 models
+> hide #!126 models
+> show #!126 models
+> hide #!126 models
+> show #!126 models
+> hide #!126 models
+> show #!126 models
+> hide #!126 models
+> show #!127 models
+> hide #!127 models
+> show #!127 models
+> hide #!127 models
+> show #!127 models
+> hide #!127 models
+> show #!127 models
+> hide #!127 models
+> hide #!133 models
+> show #!133 models
+> hide #!133 models
+> show #!133 models
+> hide #!133 models
+> hide #!134 models
+> show #!129 models
+> show #!130 models
+> show #!131 models
+> hide #!131 models
+> show #!132 models
+> hide #!132 models
+> show #!132 models
+> hide #!132 models
+> show #!133 models
+> show #!134 models
+> show #!132 models
+> hide #!132 models
+> show #!131 models
+> hide #!131 models
+> hide #!133 models
+> hide #!134 models
+> show #!122 models
+> show #!123 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> hide #!130 models
+> show #!130 models
+> hide #!122 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> hide #!130 models
+> show #!129 models
+> show #!130 models
+> hide #!129 models
+> hide #!130 models
+> show #!133 models
+> show #!134 models
+> show #!104 models
+> hide #!104 models
+> show #!103 models
+> hide #!103 models
+> show #!103 models
+> show #!102 models
+> hide #!102 models
+> show #!104 models
+> hide #!104 models
+> show #!102 models
+> hide #!103 models
+> show #!103 models
+> hide #!102 models
+> show #!101 models
+> hide #!101 models
+> show #!100 models
+> hide #!100 models
+> show #!100 models
+> hide #!103 models
+> show #!103 models
+> hide #!100 models
+> show #!100 models
+> hide #!133 models
+> hide #!134 models
+> show #!134 models
+> hide #!134 models
+> hide #!100 models
+> show #!100 models
+> hide #!100 models
+> show #!100 models
+> hide #!100 models
+> show #!100 models
+> hide #!103 models
+> show #!103 models
+> hide #!103 models
+> show #!103 models
+> hide #!103 models
+> show #!103 models
+> hide #!100 models
+> hide #!103 models
+> show #!98 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> show #!100 models
+> hide #!100 models
+> show #!101 models
+> hide #!101 models
+> show #!102 models
+> hide #!102 models
+> show #!103 models
+> hide #!103 models
+> show #!104 models
+> hide #!104 models
+> show #!129 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J876_class_00_final_volume.mrc
+Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
+,192,192, pixel 2.91, shown at level 0.504, step 1, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J880_class_00_final_volume.mrc
+Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
+,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
+> hide #!98 models
+> hide #!99 models
+> hide #!129 models
+> hide #!130 models
+> volume #206 level 0.3476
+> open /Users/cvetkom/Downloads/cryosparc_P17_J874_volume_map.mrc
+Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
+.9, shown at level 0.404, step 2, values float32
+> volume #214 step 1
+> volume #214 level 0.3304
+> open /Users/cvetkom/Downloads/cryosparc_P17_J882_volume_map.mrc
+Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
+.9, shown at level 0.4, step 2, values float32
+> volume #215 step 1
+> volume #215 level 0.347
+> volume #215 level 0.3003
+> open /Users/cvetkom/Downloads/cryosparc_P17_J878_class_00_00042_volume.mrc
+Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
+,128,128, pixel 4.36, shown at level 0.839, step 1, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J878_class_01_00042_volume.mrc
+Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
+,128,128, pixel 4.36, shown at level 1.37, step 1, values float32
+> volume #216 level 1.25
+> volume #217 level 1.171
+> volume #217 level 1
+> volume #217 level 0.9
+> volume #217 level 0.8
+> volume #217 level 0.85
+> volume #217 level 0.8
+> open /Users/cvetkom/Downloads/cryosparc_P17_J883_mask.mrc
+Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+> volume #218 color #cccc9967
+> volume #218 color #cccc9969
+> volume #218 level 1
+> volume #218 level 0.5107
+> volume #218 level 1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J884_009_volume_map.mrc
+Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
+pixel 1.9, shown at level 0.347, step 2, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J885_008_volume_map.mrc
+Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
+pixel 1.9, shown at level 0.347, step 2, values float32
+> hide #!217 models
+> hide #!218 models
+> volume #219 step 1
+> volume #220 step 1
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job506_run_class001.mrc
+Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
+.95, shown at level 0.00502, step 4, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job506_run_class001_NCP.mrc
+Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
+.95, shown at level 0.00208, step 4, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/mask_job519.mrc
+Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
+level 5e-05, step 4, values float32
+> hide #!218 models
+> hide #!220 models
+> volume #223 step 1
+> volume #223 level 0.9925
+> volume #223 color #ffb2ff80
+> volume #223 color #ffb2ff66
+> volume #222 step 1
+> volume #221 step 1
+> volume #222 level 0.002458
+> volume #222 level 0.003951
+> volume #222 level 0.004587
+> volume #222 level 0.005
+> volume #222 level 0.004508
+> volume #222 level 0.0045
+> volume #221 level 0.0045
+> hide #!223 models
+> hide #!221 models
+> show #!221 models
+> hide #!222 models
+> hide #!221 models
+> show #!222 models
+> ui tool show "Map Eraser"
+> hide #224 models
+> show #224 models
+> hide #!222 models
+Drag select of eraser sphere, 87 of 1000 triangles
+> select clear
+> show #!222 models
+> show #!221 models
+> hide #!221 models
+> show #!221 models
+> hide #!221 models
+> ui mousemode right zoom
+> select add #224
+model selected
+> ui mousemode right "translate selected models"
+> hide #224 models
+> show #224 models
+> hide #!222 models
+> show #!222 models
+> select subtract #224
+Nothing selected
+> select add #224
+model selected
+> select subtract #224
+Nothing selected
+> ui mousemode right zoom
+Drag select of eraser sphere, 27 of 1000 triangles
+> select #224
+model selected
+> select #224
+model selected
+> select clear
+> ui mousemode right "map eraser"
+> volume erase #222 center 235.13,229.91,259.65 radius 50.358
+Opened Ref3D_job506_run_class001_NCP.mrc copy as #225, grid size 588,588,588,
+pixel 0.95, shown at step 1, values float32
+> volume erase #225 center 240.34,217.6,249.39 radius 50.274
+> volume erase #225 center 249.31,217.92,185.58 radius 50.274
+> volume erase #225 center 254.34,196.31,201.83 radius 50.274
+> volume erase #225 center 244.51,226.1,178.85 radius 50.274
+> volume erase #225 center 266.29,219.21,231.39 radius 71.221
+> show #!222 models
+> hide #!222 models
+> show #!222 models
+> hide #!222 models
+> ui mousemode right zoom
+> vop gaussian #225 sdev 2.85
+Opened Ref3D_job506_run_class001_NCP.mrc copy gaussian as #224, grid size
+,588,588, pixel 0.95, shown at step 1, values float32
+> volume #224 level 0.004498
+> volume #224 level 0.004
+> volume #224 level 0.0045
+> save
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job506_run_class001_bareNCP.mrc
+> models #224
+> hide #!224 models
+> show #!224 models
+> show #!222 models
+> hide #!222 models
+> hide #!225 models
+> show #!222 models
+> hide #!222 models
+> show #!222 models
+> hide #!222 models
+> show #!222 models
+> hide #!222 models
+> show #!222 models
+> hide #!224 models
+> show #!224 models
+> hide #!224 models
+> show #!224 models
+> hide #!222 models
+> show #!222 models
+> hide #!222 models
+> show #!222 models
+> lighting full
+> hide #!222 models
+> show #!222 models
+> color #224 #d6d6d6ff models
+> color #224 darkgrey models
+> hide #!224 models
+> show #!224 models
+> hide #!222 models
+> show #!222 models
+> hide #!222 models
+> show #!222 models
+> hide #!222 models
+> show #!222 models
+> hide #!222 models
+> show #!222 models
+> hide #!222 models
+> show #!222 models
+> hide #!222 models
+> hide #!224 models
+> show #!222 models
+> show #!223 models
+> show #!221 models
+> volume #223 level 0.5133
+> volume #223 level 1
+> hide #!223 models
+> show #!223 models
+> hide #!223 models
+> show #!224 models
+> hide #!222 models
+> hide #!221 models
+> show #!221 models
+> hide #!221 models
+> show #!221 models
+> hide #!221 models
+> show #!221 models
+> hide #!221 models
+> show #!221 models
+> open /Volumes/lab-
+> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/MaskCreate/job744/mask.mrc
+Opened mask.mrc as #226, grid size 588,588,588, pixel 0.95, shown at level
+e-05, step 4, values float32
+> hide #!224 models
+> show #!224 models
+> hide #!221 models
+> volume #226 step 1
+> volume #226 color #e5bf9966
+> volume #226 level 1
+> volume #226 level 0.3859
+> volume #226 level 0.5044
+> hide #!224 models
+> show #!221 models
+> volume #226 level 1
+> hide #!226 models
+> show #!226 models
+> volume #226 level 1
+> show #!223 models
+> hide #!223 models
+> show #!223 models
+> hide #!223 models
+> show #!223 models
+> hide #!223 models
+> show #!223 models
+> hide #!223 models
+> show #!223 models
+> hide #!223 models
+> show #!223 models
+> hide #!223 models
+> volume #226 level 1
+> hide #!221 models
+> hide #!226 models
+> show #!219 models
+Error processing trigger "graphics update":
+You deleted or moved a volume file that is still open in ChimeraX.
+/Users/cvetkom/Downloads/cryosparc_P17_J884_009_volume_map.mrc
+To allow fast initial display of volume data ChimeraX does not read all data
+from the file when it is first opened, and will later read more data when
+needed. ChimeraX got an error trying to read the above file.
+> close #219-220
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J884_009_volume_map.mrc
+Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
+pixel 1.9, shown at level 0.347, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J885_008_volume_map.mrc
+Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
+pixel 1.9, shown at level 0.347, step 2, values float32
+> volume #219 step 1
+> volume #220 step 1
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J888_009_volume_map.mrc
+Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
+pixel 1.9, shown at level 0.356, step 2, values float32
+> volume #227 step 1
+> volume #219 level 0.4485
+> volume #219 level 0.4625
+> volume #219 step 2
+> volume #219 step 1
+> show #!213 models
+> hide #!213 models
+> volume #227 step 2
+> volume #227 step 1
+> close #225
+> close #226
+> hide #!219 models
+> show #!219 models
+> volume #219 step 2
+> volume #219 step 4
+> volume #219 step 1
+> volume #219 step 2
+> volume #219 level 0.4261
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
+\u2014\u2014\u2014 End of log from Thu Jul 11 13:31:37 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> hide #!219 models
+> show #!227 models
+> hide #!227 models
+> open
+> /Users/cvetkom/Downloads/cryosparc_P17_J984_class_00_00062_volume_sharp.mrc
+Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc as #225, grid size
+,128,128, pixel 3.27, shown at level 0.37, step 1, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J967_class_00_00400_volume.mrc
+Opened cryosparc_P17_J967_class_00_00400_volume.mrc as #226, grid size
+,128,128, pixel 3.27, shown at level 0.384, step 1, values float32
+> open
+> /Users/cvetkom/Downloads/cryosparc_P17_J981_class_00_00062_volume_sharp.mrc
+Opened cryosparc_P17_J981_class_00_00062_volume_sharp.mrc as #228, grid size
+,128,128, pixel 3.27, shown at level 0.327, step 1, values float32
+> show #!227 models
+> hide #!227 models
+> hide #!225 models
+> hide #!228 models
+> volume #226 level 1.133
+> volume #226 level 1.3
+> volume #226 level 1.35
+> lighting soft
+> volume #226 color darkgrey
+> volume #226 level 1.4
+> volume #226 level 1.45
+> volume #225 level 2.008
+> show #!225 models
+> hide #!225 models
+> show #!225 models
+> hide #!226 models
+> show #!226 models
+> hide #!226 models
+> show #!226 models
+> hide #!226 models
+> show #!228 models
+> volume #228 level 1.823
+> open /Users/cvetkom/Downloads/cryosparc_P17_J967_class_00_final_volume.mrc
+Opened cryosparc_P17_J967_class_00_final_volume.mrc as #229, grid size
+,192,192, pixel 2.18, shown at level 0.197, step 1, values float32
+> close #226
+> volume #229 level 1.053
+> volume #229 level 1
+> volume #229 level 0.9
+> volume #229 level 0.8
+> show #!228 models
+> show #!227 models
+> hide #!227 models
+> show #!225 models
+> hide #!229 models
+> show #!229 models
+> hide #!228 models
+> hide #!229 models
+> show #!229 models
+> volume #225 level 1.9
+> volume #225 level 1.8
+> hide #!229 models
+> show #!229 models
+> volume #225 level 1.6
+> show #!211 models
+> hide #!211 models
+> show #!211 models
+> hide #!211 models
+> show #!198 models
+> hide #!198 models
+> show #!197 models
+> hide #!197 models
+> show #!191 models
+> hide #!191 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J842_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #226, grid size
+,588,588, pixel 0.95, shown at level 0.15, step 4, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J845_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #230, grid size
+,588,588, pixel 0.95, shown at level 0.142, step 4, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J846_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #231, grid size
+,588,588, pixel 0.95, shown at level 0.14, step 4, values float32
+> hide #!225 models
+> volume #226 level 0.2956
+> volume #226 step 1
+> volume #226 level 0.334
+> show #!230 models
+> hide #!226 models
+> volume #226 level 0.33
+> show #!226 models
+> hide #!230 models
+> hide #!226 models
+> show #!230 models
+> volume #230 step 1
+> volume #230 level 0.33
+> show #!226 models
+> hide #!226 models
+> show #!226 models
+> hide #!226 models
+> show #!226 models
+> hide #!226 models
+> show #!226 models
+> hide #!226 models
+> show #!226 models
+> hide #!226 models
+> show #!226 models
+> hide #!226 models
+> volume #230 level 0.32
+> volume #230 level 0.3
+> show #!226 models
+> hide #!226 models
+> show #!226 models
+> hide #!226 models
+> show #!231 models
+> hide #!230 models
+> volume #231 step 2
+> volume #231 step 1
+> volume #231 level 0.3
+> show #!191 models
+> hide #!191 models
+> show #!190 models
+> show #!191 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!198 models
+> hide #!191 models
+> show #!191 models
+> hide #!198 models
+> hide #!191 models
+> open 1ID3 fromDatabase pdb format mmcif
+id3 title:
+Crystal structure of the yeast nucleosome core particle reveals fundamental
+differences In inter-nucleosome interactions [more info...]
+Chain information for 1id3 #232
+---
+Chain | Description | UniProt
+A E | HISTONE H3 | H3_YEAST 1-135
+B F | HISTONE H4 | H4_YEAST 1-102
+C G | HISTONE H2A.1 | H2A1_YEAST 1-131
+D H | HISTONE H2B.2 | H2B2_YEAST 1-130
+I J | PALINDROMIC 146BP DNA FRAGMENT |
+Non-standard residues in 1id3 #232
+---
+MN \u2014 manganese (II) ion
+> hide #!232 models
+> show #!232 models
+> select add #232
+atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
+> view sel
+> select subtract #232
+Nothing selected
+> show #!228 models
+> hide #!228 models
+> show #!225 models
+> hide #!225 models
+> lighting simple
+> show #!229 models
+> hide #!229 models
+> show #!225 models
+> show #!228 models
+> hide #!225 models
+> show #!225 models
+> hide #!225 models
+> show #!225 models
+> hide #!225 models
+> show #!225 models
+> hide #!225 models
+> show #!225 models
+> hide #!225 models
+> show #!225 models
+> hide #!225 models
+> show #!225 models
+> hide #!225 models
+> show #!225 models
+> hide #!228 models
+> select add #232
+atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
+> ui mousemode right "rotate selected models"
+> ui mousemode right "translate selected models"
+> view matrix models #232,1,0,0,194.77,0,1,0,198.7,0,0,1,241.66
+> select add #225
+atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 7 models selected
+> view sel
+> select subtract #225
+atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #232,0.45362,0.62002,-0.64016,176.82,-0.86856,0.46844,-0.16176,188.02,0.19958,0.62939,0.75102,238.14
+> view matrix models
+> #232,0.73516,0.67582,-0.053002,205.68,-0.43197,0.40677,-0.80495,150.64,-0.52244,0.61466,0.59097,235.27
+> view matrix models
+> #232,0.74922,0.65491,0.098772,212.99,-0.3682,0.53581,-0.75982,154.67,-0.55054,0.53291,0.64258,236.74
+> view matrix models
+> #232,0.63725,0.62725,-0.44773,185.38,-0.56763,-0.01092,-0.82321,143.6,-0.52125,0.77874,0.34909,225.69
+> ui mousemode right "translate selected models"
+> view matrix models
+> #232,0.63725,0.62725,-0.44773,108.34,-0.56763,-0.01092,-0.82321,126.58,-0.52125,0.77874,0.34909,223.48
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #232,0.69009,0.70479,0.16445,140.62,-0.26062,0.454,-0.85204,130.7,-0.67517,0.54512,0.49698,228.24
+> view matrix models
+> #232,0.021212,0.98524,0.16984,150.87,-0.50552,0.15714,-0.84839,127.69,-0.86256,-0.067863,0.50139,219.42
+> view matrix models
+> #232,0.026211,0.99233,-0.12082,136.06,-0.53573,-0.088094,-0.83978,124.17,-0.84398,0.086736,0.52931,223.35
+> view matrix models
+> #232,0.0051654,0.11484,-0.99337,76.495,-0.63253,-0.76903,-0.092196,151.55,-0.77452,0.62881,0.068669,208.5
+> view matrix models
+> #232,0.026817,-0.97752,0.20912,119.22,-0.36995,0.18463,0.91052,217.22,-0.92866,-0.10178,-0.35669,175.39
+> view matrix models
+> #232,-0.0985,-0.93943,0.32829,126.94,0.94539,0.014666,0.32562,174.18,-0.31071,0.34244,0.88668,241.92
+> view matrix models
+> #232,0.23695,-0.92136,0.30814,123.63,0.84083,0.035592,-0.54013,130.99,0.48669,0.38708,0.78314,231.21
+> view matrix models
+> #232,0.37181,-0.91507,0.15625,114.91,0.42362,0.017477,-0.90567,115.18,0.82602,0.40293,0.39414,208.93
+> view matrix models
+> #232,0.30529,-0.94633,-0.10613,101.45,0.56154,0.26891,-0.78253,124.73,0.76907,0.1793,0.6135,216.78
+> view matrix models
+> #232,0.059237,0.85249,0.51938,166.21,0.47573,-0.48152,0.73609,190.34,0.8776,0.20348,-0.43407,162.69
+> view matrix models
+> #232,0.24626,-0.51664,-0.82003,72.694,0.61898,0.73489,-0.27712,158.16,0.7458,-0.43934,0.50076,200.59
+> view matrix models
+> #232,-0.067706,-0.98402,0.16471,117.56,0.51804,-0.17576,-0.83711,114.66,0.85268,0.028649,0.52165,208.85
+> volume flip #225
+Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip as #233, grid
+size 128,128,128, pixel 3.27, shown at step 1, values float32
+> view matrix models
+> #232,-0.086674,-0.98325,0.16032,117.49,0.60367,-0.17985,-0.77669,117.02,0.79251,0.02946,0.60914,213.81
+> view matrix models
+> #232,-0.20892,-0.97186,0.10878,115.99,0.81932,-0.11321,0.56205,185.07,-0.53392,0.20655,0.81992,237.89
+> view matrix models
+> #232,-0.0034667,-0.99986,-0.016272,107.52,0.52919,-0.015641,0.84836,203.66,-0.8485,-0.0056699,0.52917,221.79
+> view matrix models
+> #232,0.10405,-0.99333,-0.049687,105.09,0.51074,0.010501,0.85967,204.82,-0.85341,-0.11483,0.50843,218.9
+> view matrix models
+> #232,0.155,-0.97565,0.1552,115.49,0.4679,0.21087,0.85826,208.52,-0.87008,-0.060414,0.48919,218.98
+> view matrix models
+> #232,0.045605,-0.97983,0.19456,118.28,0.53868,0.18814,0.82123,205.68,-0.84127,0.067353,0.5364,223.36
+> ui mousemode right "translate selected models"
+> view matrix models
+> #232,0.045605,-0.97983,0.19456,194.24,0.53868,0.18814,0.82123,258.89,-0.84127,0.067353,0.5364,231.26
+> view matrix models
+> #232,0.045605,-0.97983,0.19456,195.08,0.53868,0.18814,0.82123,259.08,-0.84127,0.067353,0.5364,236.86
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #232,-0.039543,-0.99451,0.096893,190.48,-0.23842,0.10356,0.96562,271.04,-0.97036,0.015082,-0.24121,197.13
+> view matrix models
+> #232,-0.078672,-0.98952,0.12105,192.1,-0.5971,0.14401,0.78913,265.46,-0.7983,-0.010198,-0.60217,176.87
+> view matrix models
+> #232,-0.14713,-0.98779,0.051262,189.09,-0.8147,0.15042,0.56004,255.52,-0.56091,0.040637,-0.82688,164.4
+> select subtract #232
+Nothing selected
+> ui tool show "Fit in Map"
+> fitmap #232 inMap #233
+Fit molecule 1id3 (#232) to map
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 12124
+atoms
+average map value = 1.802, steps = 72
+shifted from previous position = 12.2
+rotated from previous position = 11.2 degrees
+atoms outside contour = 5403, contour level = 1.6
+Position of 1id3 (#232) relative to
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
+Matrix rotation and translation
+-0.03585182 -0.99591182 0.08291139 194.40297797
+-0.72260858 0.08314376 0.68623899 250.19258695
+-0.69032709 -0.03530956 -0.72263528 174.98991176
+Axis -0.66054809 0.70786809 0.25019790
+Axis point 245.81431621 -0.00000000 -10.35559013
+Rotation angle (degrees) 146.89506394
+Shift along axis 92.47294040
+> volume #233 level 1.5
+> volume #233 level 1.4
+> ui mousemode right "translate selected models"
+> select add #232
+atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
+> view matrix models
+> #232,-0.035852,-0.99591,0.082911,187.84,-0.72261,0.083144,0.68624,334.95,-0.69033,-0.03531,-0.72264,195.33
+> lighting soft
+> view matrix models
+> #232,-0.035852,-0.99591,0.082911,189.25,-0.72261,0.083144,0.68624,329.81,-0.69033,-0.03531,-0.72264,193.67
+> lighting simple
+> view matrix models
+> #232,-0.035852,-0.99591,0.082911,207.89,-0.72261,0.083144,0.68624,254.31,-0.69033,-0.03531,-0.72264,174.46
+> view matrix models
+> #232,-0.035852,-0.99591,0.082911,196.79,-0.72261,0.083144,0.68624,255.92,-0.69033,-0.03531,-0.72264,174.52
+> fitmap #232 inMap #233
+Fit molecule 1id3 (#232) to map
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 12124
+atoms
+average map value = 1.802, steps = 52
+shifted from previous position = 6.21
+rotated from previous position = 0.0558 degrees
+atoms outside contour = 4425, contour level = 1.4
+Position of 1id3 (#232) relative to
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
+Matrix rotation and translation
+-0.03529330 -0.99599473 0.08215154 194.42252609
+-0.72248530 0.08222358 0.68647963 250.18011940
+-0.69048489 -0.03512516 -0.72249349 174.98679362
+Axis -0.66080361 0.70753542 0.25046400
+Axis point 245.92146757 -0.00000000 -10.42218197
+Rotation angle (degrees) 146.90659877
+Shift along axis 92.36408147
+> fitmap #232 inMap #233
+Fit molecule 1id3 (#232) to map
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 12124
+atoms
+average map value = 1.802, steps = 48
+shifted from previous position = 0.0262
+rotated from previous position = 0.0179 degrees
+atoms outside contour = 4427, contour level = 1.4
+Position of 1id3 (#232) relative to
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
+Matrix rotation and translation
+-0.03522647 -0.99601286 0.08196018 194.43601851
+-0.72265585 0.08203483 0.68632267 250.16027535
+-0.69030980 -0.03505228 -0.72266432 174.97347823
+Axis -0.66086507 0.70749095 0.25042747
+Axis point 245.92434501 0.00000000 -10.39497167
+Rotation angle (degrees) 146.92196206
+Shift along axis 92.30832410
+> select subtract #232
+Nothing selected
+> hide #!232 atoms
+> show #!232 cartoons
+> hide #!233 models
+> show #!233 models
+> fitmap #232 inMap #233
+Fit molecule 1id3 (#232) to map
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 12124
+atoms
+average map value = 1.802, steps = 44
+shifted from previous position = 0.00249
+rotated from previous position = 0.0128 degrees
+atoms outside contour = 4428, contour level = 1.4
+Position of 1id3 (#232) relative to
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
+Matrix rotation and translation
+-0.03534401 -0.99599682 0.08210439 194.44302789
+-0.72273427 0.08221501 0.68621853 250.15752046
+-0.69022169 -0.03508594 -0.72274684 174.96686637
+Axis -0.66081898 0.70756214 0.25034793
+Axis point 245.90230259 0.00000000 -10.37331191
+Rotation angle (degrees) 146.92300591
+Shift along axis 92.31293996
+> fitmap #232 inMap #233
+Fit molecule 1id3 (#232) to map
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 12124
+atoms
+average map value = 1.802, steps = 48
+shifted from previous position = 0.0672
+rotated from previous position = 0.0319 degrees
+atoms outside contour = 4424, contour level = 1.4
+Position of 1id3 (#232) relative to
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
+Matrix rotation and translation
+-0.03562336 -0.99595084 0.08254033 194.40523233
+-0.72285407 0.08271076 0.68603274 250.17963983
+-0.69008186 -0.03522582 -0.72287355 174.97000524
+Axis -0.66069357 0.70774412 0.25016449
+Axis point 245.83818539 0.00000000 -10.32676146
+Rotation angle (degrees) 146.91829753
+Shift along axis 92.39216339
+> volume #233 color #b2b2b2db
+> volume #233 color #b2b2b2b0
+> volume #233 color #b2b2b29a
+> volume #233 color #b2b2b299
+> volume #233 color #b2b2b2b2
+> volume #233 color #b2b2b2cc
+> combine #232
+> hide #!232 models
+> hide #!234 models
+> show #!234 models
+> select #234/I
+atoms, 3354 bonds, 3 pseudobonds, 162 residues, 2 models selected
+> delete atoms (#!234 & sel)
+> delete bonds (#!234 & sel)
+> select #234/J
+atoms, 3354 bonds, 6 pseudobonds, 160 residues, 2 models selected
+> delete atoms (#!234 & sel)
+> delete bonds (#!234 & sel)
+> hide #!233 models
+> show #!233 models
+> fitmap #234 inMap #233
+Fit molecule copy of 1id3 (#234) to map
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 6114
+atoms
+average map value = 1.618, steps = 48
+shifted from previous position = 0.869
+rotated from previous position = 6.47 degrees
+atoms outside contour = 2277, contour level = 1.4
+Position of copy of 1id3 (#234) relative to
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
+Matrix rotation and translation
+-0.05927763 -0.99809265 0.01724050 190.79692871
+-0.66015313 0.05215041 0.74931847 251.66034038
+-0.74878836 0.03303645 -0.66198534 180.19394497
+Axis -0.65007489 0.69522355 0.30670320
+Axis point 244.94027053 -0.00000000 -21.53118005
+Rotation angle (degrees) 146.56966321
+Shift along axis 106.19396109
+> volume #233 color #b2b2b280
+> volume #233 color #b2b2b29a
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!234 models
+> hide #!233 models
+> show #!233 models
+> hide #!232 models
+> hide #!233 models
+> show #!129 models
+> select add #129
+models selected
+> view clip false
+> select subtract #129
+Nothing selected
+> show #!130 models
+> show #!227 models
+> hide #!227 models
+> show #!227 models
+> hide #!227 models
+> show #!227 models
+> hide #!227 models
+> volume flip #227
+Opened cryosparc_P17_J888_009_volume_map.mrc z flip as #235, grid size
+,294,294, pixel 1.9, shown at step 1, values float32
+> select add #235
+models selected
+> ui mousemode right "move picked models"
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #235,0.84663,0.46913,0.25127,-169.59,0.42608,-0.88042,0.20812,364.8,0.31886,-0.069133,-0.94528,519.57
+> view matrix models
+> #235,-0.53578,-0.80769,-0.24613,731.78,-0.84162,0.48737,0.23271,310.31,-0.067998,0.33183,-0.94089,508.65
+> view matrix models
+> #235,-0.9965,-0.022294,-0.080596,581.12,-0.043426,0.96162,0.27092,-58.716,0.071463,0.27347,-0.95922,492.67
+> ui mousemode right "translate selected models"
+> view matrix models
+> #235,-0.9965,-0.022294,-0.080596,577.57,-0.043426,0.96162,0.27092,-52.189,0.071463,0.27347,-0.95922,460.39
+> volume #235 step 2
+> select subtract #235
+Nothing selected
+> fitmap #235 inMap #130
+Fit map cryosparc_P17_J888_009_volume_map.mrc z flip in map
+Cl3D_j591_run_it025_class002.mrc using 31742 points
+correlation = 0.9449, correlation about mean = 0.3834, overlap = 384.9
+steps = 216, shift = 20, angle = 24.3 degrees
+Position of cryosparc_P17_J888_009_volume_map.mrc z flip (#235) relative to
+Cl3D_j591_run_it025_class002.mrc (#130) coordinates:
+Matrix rotation and translation
+-0.97670485 -0.09877980 -0.19049983 628.35061820
+-0.19630370 0.76986862 0.60726203 -34.18266636
+.08667462 0.63051159 -0.77132526 290.90888037
+Axis 0.07887912 -0.94037367 -0.33087073
+Axis point 301.47094386 0.00000000 176.26702948
+Rotation angle (degrees) 171.52518698
+Shift along axis -14.54501139
+> hide #!130 models
+> show #!130 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> hide #!130 models
+> show #!98 models
+> show #!99 models
+> show #!219 models
+> hide #!219 models
+> volume flip #219
+Opened cryosparc_P17_J884_009_volume_map.mrc z flip as #236, grid size
+,294,294, pixel 1.9, shown at step 1, values float32
+> select add #236
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,-0.14,0.86518,0.48153,-32.729,-0.98201,-0.059076,-0.17936,602.39,-0.12673,-0.49797,0.85788,204
+> view matrix models
+> #236,-0.95021,0.22201,0.21868,433.84,-0.29489,-0.86749,-0.40063,679.42,0.10076,-0.44517,0.88976,117.62
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,-0.95021,0.22201,0.21868,442.55,-0.29489,-0.86749,-0.40063,714.68,0.10076,-0.44517,0.88976,125.94
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,-0.96826,0.24636,0.042262,487.62,-0.23836,-0.85916,-0.4528,710.28,-0.07524,-0.4485,0.89061,176.2
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,-0.96826,0.24636,0.042262,471.31,-0.23836,-0.85916,-0.4528,704.57,-0.07524,-0.4485,0.89061,178.79
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> select clear
+> fitmap #236 inMap #98
+Fit map cryosparc_P17_J884_009_volume_map.mrc z flip in map
+Cl3D_j581_run_it025_class001.mrc using 185363 points
+correlation = 0.8766, correlation about mean = 0.02403, overlap = 2112
+steps = 192, shift = 22.6, angle = 21.2 degrees
+Position of cryosparc_P17_J884_009_volume_map.mrc z flip (#236) relative to
+Cl3D_j581_run_it025_class001.mrc (#98) coordinates:
+Matrix rotation and translation
+-0.84354066 0.50422936 0.18491053 314.97189258
+-0.50932699 -0.64184531 -0.57325441 772.53341394
+-0.17036775 -0.57774333 0.79824024 267.14568387
+Axis -0.00417951 0.33079007 -0.94369511
+Axis point 276.01471701 384.47498501 0.00000000
+Rotation angle (degrees) 147.51935105
+Shift along axis 2.12587651
+> hide #!98 models
+> hide #!99 models
+> volume flip #236
+Opened cryosparc_P17_J884_009_volume_map.mrc z flip z flip as #237, grid size
+,294,294, pixel 1.9, shown at step 1, values float32
+> close #236
+> show #!98 models
+> show #!99 models
+> select add #237
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #237,0.96723,0.12731,-0.21969,22.54,0.15273,-0.9829,0.10285,476.95,-0.20284,-0.13303,-0.97013,678.92
+> view matrix models
+> #237,0.98911,0.12697,-0.074375,-26.233,0.1345,-0.98512,0.10698,481.46,-0.059685,-0.11582,-0.99148,640.32
+> view matrix models
+> #237,0.99344,0.076053,-0.08539,-10.83,0.10378,-0.91318,0.39411,386.84,-0.048004,-0.40039,-0.91509,689.4
+> ui mousemode right "translate selected models"
+> view matrix models
+> #237,0.99344,0.076053,-0.08539,-17.742,0.10378,-0.91318,0.39411,419.91,-0.048004,-0.40039,-0.91509,662.61
+> view matrix models
+> #237,0.99344,0.076053,-0.08539,-17.954,0.10378,-0.91318,0.39411,412.57,-0.048004,-0.40039,-0.91509,657.54
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #237,0.99498,0.052431,-0.085289,-12.206,0.089013,-0.85322,0.5139,365.78,-0.045827,-0.51891,-0.8536,670.02
+> ui mousemode right "translate selected models"
+> view matrix models
+> #237,0.99498,0.052431,-0.085289,4.4691,0.089013,-0.85322,0.5139,363.94,-0.045827,-0.51891,-0.8536,680.57
+> select subtract #237
+Nothing selected
+> fitmap #237 inMap #98
+Fit map cryosparc_P17_J884_009_volume_map.mrc z flip z flip in map
+Cl3D_j581_run_it025_class001.mrc using 185363 points
+correlation = 0.9464, correlation about mean = 0.3043, overlap = 2607
+steps = 148, shift = 5.24, angle = 12.2 degrees
+Position of cryosparc_P17_J884_009_volume_map.mrc z flip z flip (#237)
+relative to Cl3D_j581_run_it025_class001.mrc (#98) coordinates:
+Matrix rotation and translation
+.95506772 0.17454310 -0.23954199 25.26355402
+.28049806 -0.79336127 0.54027653 283.68421592
+-0.09574180 -0.58319174 -0.80667274 694.76834568
+Axis -0.98759585 -0.12640897 0.09314076
+Axis point 0.00000000 249.94675701 303.67322404
+Rotation angle (degrees) 145.33414419
+Shift along axis 3.90083895
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> hide #!99 models
+> volume #237 step 2
+> volume #237 level 0.3935
+> volume #237 level 0.3609
+> volume #237 level 0.3342
+> show #!98 models
+> show #!97 models
+> hide #!97 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> hide #!98 models
+> show #!98 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> hide #!99 models
+> show #!129 models
+> show #!130 models
+> hide #!129 models
+> hide #!130 models
+> show #!173 models
+> show #!205 models
+> hide #!173 models
+> ui mousemode right zoom
+> lighting soft
+> show #!204 models
+> hide #!205 models
+> show #!205 models
+> hide #!204 models
+> show #!204 models
+> show #!206 models
+> hide #!205 models
+> hide #!206 models
+> hide #!204 models
+> show #!204 models
+> show #!205 models
+> hide #!204 models
+> hide #!205 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> show #!228 models
+> hide #!228 models
+> show #!225 models
+> hide #!225 models
+> show #!233 models
+> show #!232 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> hide #!233 models
+> hide #!232 models
+> show #!225 models
+> show #!233 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> color #233 #b2b2b2b7 models
+> color #233 #b2b2b2c0 models
+> color #233 #b2b2b2c6 models
+> color #233 #b2b2b2ca models
+> color #233 #b2b2b2cb models
+> color #233 #b2b2b2cc models
+> color #233 #b2b2b2ff models
+> color #233 #b2b2b2f3 models
+> color #233 #b2b2b2ff models
+> color #233 #b2b2b2ee models
+> color #233 #b2b2b2a5 models
+> color #233 #b2b2b2ff models
+> color #233 #b2b2b283 models
+> color #233 #b2b2b298 models
+> color #233 #b2b2b2ff models
+[Repeated 2 time(s)]
+> color #233 #b2b2b216 models
+> color #233 #b2b2b22a models
+> color #233 #b2b2b268 models
+> color #233 #b2b2b24e models
+> color #233 #b2b2b27c models
+> color #233 #b2b2b236 models
+> color #233 #b2b2b280 models
+> color #233 #b2b2b2ff models
+> hide #!233 models
+> show #!233 models
+> select #234/A
+atoms, 813 bonds, 102 residues, 1 model selected
+> volume flip #236sel #234/A,E
+Missing or invalid "volumes" argument: only initial part "#236" of atom
+specifier valid
+> select #234/A,E
+atoms, 1626 bonds, 205 residues, 1 model selected
+> color sel orange
+> select #234/B,F
+atoms, 1326 bonds, 173 residues, 1 model selected
+> color sel orange red
+> select clear
+> show #!233 models
+> hide #!237 models
+> color #233 #b2b2b272 models
+> color #233 #b2b2b27c models
+> show #!179 models
+> hide #!179 models
+> show #!178 models
+> hide #!178 models
+> show #!179 models
+> hide #!179 models
+> combine #179
+No structures specified
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J544_007_volume_map_zflip.mrc
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
+,588,588, pixel 0.95, shown at level 0.158, step 4, values float32
+> select add #236
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,-0.012453,0.9963,-0.085041,38.532,-0.99954,-0.014744,-0.026367,562,-0.027524,0.084674,0.99603,-14.052
+> view matrix models
+> #236,0.059878,0.99536,-0.075321,15.571,-0.99446,0.066013,0.081795,504.47,0.086388,0.070006,0.9938,-41.09
+> view matrix models
+> #236,0.76783,0.50486,-0.39441,52.38,-0.29922,0.82696,0.47602,-20.228,0.56648,-0.24749,0.78603,-22.96
+> lighting simple
+> view matrix models
+> #236,-0.88103,0.27074,-0.38793,573.03,-0.025569,0.79159,0.61052,-129.36,0.47237,0.5478,-0.69049,254.3
+> view matrix models
+> #236,-0.16658,-0.56618,-0.80728,733.71,-0.98446,0.049393,0.16849,478.79,-0.055524,0.8228,-0.56561,287.22
+> view matrix models
+> #236,0.4492,-0.45163,-0.77088,519.64,-0.80916,-0.57146,-0.13671,694.91,-0.37879,0.68517,-0.62214,432.45
+> view matrix models
+> #236,0.65993,-0.46974,-0.58638,407.54,-0.74905,-0.47202,-0.46488,754.94,-0.058416,0.74602,-0.66336,339.76
+> view matrix models
+> #236,0.53079,-0.4452,-0.72115,479.45,-0.83669,-0.41075,-0.36226,730.28,-0.13493,0.79566,-0.59052,324.57
+> view matrix models
+> #236,0.35401,-0.88851,0.29195,328.65,-0.68389,-0.033001,0.72884,240.28,-0.63794,-0.45768,-0.61932,813.79
+> view matrix models
+> #236,0.42906,-0.90235,0.040822,390.9,-0.42585,-0.16222,0.89013,152.48,-0.79659,-0.3993,-0.45387,789.83
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.42906,-0.90235,0.040822,224.14,-0.42585,-0.16222,0.89013,22.814,-0.79659,-0.3993,-0.45387,720.65
+> view matrix models
+> #236,0.42906,-0.90235,0.040822,264.42,-0.42585,-0.16222,0.89013,-12.91,-0.79659,-0.3993,-0.45387,709.48
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,0.35817,-0.93201,-0.055435,322.64,-0.41443,-0.21191,0.88507,-1.0118,-0.83664,-0.29403,-0.46215,694.69
+> view matrix models
+> #236,0.67931,-0.62117,-0.39075,254.89,-0.16273,-0.64672,0.74516,91.098,-0.71558,-0.44261,-0.54041,726.03
+> view matrix models
+> #236,0.71295,-0.55192,-0.43253,239.94,-0.10993,-0.69717,0.70842,101.7,-0.69254,-0.45753,-0.55772,729.13
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.71295,-0.55192,-0.43253,297.54,-0.10993,-0.69717,0.70842,100.6,-0.69254,-0.45753,-0.55772,732.73
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,0.68046,-0.63817,-0.36017,307.11,0.13892,-0.37025,0.91849,-123.81,-0.7195,-0.67503,-0.16328,674.54
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.68046,-0.63817,-0.36017,294.76,0.13892,-0.37025,0.91849,-125.98,-0.7195,-0.67503,-0.16328,621.96
+> view matrix models
+> #236,0.68046,-0.63817,-0.36017,302.19,0.13892,-0.37025,0.91849,-125.89,-0.7195,-0.67503,-0.16328,622.96
+> view matrix models
+> #236,0.68046,-0.63817,-0.36017,303.09,0.13892,-0.37025,0.91849,-124.21,-0.7195,-0.67503,-0.16328,623.52
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,0.68673,-0.57216,-0.44837,311.32,0.2108,-0.43355,0.87613,-113.66,-0.69568,-0.69618,-0.17711,627
+> view matrix models
+> #236,0.6869,-0.56458,-0.45762,312.14,0.21863,-0.43999,0.87099,-112.46,-0.69308,-0.69833,-0.1788,627.39
+> view matrix models
+> #236,0.68383,-0.61388,-0.39437,306.37,0.16624,-0.39519,0.90343,-120.29,-0.71045,-0.68336,-0.16819,624.81
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.68383,-0.61388,-0.39437,314.45,0.16624,-0.39519,0.90343,-114.46,-0.71045,-0.68336,-0.16819,626.72
+> view matrix models
+> #236,0.68383,-0.61388,-0.39437,313.59,0.16624,-0.39519,0.90343,-113.76,-0.71045,-0.68336,-0.16819,626.96
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,0.68659,-0.57615,-0.44344,318.1,0.20666,-0.4301,0.87881,-107.76,-0.69705,-0.69503,-0.17624,628.94
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.68659,-0.57615,-0.44344,327.07,0.20666,-0.4301,0.87881,-108.47,-0.69705,-0.69503,-0.17624,628.68
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,0.63818,-0.60887,-0.47118,358.2,0.24341,-0.42105,0.87377,-119.57,-0.7304,-0.67231,-0.1205,614.18
+> view matrix models
+> #236,0.63577,-0.5548,-0.53665,364.9,0.29495,-0.46787,0.83313,-108.37,-0.7133,-0.68796,-0.13382,617.88
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.63577,-0.5548,-0.53665,372.36,0.29495,-0.46787,0.83313,-107.39,-0.7133,-0.68796,-0.13382,618.18
+> hide #!234 models
+> hide #!233 models
+> show #!233 models
+> color #233 #b2b2b2ff models
+> select subtract #236
+Nothing selected
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> volume #236 step 1
+> volume #236 level 0.1732
+> volume #236 color #009193
+[Repeated 1 time(s)]
+> select add #236
+models selected
+> view matrix models
+> #236,0.63577,-0.5548,-0.53665,371.67,0.29495,-0.46787,0.83313,-109.23,-0.7133,-0.68796,-0.13382,606.22
+> hide #!236 models
+> show #!236 models
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,0.64925,-0.56021,-0.51443,362.37,0.19972,-0.52706,0.82603,-64.458,-0.73388,-0.63904,-0.23031,629.16
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.64925,-0.56021,-0.51443,360.82,0.19972,-0.52706,0.82603,-64.722,-0.73388,-0.63904,-0.23031,636.2
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,0.65709,-0.56493,-0.49909,355.08,0.13448,-0.56361,0.81502,-33.193,-0.74172,-0.60266,-0.29436,648.75
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.65709,-0.56493,-0.49909,353.84,0.13448,-0.56361,0.81502,-29.68,-0.74172,-0.60266,-0.29436,652.83
+> select subtract #236
+Nothing selected
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> ui mousemode right "rotate selected models"
+> select add #236
+models selected
+> view matrix models
+> #236,0.66843,-0.53922,-0.5123,347.9,0.2468,-0.48895,0.83667,-87.981,-0.70163,-0.68569,-0.19375,632.36
+> select subtract #236
+Nothing selected
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!236 models
+> show #!236 models
+> select add #236
+models selected
+> view matrix models
+> #236,0.6648,-0.54898,-0.50663,349.76,0.17003,-0.54919,0.81822,-44.49,-0.72742,-0.63009,-0.27176,649.12
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.6648,-0.54898,-0.50663,348.92,0.17003,-0.54919,0.81822,-46.742,-0.72742,-0.63009,-0.27176,656.36
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,0.66754,-0.54182,-0.5107,347.51,0.22647,-0.50565,0.83248,-78.738,-0.70929,-0.67138,-0.21483,644.51
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.66754,-0.54182,-0.5107,347.63,0.22647,-0.50565,0.83248,-82.762,-0.70929,-0.67138,-0.21483,639.69
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,0.67038,-0.53268,-0.51657,346.22,0.29731,-0.44502,0.84473,-122.74,-0.67985,-0.71987,-0.13996,620.98
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.67038,-0.53268,-0.51657,347.56,0.29731,-0.44502,0.84473,-116.97,-0.67985,-0.71987,-0.13996,611.3
+> select subtract #236
+Nothing selected
+> select add #236
+models selected
+> view matrix models
+> #236,0.67038,-0.53268,-0.51657,347.92,0.29731,-0.44502,0.84473,-119.74,-0.67985,-0.71987,-0.13996,610.38
+> select subtract #236
+Nothing selected
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> select add #236
+models selected
+> view matrix models
+> #236,0.67038,-0.53268,-0.51657,348.46,0.29731,-0.44502,0.84473,-117.4,-0.67985,-0.71987,-0.13996,603.72
+> select subtract #236
+Nothing selected
+> hide #!233 models
+> show #!233 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> ui mousemode right "rotate selected models"
+> select add #236
+models selected
+> view matrix models
+> #236,0.66305,-0.53587,-0.5227,353.3,0.32847,-0.41917,0.84641,-133.6,-0.67266,-0.7329,-0.10191,593.24
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.66305,-0.53587,-0.5227,353.67,0.32847,-0.41917,0.84641,-133.02,-0.67266,-0.7329,-0.10191,590.06
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,0.68404,-0.53709,-0.49359,338.97,0.31215,-0.39604,0.86355,-140.12,-0.65928,-0.74477,-0.10325,589.96
+> view matrix models
+> #236,0.68758,-0.51714,-0.50971,337.68,0.32634,-0.40699,0.85315,-137.85,-0.64864,-0.75294,-0.11107,591.67
+> view matrix models
+> #236,0.68393,-0.51897,-0.51275,340.15,0.34156,-0.39327,0.85363,-145.94,-0.64466,-0.75895,-0.091709,586.07
+> hide #!233 models
+> show #!233 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> select subtract #236
+Nothing selected
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!233 models
+> show #!233 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!236 models
+> show #!236 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!236 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> show #!235 models
+> hide #!235 models
+> ui tool show Matchmaker
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> hide #!232 models
+> show #!234 models
+> select #234/C,G
+atoms, 1700 bonds, 2 pseudobonds, 231 residues, 2 models selected
+> color (#!234 & sel) light gray
+> select clear
+> select #234/D,H
+atoms, 1494 bonds, 1 pseudobond, 203 residues, 2 models selected
+> color (#!234 & sel) dim gray
+> select clear
+> show #!236 models
+> hide #!236 models
+> show #!233 models
+> hide #!233 models
+> show #!235 models
+> hide #!235 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> color #233 #b2b2b2cb models
+> color #233 #b2b2b2be models
+> color #233 #b2b2b2c0 models
+> color #233 #b2b2b2bf models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> lighting soft
+[Repeated 1 time(s)]
+> lighting full
+> lighting simple
+> lighting full
+[Repeated 1 time(s)]
+> lighting soft
+> lighting full
+[Repeated 6 time(s)]
+> color #233 #b2b2b2ed models
+> color #233 #b2b2b2ff models
+> lighting soft
+> show #!236 models
+> select add #236
+models selected
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.68393,-0.51897,-0.51275,340.34,0.34156,-0.39327,0.85363,-144.79,-0.64466,-0.75895,-0.091709,589.32
+> select subtract #236
+Nothing selected
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!234 models
+> show #!234 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!234 models
+> show #!234 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> ui mousemode right zoom
+> hide #!233 models
+> hide #!236 models
+> show #!98 models
+> show #!99 models
+> show #!129 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!130 models
+> show #!130 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> hide #!99 models
+> hide #!129 models
+> hide #!130 models
+> show #!98 models
+> show #!99 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!130 models
+> hide #!130 models
+> show #!129 models
+> hide #!129 models
+> show #!130 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> hide #!98 models
+> hide #!99 models
+> show #!173 models
+> volume flip #173
+Opened cryosparc_P17_J858_007_volume_map.mrc z flip as #238, grid size
+,588,588, pixel 0.95, shown at step 1, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J864_007_volume_map.mrc
+Opened cryosparc_P17_J864_007_volume_map.mrc as #239, grid size 588,588,588,
+pixel 0.95, shown at level 0.153, step 4, values float32
+> volume #239 step 1
+> show #!173 models
+Error processing trigger "graphics update":
+You deleted or moved a volume file that is still open in ChimeraX.
+/Users/cvetkom/Downloads/cryosparc_P17_J858_007_volume_map.mrc
+To allow fast initial display of volume data ChimeraX does not read all data
+from the file when it is first opened, and will later read more data when
+needed. ChimeraX got an error trying to read the above file.
+> hide #!173 models
+> show #!173 models
+> hide #!173 models
+> show #!173 models
+> hide #!173 models
+> show #!173 models
+> hide #!173 models
+> volume flip #239
+Opened cryosparc_P17_J864_007_volume_map.mrc z flip as #240, grid size
+,588,588, pixel 0.95, shown at step 1, values float32
+> hide #!240 models
+> show #!240 models
+> show #!239 models
+> hide #!239 models
+> hide #!240 models
+> show #!240 models
+> close #238
+> volume #240 level 0.1562
+> hide #!240 models
+> show #!240 models
+> select add #240
+models selected
+> select subtract #240
+Nothing selected
+> view #240 clip false
+No displayed objects specified.
+> show #!237 models
+> hide #!237 models
+> close #237
+> hide #!240 models
+> show #!240 models
+> close #240
+> show #!239 models
+> volume flip #239
+Opened cryosparc_P17_J864_007_volume_map.mrc z flip as #237, grid size
+,588,588, pixel 0.95, shown at step 1, values float32
+> hide #!237 models
+> show #!237 models
+> show #!233 models
+> hide #!233 models
+> hide #!237 models
+> show #!237 models
+> close #237
+> show #!233 models
+> save
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc
+> models #233
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!235 models
+> show #!236 models
+> show #!234 models
+> hide #!234 models
+> show #!233 models
+> hide #!233 models
+> hide #!235 models
+> hide #!236 models
+> show #!235 models
+> hide #!235 models
+> show #!235 models
+> close #235
+> volume flip #239
+Opened cryosparc_P17_J864_007_volume_map.mrc z flip as #235, grid size
+,588,588, pixel 0.95, shown at step 1, values float32
+> hide #!235 models
+> show #!235 models
+> close #235
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
+\u2014\u2014\u2014 End of log from Thu Jul 18 17:16:17 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> show #!236 models
+> hide #!236 models
+> show #!233 models
+> show #!236 models
+> hide #!236 models
+> hide #!233 models
+> show #!239 models
+> lighting simple
+> volume flip #239
+Opened cryosparc_P17_J864_007_volume_map.mrc z flip as #235, grid size
+,588,588, pixel 0.95, shown at step 1, values float32
+> save
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J864_007_volume_map_zflip.mrc
+> models #235
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
+[Repeated 1 time(s)]
+\u2014\u2014\u2014 End of log from Thu Jul 18 19:11:33 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> show #!236 models
+> hide #!236 models
+> hide #!235 models
+> show #!236 models
+> show #!233 models
+> hide #!236 models
+> hide #!233 models
+> open /Users/cvetkom/Documents/AlphaFold/Mrc1_Ctf4CTD/ranked_0.pdb
+Chain information for ranked_0.pdb #237
+---
+Chain | Description
+A | No description available
+B C D | No description available
+> open /Users/cvetkom/Documents/AlphaFold/Mrc1_Ctf4CTD/ranked_1.pdb
+Chain information for ranked_1.pdb #238
+---
+Chain | Description
+A | No description available
+B C D | No description available
+> open /Users/cvetkom/Documents/AlphaFold/Mrc1_Ctf4CTD/ranked_2.pdb
+Chain information for ranked_2.pdb #240
+---
+Chain | Description
+A | No description available
+B C D | No description available
+> open /Users/cvetkom/Documents/AlphaFold/Mrc1_Ctf4CTD/ranked_3.pdb
+Chain information for ranked_3.pdb #241
+---
+Chain | Description
+A | No description available
+B C D | No description available
+> open /Users/cvetkom/Documents/AlphaFold/Mrc1_Ctf4CTD/ranked_4.pdb
+Chain information for ranked_4.pdb #242
+---
+Chain | Description
+A | No description available
+B C D | No description available
+> hide #237 models
+> show #237 models
+> view #237 clip false
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!235 models
+> hide #!235 models
+> select add #237
+atoms, 39489 bonds, 2467 residues, 1 model selected
+> cofr sel
+> select subtract #237
+Nothing selected
+> select add #237
+atoms, 39489 bonds, 2467 residues, 1 model selected
+> select subtract #237
+Nothing selected
+> hide #238 models
+> hide #240 models
+> hide #241 models
+> hide #242 models
+> show #238 models
+> hide #238 models
+> show #238 models
+> hide #238 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> show #238 models
+> hide #238 models
+> show #240 models
+> ui tool show Matchmaker
+> hide #240 models
+> show #237 models
+> hide #237 models
+> show #!211 models
+> select add #211
+models selected
+> cofr sel
+> view sel
+> select subtract #211
+Nothing selected
+> show #!221 models
+> hide #!221 models
+> show #!177 models
+> hide #!177 models
+> show #!191 models
+> hide #!211 models
+> show #!211 models
+> hide #!211 models
+> show #!211 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> show #!197 models
+> hide #!197 models
+> show #!198 models
+> hide #!191 models
+> show #!191 models
+> hide #!198 models
+> hide #!191 models
+> show #!191 models
+> select add #191
+models selected
+> select subtract #191
+Nothing selected
+> select add #211
+models selected
+Drag select of 211 cryosparc_P17_J843_008_volume_map_sharp.mrc
+> ui mousemode right "translate selected models"
+> select #211
+models selected
+> view matrix models #211,1,0,0,23.591,0,1,0,56.577,0,0,1,-51.52
+> view matrix models #211,1,0,0,22.768,0,1,0,47.717,0,0,1,-59.573
+> ui tool show "Fit in Map"
+> fitmap #211 inMap #191
+Fit map cryosparc_P17_J843_008_volume_map_sharp.mrc in map
+cryosparc_P17_J803_005_volume_map_sharp.mrc using 95383 points
+correlation = 0.8844, correlation about mean = 0.6114, overlap = 1.144e+05
+steps = 204, shift = 6.18, angle = 0.216 degrees
+Position of cryosparc_P17_J843_008_volume_map_sharp.mrc (#211) relative to
+cryosparc_P17_J803_005_volume_map_sharp.mrc (#191) coordinates:
+Matrix rotation and translation
+.99999559 -0.00221335 -0.00198223 26.85415332
+.00221794 0.99999485 0.00231772 45.03607037
+.00197709 -0.00232210 0.99999535 -64.65124874
+Axis -0.61542026 -0.52516117 0.58776156
+Axis point 0.00000000 -8050.27859560 -1735.24699520
+Rotation angle (degrees) 0.21598457
+Shift along axis -78.17730413
+> select subtract #211
+Nothing selected
+> hide #!191 models
+> show #!191 models
+> ui mousemode right zoom
+[Repeated 1 time(s)]
+> lighting soft
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> show #!198 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> hide #!198 models
+> hide #!211 models
+> show #!190 models
+> show #!226 models
+> hide #!226 models
+> show #!226 models
+> color #226 #9437ffff models
+> lighting simple
+> hide #!190 models
+> show #!190 models
+> select add #226
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #226,-0.69587,-0.71701,-0.040702,705.69,-0.14519,0.19596,-0.9698,554.35,0.70334,-0.66895,-0.24047,350.03
+> view matrix models
+> #226,-0.55466,-0.80613,-0.20617,738.49,-0.80542,0.58236,-0.11025,383.62,0.20894,0.1049,-0.97229,500.26
+> view matrix models
+> #226,-0.93544,-0.34201,0.089373,633.42,-0.33939,0.93964,0.043527,102.84,-0.098865,0.010385,-0.99505,623.13
+> ui mousemode right "translate selected models"
+> view matrix models
+> #226,-0.93544,-0.34201,0.089373,607.14,-0.33939,0.93964,0.043527,107.99,-0.098865,0.010385,-0.99505,615.3
+> view matrix models
+> #226,-0.93544,-0.34201,0.089373,604.94,-0.33939,0.93964,0.043527,90.344,-0.098865,0.010385,-0.99505,582.38
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #226,-0.92949,-0.35318,0.10634,601.2,-0.35497,0.93487,0.0022278,108.57,-0.1002,-0.035677,-0.99433,595.25
+> ui mousemode right "translate selected models"
+> view matrix models
+> #226,-0.92949,-0.35318,0.10634,600.67,-0.35497,0.93487,0.0022278,112.16,-0.1002,-0.035677,-0.99433,599.08
+> view matrix models
+> #226,-0.92949,-0.35318,0.10634,604.71,-0.35497,0.93487,0.0022278,115.64,-0.1002,-0.035677,-0.99433,597.23
+> fitmap #226 inMap #190
+Fit map cryosparc_P17_J842_005_volume_map_sharp.mrc in map
+cryosparc_P17_J803_005_volume_map.mrc using 488089 points
+correlation = 0.9693, correlation about mean = 0.8115, overlap = 1.318e+05
+steps = 208, shift = 8.45, angle = 11.9 degrees
+Position of cryosparc_P17_J842_005_volume_map_sharp.mrc (#226) relative to
+cryosparc_P17_J803_005_volume_map.mrc (#190) coordinates:
+Matrix rotation and translation
+-0.97649779 -0.20178090 0.07573987 585.60429131
+-0.21091477 0.96696460 -0.14315876 117.19127531
+-0.04435107 -0.15576887 -0.98679737 611.32765515
+Axis -0.10413305 0.99169911 -0.07542663
+Axis point 308.30518170 0.00000000 301.15926555
+Rotation angle (degrees) 176.52872801
+Shift along axis 9.12733602
+> select subtract #226
+Nothing selected
+> hide #!190 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!190 models
+> hide #!226 models
+> show #!230 models
+> show #!231 models
+> select add #230
+models selected
+> select add #231
+models selected
+> view matrix models
+> #230,1,0,0,6.1821,0,1,0,2.3092,0,0,1,0.16596,#231,1,0,0,6.1821,0,1,0,2.3092,0,0,1,0.16596
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #230,-0.89534,0.44297,-0.046301,393.57,0.44479,0.88392,-0.14437,-39.265,-0.023027,-0.14986,-0.98844,641.69,#231,-0.89534,0.44297,-0.046301,393.57,0.44479,0.88392,-0.14437,-39.265,-0.023027,-0.14986,-0.98844,641.69
+> ui mousemode right "translate selected models"
+> view matrix models
+> #230,-0.89534,0.44297,-0.046301,320.22,0.44479,0.88392,-0.14437,-44.069,-0.023027,-0.14986,-0.98844,639.1,#231,-0.89534,0.44297,-0.046301,320.22,0.44479,0.88392,-0.14437,-44.069,-0.023027,-0.14986,-0.98844,639.1
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #230,-0.91848,0.23415,0.31871,274.41,0.27736,0.95585,0.097055,-92.686,-0.28191,0.17754,-0.94287,602.62,#231,-0.91848,0.23415,0.31871,274.41,0.27736,0.95585,0.097055,-92.686,-0.28191,0.17754,-0.94287,602.62
+> ui mousemode right "translate selected models"
+> view matrix models
+> #230,-0.91848,0.23415,0.31871,357.45,0.27736,0.95585,0.097055,-82.118,-0.28191,0.17754,-0.94287,602.24,#231,-0.91848,0.23415,0.31871,357.45,0.27736,0.95585,0.097055,-82.118,-0.28191,0.17754,-0.94287,602.24
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #230,-0.9953,-0.08301,0.049969,545.27,-0.075504,0.9877,0.13689,-11.072,-0.060718,0.13247,-0.98933,571.06,#231,-0.9953,-0.08301,0.049969,545.27,-0.075504,0.9877,0.13689,-11.072,-0.060718,0.13247,-0.98933,571.06
+> ui mousemode right "translate selected models"
+> view matrix models
+> #230,-0.9953,-0.08301,0.049969,559.93,-0.075504,0.9877,0.13689,-6.7949,-0.060718,0.13247,-0.98933,569.44,#231,-0.9953,-0.08301,0.049969,559.93,-0.075504,0.9877,0.13689,-6.7949,-0.060718,0.13247,-0.98933,569.44
+> view matrix models
+> #230,-0.9953,-0.08301,0.049969,568.3,-0.075504,0.9877,0.13689,-40.558,-0.060718,0.13247,-0.98933,526.44,#231,-0.9953,-0.08301,0.049969,568.3,-0.075504,0.9877,0.13689,-40.558,-0.060718,0.13247,-0.98933,526.44
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #230,-0.99234,-0.11444,0.046504,577.22,-0.10693,0.9843,0.14046,-32.528,-0.061848,0.13441,-0.98899,526.1,#231,-0.99234,-0.11444,0.046504,577.22,-0.10693,0.9843,0.14046,-32.528,-0.061848,0.13441,-0.98899,526.1
+> view matrix models
+> #230,-0.98137,-0.13006,0.14143,550.27,-0.15125,0.97687,-0.15114,68.276,-0.1185,-0.16971,-0.97834,621.31,#231,-0.98137,-0.13006,0.14143,550.27,-0.15125,0.97687,-0.15114,68.276,-0.1185,-0.16971,-0.97834,621.31
+> ui mousemode right "translate selected models"
+> view matrix models
+> #230,-0.98137,-0.13006,0.14143,541.12,-0.15125,0.97687,-0.15114,98.697,-0.1185,-0.16971,-0.97834,633.01,#231,-0.98137,-0.13006,0.14143,541.12,-0.15125,0.97687,-0.15114,98.697,-0.1185,-0.16971,-0.97834,633.01
+> fitmap #230 inMap #190
+Fit map cryosparc_P17_J845_005_volume_map_sharp.mrc in map
+cryosparc_P17_J803_005_volume_map.mrc using 572767 points
+correlation = 0.9702, correlation about mean = 0.8247, overlap = 1.352e+05
+steps = 108, shift = 7.64, angle = 5.67 degrees
+Position of cryosparc_P17_J845_005_volume_map_sharp.mrc (#230) relative to
+cryosparc_P17_J803_005_volume_map.mrc (#190) coordinates:
+Matrix rotation and translation
+-0.97635603 -0.20284331 0.07472287 586.20276261
+-0.21174871 0.96698095 -0.14181092 117.11563644
+-0.04349020 -0.15428042 -0.98706949 610.85909501
+Axis -0.10460810 0.99170348 -0.07470851
+Axis point 308.47483717 0.00000000 301.01098483
+Rotation angle (degrees) 176.58308850
+Shift along axis 9.18605482
+> fitmap #231 inMap #190
+Fit map cryosparc_P17_J846_005_volume_map_sharp.mrc in map
+cryosparc_P17_J803_005_volume_map.mrc using 570393 points
+correlation = 0.9715, correlation about mean = 0.8289, overlap = 1.331e+05
+steps = 120, shift = 7.62, angle = 5.66 degrees
+Position of cryosparc_P17_J846_005_volume_map_sharp.mrc (#231) relative to
+cryosparc_P17_J803_005_volume_map.mrc (#190) coordinates:
+Matrix rotation and translation
+-0.97634464 -0.20282850 0.07491170 586.12671435
+-0.21175571 0.96700450 -0.14163978 117.05949264
+-0.04371137 -0.15415222 -0.98707974 610.90239310
+Axis -0.10460616 0.99170937 -0.07463300
+Axis point 308.46618437 0.00000000 300.99661437
+Rotation angle (degrees) 176.57124371
+Shift along axis 9.18305466
+> select subtract #231
+models selected
+> select subtract #230
+Nothing selected
+> hide #!231 models
+> show #!231 models
+> hide #!231 models
+> hide #!230 models
+> show #!230 models
+> hide #!230 models
+> show #!177 models
+> select add #177
+atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
+> view matrix models #177,1,0,0,79.796,0,1,0,51.72,0,0,1,-8.0933
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #177,0.69184,0.051639,0.7202,1.2453,0.39268,0.81013,-0.4353,88.033,-0.60594,0.58396,0.54021,85.465
+> view matrix models
+> #177,0.68848,0.040322,0.72414,3.3706,0.40239,0.80944,-0.42765,84.826,-0.60339,0.58581,0.54106,84.445
+> ui mousemode right "translate selected models"
+> view matrix models
+> #177,0.68848,0.040322,0.72414,-24.721,0.40239,0.80944,-0.42765,124.91,-0.60339,0.58581,0.54106,181.95
+> fitmap #177 inMap #190
+Fit molecule 6skl (#177) to map cryosparc_P17_J803_005_volume_map.mrc (#190)
+using 118220 atoms
+average map value = 0.2974, steps = 296
+shifted from previous position = 36.4
+rotated from previous position = 17.9 degrees
+atoms outside contour = 74597, contour level = 0.30132
+Position of 6skl (#177) relative to cryosparc_P17_J803_005_volume_map.mrc
+(#190) coordinates:
+Matrix rotation and translation
+.46579535 -0.09937691 0.87929456 48.24974596
+.51662113 0.83728469 -0.17904461 61.91426409
+-0.71842697 0.53766029 0.44134352 233.27290342
+Axis 0.38609415 0.86070423 0.33184263
+Axis point 168.02643327 0.00000000 112.77870008
+Rotation angle (degrees) 68.14791182
+Shift along axis 149.32870821
+> select subtract #177
+Nothing selected
+> ui mousemode right zoom
+> select add #177
+atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
+> hide (#!177 & sel) target a
+> cartoon (#!177 & sel)
+> select subtract #177
+Nothing selected
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!191 models
+> hide #!177 models
+> show #!177 models
+> fitmap #177 inMap #191
+Fit molecule 6skl (#177) to map cryosparc_P17_J803_005_volume_map_sharp.mrc
+(#191) using 118220 atoms
+average map value = 0.3767, steps = 56
+shifted from previous position = 0.0922
+rotated from previous position = 0.0581 degrees
+atoms outside contour = 80226, contour level = 0.39
+Position of 6skl (#177) relative to
+cryosparc_P17_J803_005_volume_map_sharp.mrc (#191) coordinates:
+Matrix rotation and translation
+.46578087 -0.09837126 0.87941531 48.10212088
+.51628561 0.83733279 -0.17978591 62.07532586
+-0.71867751 0.53777030 0.44080126 233.33404225
+Axis 0.38651030 0.86080969 0.33108377
+Axis point 168.00088480 0.00000000 112.96763857
+Rotation angle (degrees) 68.16361025
+Shift along axis 149.28012082
+> hide #!177 models
+> show #!177 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
+> show #237 models
+> hide #237 models
+> show #237 models
+> matchmaker #237/B to #177/H pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain H (#177) with ranked_0.pdb, chain B (#237), sequence
+alignment score = 2258
+RMSD between 412 pruned atom pairs is 0.645 angstroms; (across all 425 pairs:
+.877)
+> hide #237 models
+> show #237 models
+> show #238 models
+> matchmaker #238/B to #177/H pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain H (#177) with ranked_1.pdb, chain B (#238), sequence
+alignment score = 2254.4
+RMSD between 411 pruned atom pairs is 0.626 angstroms; (across all 425 pairs:
+.888)
+> matchmaker #240/B to #177/H pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain H (#177) with ranked_2.pdb, chain B (#240), sequence
+alignment score = 2264.6
+RMSD between 414 pruned atom pairs is 0.635 angstroms; (across all 425 pairs:
+.838)
+> show #240 models
+> hide #240 models
+> hide #237 models
+> hide #238 models
+> show #240 models
+> hide #!177 models
+> matchmaker #240/C to #177/H pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain H (#177) with ranked_2.pdb, chain C (#240), sequence
+alignment score = 2261.6
+RMSD between 413 pruned atom pairs is 0.630 angstroms; (across all 425 pairs:
+.840)
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #240 models
+> show #241 models
+> matchmaker #242/B to #177/H pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain H (#177) with ranked_4.pdb, chain B (#242), sequence
+alignment score = 2243.6
+RMSD between 412 pruned atom pairs is 0.623 angstroms; (across all 425 pairs:
+.828)
+> show #242 models
+> matchmaker #241/B to #177/H pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain H (#177) with ranked_3.pdb, chain B (#241), sequence
+alignment score = 2265.2
+RMSD between 410 pruned atom pairs is 0.661 angstroms; (across all 425 pairs:
+.961)
+> hide #242 models
+> hide #241 models
+> show #242 models
+> hide #242 models
+> show #241 models
+> show #242 models
+> hide #241 models
+> hide #242 models
+> show #237 models
+> hide #!177 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!177 models
+> hide #!177 models
+> select #237/A#238/A#240/A#241/A#242/A
+atoms, 87105 bonds, 5480 residues, 5 models selected
+> select #237/B#238/B#240/B#241/B#242/B
+atoms, 36780 bonds, 2285 residues, 5 models selected
+> ui tool show "Color Actions"
+> color sel lime green
+> select #237/C#238/C#240/C#241/C#242/C
+atoms, 36780 bonds, 2285 residues, 5 models selected
+> color sel lime green
+> select #237/D#238/D#240/D#241/D#242/D
+atoms, 36780 bonds, 2285 residues, 5 models selected
+> color sel lime green
+> select #237/A#238/A#240/A#241/A#242/A
+atoms, 87105 bonds, 5480 residues, 5 models selected
+> show #!177 models
+> color sel medium blue
+> color sel dark blue
+> color sel medium blue
+[Repeated 1 time(s)]
+> color sel purple
+> color sel blue
+> color sel medium blue
+[Repeated 1 time(s)]
+> select clear
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #238 models
+> hide #238 models
+> show #238 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #238 models
+> show #238 models
+> hide #238 models
+> show #238 models
+> hide #238 models
+> hide #237 models
+> show #240 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #240 models
+> show #240 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> hide #240 models
+> show #241 models
+> show #240 models
+> hide #240 models
+> show #240 models
+> hide #240 models
+> show #240 models
+> hide #240 models
+> show #242 models
+> hide #242 models
+> show #242 models
+> hide #241 models
+> show #241 models
+> hide #241 models
+> show #241 models
+> hide #242 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #241 models
+> show #241 models
+> hide #241 models
+> show #241 models
+> hide #237 models
+> hide #241 models
+> show #237 models
+> hide #237 models
+> show #238 models
+> show #237 models
+> hide #238 models
+> show #238 models
+> hide #237 models
+> hide #238 models
+> show #240 models
+> show #237 models
+> hide #237 models
+> hide #240 models
+> show #237 models
+> hide #237 models
+> show #238 models
+> hide #238 models
+> show #!239 models
+> hide #!239 models
+> show #240 models
+> hide #240 models
+> show #237 models
+> hide #237 models
+> show #238 models
+> hide #238 models
+> show #237 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #237/A
+Alignment identifier is 237/A
+> select #237/A:746
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #237/A:746-757
+atoms, 193 bonds, 12 residues, 1 model selected
+> show sel target ab
+> style sel ball
+Changed 193 atom styles
+> style sel sphere
+Changed 193 atom styles
+> style sel ball
+Changed 193 atom styles
+> select ~sel & ##selected
+atoms, 39296 bonds, 2455 residues, 1 model selected
+> hide sel target a
+> cartoon hide sel
+> select #237/A#238/A#240/A#241/A#242/A
+atoms, 87105 bonds, 5480 residues, 5 models selected
+> ui tool show "Color Actions"
+> color sel cornflower blue
+> color sel royal blue
+> select clear
+> show #238 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> hide #238 models
+> show #240 models
+> show #237 models
+> hide #240 models
+> show #240 models
+> hide #240 models
+> show #240 models
+> hide #240 models
+> hide #!177 models
+> select add #237
+atoms, 39489 bonds, 2467 residues, 1 model selected
+> select subtract #237
+Nothing selected
+> select add #237
+atoms, 39489 bonds, 2467 residues, 1 model selected
+> show sel target ab
+> hide sel target a
+> cartoon sel
+> ui tool show "Show Sequence Viewer"
+> sequence chain #237/A
+Alignment identifier is 237/A
+> select subtract #237
+Nothing selected
+> select #237/A:746-747
+atoms, 22 bonds, 2 residues, 1 model selected
+> select #237/A:746-757
+atoms, 193 bonds, 12 residues, 1 model selected
+> select #237/A:744
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #237/A:744-759
+atoms, 255 bonds, 16 residues, 1 model selected
+> show sel target ab
+> combine #237
+> hide #237 models
+> show #237 models
+> hide #243 models
+> select #237/A:743
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #237/A:1-743
+atoms, 11702 bonds, 743 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select #237/A:761
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #237/A:761-1096
+atoms, 5441 bonds, 336 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select #237/A:744
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #237/A
+atoms, 276 bonds, 17 residues, 1 model selected
+> show sel target ab
+> style sel ball
+Changed 274 atom styles
+> select clear
+> show #!211 models
+> lighting soft
+> color #211 #ffffb27e models
+> color #211 #ffffb2c3 models
+> color #211 #ffffb2ad models
+> color #211 #ffffb29d models
+> color #211 #ffffb28e models
+> color #211 #ffffb28f models
+> lighting full
+> lighting simple
+> set bgColor white
+> set bgColor #ffffff00
+> graphics silhouettes true
+> color #211 #ffffb2b0 models
+> color #211 #ffffb2d5 models
+> color #211 #ffffb2ec models
+> color #211 #ffffb2ca models
+> color #211 #ffffb227 models
+> color #211 #ffffb290 models
+> color #211 #ffffb2b1 models
+> color #211 #ffffb282 models
+> color #211 #ffffb2ff models
+> lighting soft
+> volume #211 level 0.6913
+> volume #211 level 0.65
+> show #!230 models
+> hide #!230 models
+> show #!230 models
+> hide #!230 models
+> show #!230 models
+> hide #!230 models
+> show #!230 models
+> hide #!230 models
+> show #!230 models
+> hide #!230 models
+> show #!230 models
+> hide #!230 models
+> show #!230 models
+> hide #!230 models
+> show #!230 models
+> show #!231 models
+> hide #!230 models
+> hide #!231 models
+> show #!231 models
+> hide #!231 models
+> show #!231 models
+> hide #!231 models
+> show #!231 models
+> hide #!231 models
+> show #!231 models
+> hide #!231 models
+> show #!231 models
+> hide #!231 models
+> show #!231 models
+> color #231 #b2ffb2d9 models
+> color #231 #b2ffb2c1 models
+> color #231 #b2ffb2a3 models
+> color #231 #b2ffb27f models
+> color #231 #b2ffb26e models
+> color #231 #b2ffb2ff models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> hide #!231 models
+> show #!231 models
+> hide #!231 models
+> show #!231 models
+> hide #!231 models
+> show #!231 models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> hide #!231 models
+> show #!231 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> set bgColor black
+> set bgColor transparent
+> ui tool show "Fit in Map"
+> show #243 models
+> hide #243 models
+> show #237 models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> hide #!231 models
+> show #!231 models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> fitmap #237 inMap #231
+Fit molecule ranked_0.pdb (#237) to map
+cryosparc_P17_J846_005_volume_map_sharp.mrc (#231) using 22081 atoms
+average map value = 0.3487, steps = 116
+shifted from previous position = 1.47
+rotated from previous position = 1.84 degrees
+atoms outside contour = 10270, contour level = 0.3
+Position of ranked_0.pdb (#237) relative to
+cryosparc_P17_J846_005_volume_map_sharp.mrc (#231) coordinates:
+Matrix rotation and translation
+.07105997 -0.95640246 -0.28327514 285.99602561
+.71998545 0.24572901 -0.64902865 297.83602531
+.69034152 -0.15783402 0.70605736 373.36846355
+Axis 0.24561334 -0.48684010 0.83824865
+Axis point -161.36898166 394.59093851 0.00000000
+Rotation angle (degrees) 89.34548655
+Shift along axis 238.22153124
+> hide #237 models
+> show #237 models
+> color #231 #b2ffb283 models
+> set bgColor white
+> set bgColor #ffffff00
+> color #231 #b2ffb282 models
+> color #231 #b2ffb292 models
+> color #231 #b2ffb2ae models
+> color #231 #b2ffb2bd models
+> color #231 #b2ffb295 models
+> lighting full
+> lighting simple
+> color #231 #b2ffb2ff models
+> color #231 #b2ffb29d models
+> color #231 #b2ffb2d4 models
+> color #231 #b2ffb2af models
+> color #231 #b2ffb2ff models
+> lighting soft
+> lighting full
+> lighting soft
+> hide #237 models
+> set bgColor black
+> set bgColor transparent
+> hide #!231 models
+> show #!230 models
+> show #!231 models
+> hide #!231 models
+> show #!231 models
+> hide #!231 models
+> show #!226 models
+> hide #!230 models
+> show #!231 models
+> hide #!226 models
+> hide #!231 models
+> show #!211 models
+> show #!232 models
+> hide #!232 models
+> hide #!211 models
+> show #!235 models
+> hide #!235 models
+> show #!233 models
+> show #!232 models
+> show #!236 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!232 models
+> show #!232 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> show #!236 models
+> hide #!232 models
+> hide #!233 models
+> show #!233 models
+> hide #!236 models
+> select add #233
+models selected
+> cofr sel
+> select subtract #233
+Nothing selected
+> show #!236 models
+> show #!232 models
+> hide #!232 models
+> show #!234 models
+> hide #!234 models
+> show #!232 models
+> show #!231 models
+> hide #!231 models
+> show #!230 models
+> hide #!230 models
+> show #!231 models
+> hide #!231 models
+> hide #!236 models
+> show #!236 models
+> show #!234 models
+> hide #!234 models
+> hide #!236 models
+> color #233 #b2b2b2b0 models
+> hide #!233 models
+> hide #!232 models
+> show #!191 models
+> hide #!191 models
+> show #!211 models
+> hide #!211 models
+> show #!231 models
+> show #!177 models
+> hide #!177 models
+> show #237 models
+> hide #237 models
+> hide #!231 models
+> show #!233 models
+> color #233 #b2b2b2ff models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> open /Volumes/lab-
+> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Refine3D/job814/run_class001.mrc
+Opened run_class001.mrc as #244, grid size 588,588,588, pixel 0.95, shown at
+level 0.00486, step 4, values float32
+> close #244
+> hide #!236 models
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> lighting shadows true intensity 0.5
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> lighting soft
+> lighting full
+> lighting soft
+> lighting full
+> show #!236 models
+> lighting soft
+> lighting simple
+> lighting full
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> hide #!236 models
+> show #!236 models
+> hide #!233 models
+> show #!233 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
+\u2014\u2014\u2014 End of log from Wed Jul 24 16:21:27 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> hide #!236 models
+> hide #!233 models
+> show #!98 models
+> lighting simple
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!100 models
+> hide #!100 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> hide #!99 models
+> show #!99 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> hide #!99 models
+> show #!32 models
+> show #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> hide #!34 models
+> show #!129 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!129 models
+> hide #!130 models
+> show #!74 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!74 models
+> show #!75 models
+> hide #!75 models
+> hide #!74 models
+> show #!110 models
+> show #!111 models
+> hide #!110 models
+> show #!110 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> hide #!110 models
+> show #!122 models
+> show #!129 models
+> hide #!122 models
+> show #!122 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!122 models
+> show #!122 models
+> hide #!129 models
+> show #!123 models
+> hide #!122 models
+> hide #!123 models
+> show #!123 models
+> show #!124 models
+> hide #!124 models
+> show #!122 models
+> hide #!122 models
+> show #!130 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!130 models
+> hide #!123 models
+> show #!123 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!123 models
+> show #!123 models
+> hide #!110 models
+> show #!110 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!123 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!34 models
+> show #!32 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!112 models
+> hide #!112 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!110 models
+> show #!110 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!110 models
+> hide #!111 models
+> hide #!32 models
+> hide #!34 models
+> show #!123 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!129 models
+> hide #!129 models
+> show #!130 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!75 models
+> show #!75 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> show #!122 models
+> hide #!122 models
+> show #!122 models
+> hide #!122 models
+> show #!122 models
+> hide #!122 models
+> show #!122 models
+> hide #!122 models
+> show #!122 models
+> hide #!122 models
+> show #!122 models
+> hide #!122 models
+> show #!122 models
+> hide #!122 models
+> show #!122 models
+> hide #!123 models
+> show #!123 models
+> hide #!122 models
+> hide #!74 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!123 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> hide #!130 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J368_007_volume_map.mrc
+Opened cryosparc_P17_J368_007_volume_map.mrc as #244, grid size 294,294,294,
+pixel 1.9, shown at level 0.37, step 2, values float32
+> lighting simple
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #244 step 1
+> volume #244 level 0.344
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J685_007_volume_map.mrc
+Opened cryosparc_P17_J685_007_volume_map.mrc as #245, grid size 294,294,294,
+pixel 1.9, shown at level 0.361, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J690_006_volume_map.mrc
+Opened cryosparc_P17_J690_006_volume_map.mrc as #246, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 2, values float32
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #245 step 1
+> volume #245 level 0.3413
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #246 step 1
+> show #!245 models
+> hide #!245 models
+> show #!245 models
+> select add #245
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #245,0.24392,0.87788,0.4121,-128.61,0.92708,-0.086349,-0.36479,125.94,-0.28466,0.47103,-0.83493,401.32
+> view matrix models
+> #245,0.64106,-0.054068,-0.76558,302.83,0.031113,-0.99486,0.096313,510.77,-0.76686,-0.085561,-0.63609,638.94
+> view matrix models
+> #245,0.9162,-0.026949,-0.39982,128.81,0.14241,-0.91071,0.38773,385.27,-0.37456,-0.41217,-0.83055,665.84
+> view matrix models
+> #245,0.91682,-0.37423,-0.13924,159.29,-0.35009,-0.92108,0.17043,579.11,-0.19203,-0.1075,-0.97548,567.39
+> ui mousemode right "translate selected models"
+> view matrix models
+> #245,0.91682,-0.37423,-0.13924,163.24,-0.35009,-0.92108,0.17043,567.35,-0.19203,-0.1075,-0.97548,639.7
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #245,0.98493,-0.05987,-0.16227,64.254,-0.032068,-0.98512,0.16883,496.24,-0.16996,-0.16108,-0.9722,647.31
+> ui mousemode right "translate selected models"
+> view matrix models
+> #245,0.98493,-0.05987,-0.16227,72.788,-0.032068,-0.98512,0.16883,503.81,-0.16996,-0.16108,-0.9722,638.94
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #245,0.96022,0.026881,-0.27794,84.445,0.064645,-0.98972,0.12761,488.12,-0.27165,-0.1405,-0.95208,656.85
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #245,0.96845,0.06341,-0.24101,63.142,0.079191,-0.99527,0.056358,503.03,-0.23629,-0.073665,-0.96889,632.88
+> ui mousemode right "translate selected models"
+> view matrix models
+> #245,0.96845,0.06341,-0.24101,55.646,0.079191,-0.99527,0.056358,515.43,-0.23629,-0.073665,-0.96889,633.64
+> select subtract #245
+Nothing selected
+> hide #!245 models
+> show #!246 models
+> select add #246
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #246,-0.94249,-0.14738,0.29999,492.53,0.01794,-0.91854,-0.39491,640.24,0.33376,-0.36682,0.86836,47.073
+> view matrix models
+> #246,-0.98683,-0.012271,0.16129,511.21,-0.0067172,-0.99315,-0.11666,581.14,0.16162,-0.11621,0.97999,-7.5123
+> view matrix models
+> #246,-0.99462,-0.028395,0.099663,536.91,0.012491,-0.98757,-0.15671,586.65,0.10287,-0.15462,0.9826,18.639
+> select subtract #246
+Nothing selected
+> select add #246
+models selected
+> select subtract #246
+Nothing selected
+> show #!245 models
+> ui tool show "Fit in Map"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+[Repeated 1 time(s)]
+> fitmap #245 inMap #244
+Fit map cryosparc_P17_J685_007_volume_map.mrc in map
+cryosparc_P17_J368_007_volume_map.mrc using 271515 points
+correlation = 0.9949, correlation about mean = 0.9457, overlap = 9.464e+04
+steps = 188, shift = 2.56, angle = 15.2 degrees
+Position of cryosparc_P17_J685_007_volume_map.mrc (#245) relative to
+cryosparc_P17_J368_007_volume_map.mrc (#244) coordinates:
+Matrix rotation and translation
+.99981329 -0.01923951 0.00179460 4.69427957
+-0.01931352 -0.99208863 0.12404490 525.91853508
+-0.00060616 -0.12405640 -0.99227498 588.72614471
+Axis -0.99995314 0.00967608 -0.00029828
+Axis point 0.00000000 281.31245766 277.98752927
+Rotation angle (degrees) 172.87372921
+Shift along axis 0.21916772
+> fitmap #246 inMap #244
+Fit map cryosparc_P17_J690_006_volume_map.mrc in map
+cryosparc_P17_J368_007_volume_map.mrc using 254434 points
+correlation = 0.9952, correlation about mean = 0.9446, overlap = 9.256e+04
+steps = 120, shift = 8.54, angle = 6.45 degrees
+Position of cryosparc_P17_J690_006_volume_map.mrc (#246) relative to
+cryosparc_P17_J368_007_volume_map.mrc (#244) coordinates:
+Matrix rotation and translation
+-0.99997157 0.00691924 -0.00299642 557.81739805
+-0.00648161 -0.99184550 -0.12728119 593.36152310
+-0.00385267 -0.12725815 0.99186215 38.74337635
+Axis 0.00171577 0.06376541 -0.99796344
+Axis point 279.94000643 296.98029450 0.00000000
+Rotation angle (degrees) 179.61530751
+Shift along axis 0.12855455
+> hide #!246 models
+> hide #!244 models
+> show #!246 models
+> ui mousemode right zoom
+> lighting soft
+> hide #!245 models
+> show #!245 models
+> hide #!246 models
+> show #!246 models
+> hide #!246 models
+> show #!246 models
+> hide #!246 models
+> show #!246 models
+> hide #!245 models
+> show #!245 models
+> hide #!246 models
+> hide #!245 models
+> show #!244 models
+> show #!246 models
+> hide #!246 models
+> show #!246 models
+> hide #!244 models
+> show #!244 models
+> hide #!244 models
+> show #!244 models
+> volume #244 level 0.36
+> hide #!246 models
+> show #!246 models
+> hide #!246 models
+> show #!246 models
+> hide #!244 models
+> show #!244 models
+> hide #!244 models
+> show #!244 models
+> hide #!246 models
+> show #!246 models
+> hide #!244 models
+> show #!245 models
+> show #!244 models
+> hide #!246 models
+> hide #!245 models
+> show #!245 models
+> volume #245 level 0.36
+> hide #!244 models
+> show #!246 models
+> hide #!246 models
+> show #!246 models
+> hide #!245 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J697_006_volume_map.mrc
+Opened cryosparc_P17_J697_006_volume_map.mrc as #247, grid size 294,294,294,
+pixel 1.9, shown at level 0.358, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J712_007_volume_map.mrc
+Opened cryosparc_P17_J712_007_volume_map.mrc as #248, grid size 294,294,294,
+pixel 1.9, shown at level 0.349, step 2, values float32
+> hide #!246 models
+> show #!246 models
+> hide #!246 models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #247 step 1
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #248 step 1
+> volume #247 level 0.36
+> volume #248 level 0.36
+> close #248
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J362_007_volume_map.mrc
+Opened cryosparc_P17_J362_007_volume_map.mrc as #248, grid size 294,294,294,
+pixel 1.9, shown at level 0.368, step 2, values float32
+> hide #!247 models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #248 step 1
+> volume #248 level 0.36
+> show #!244 models
+> hide #!248 models
+> show #!248 models
+> hide #!244 models
+> show #!244 models
+> hide #!248 models
+> show #!248 models
+> hide #!244 models
+> hide #!248 models
+> show #!248 models
+> show #!246 models
+> show #!247 models
+> hide #!247 models
+> hide #!248 models
+> show #!248 models
+> hide #!248 models
+> show #!248 models
+> hide #!246 models
+> show #!246 models
+> hide #!248 models
+> hide #!246 models
+> show #!98 models
+> show #!110 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> show #!34 models
+> hide #!32 models
+> hide #!98 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!110 models
+> show #!111 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> show #!219 models
+> show #!220 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> hide #!34 models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #219 step 1
+> volume #220 level 0.35
+> volume #219 level 0.35
+> volume #219 step 2
+> volume #219 step 1
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #220 step 2
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1103_006_volume_map.mrc
+Opened cryosparc_P17_J1103_006_volume_map.mrc as #249, grid size 294,294,294,
+pixel 1.9, shown at level 0.358, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1105_008_volume_map.mrc
+Opened cryosparc_P17_J1105_008_volume_map.mrc as #250, grid size 294,294,294,
+pixel 1.9, shown at level 0.362, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1106_006_volume_map.mrc
+Opened cryosparc_P17_J1106_006_volume_map.mrc as #251, grid size 294,294,294,
+pixel 1.9, shown at level 0.357, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1107_006_volume_map.mrc
+Opened cryosparc_P17_J1107_006_volume_map.mrc as #252, grid size 294,294,294,
+pixel 1.9, shown at level 0.356, step 2, values float32
+> hide #!219 models
+> hide #!220 models
+> hide #!249 models
+> hide #!250 models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #251 step 1
+> volume #251 level 0.3333
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #252 step 1
+> volume #252 level 0.33
+> volume #252 level 0.35
+> volume #252 level 0.34
+> hide #!252 models
+> show #!32 models
+> show #!33 models
+> hide #!33 models
+> show #!33 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!33 models
+> show #!33 models
+> hide #!33 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!34 models
+> show #!34 models
+> hide #!32 models
+> hide #!34 models
+> show #!98 models
+> show #!99 models
+> hide #!99 models
+> hide #!98 models
+> show #!99 models
+> show #!98 models
+> hide #!99 models
+> hide #!98 models
+> show #!99 models
+> hide #!99 models
+> show #!110 models
+> show #!111 models
+> hide #!110 models
+> show #!110 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> hide #!110 models
+> show #!246 models
+> hide #!246 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
+\u2014\u2014\u2014 End of log from Tue Jul 30 11:34:25 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> show #!232 models
+> hide #!232 models
+> show #!234 models
+> show #!236 models
+> lighting simple
+> close #1-18
+> close #22-27,32-75
+> close #98-135
+> close #85-90
+> show #!244 models
+> hide #!244 models
+> close #244-252
+> show #!19 models
+> hide #!19 models
+> open 8XGC fromDatabase pdb format mmcif
+xgc title:
+Structure of yeast replisome associated with FACT and histone hexamer,
+Composite map [more info...]
+Chain information for 8xgc #1
+---
+Chain | Description | UniProt
+| DNA replication licensing factor MCM2 | A0A6A5Q1S9_YEASX 1-868
+| DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
+| DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
+| Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
+| DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
+| DNA replication licensing factor MCM7 | A0A8H4BTB2_YEASX 1-845
+| DNA polymerase epsilon catalytic subunit A | DPOE_YEAST 1-2222
+| DNA polymerase epsilon subunit B | DPB2_YEAST 1-689
+A | DNA replication complex GINS protein PSF1 | PSF1_YEAST 1-208
+B | DNA replication complex GINS protein PSF2 |
+C | DNA replication complex GINS protein PSF3 | PSF3_YEAST 1-194
+D | DNA replication complex GINS protein SLD5 | SLD5_YEAST 1-294
+E | Cell division control protein 45 | CDC45_YEAST 1-650
+F G H | DNA polymerase alpha-binding protein | CTF4_YEAST 1-927
+I | Topoisomerase 1-associated factor 1 | TOF1_YEAST 1-1238
+J | Chromosome segregation in meiosis protein 3 | CSM3_YEAST 1-317
+K | Mediator of replication checkpoint protein 1 | MRC1_YEAST 1-1096
+L | FACT complex subunit SPT16 | SPT16_YEAST 1-1035
+M | FACT complex subunit POB3 | POB3_YEAST 1-552
+N R | Histone H3 | A0A6A5Q536_YEASX 1-136
+O S | Histone H4 | H4_YEAST 1-103
+P | Histone H2A.1 | H2A1_YEAST 1-132
+Q | Histone H2B.2 | H2B2_YEAST 1-131
+X | DNA (51-MER) |
+Y | DNA (39-MER) |
+Non-standard residues in 8xgc #1
+---
+ADP \u2014 adenosine-5'-diphosphate
+ZN \u2014 zinc ion
+> select add #1
+atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
+> hide (#!1 & sel) target a
+> cartoon (#!1 & sel)
+> cartoon style (#!1 & sel) modeHelix tube sides 20
+> select clear
+> select add #1
+atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
+> ui mousemode right "translate selected models"
+> view matrix models #1,1,0,0,47.645,0,1,0,-186.91,0,0,1,-225.38
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #1,0.58597,0.26748,0.76491,-77.764,-0.68071,0.6746,0.28556,-31.019,-0.43963,-0.68802,0.57737,101.42
+> view matrix models
+> #1,-0.63049,-0.77581,0.02448,555.31,-0.40378,0.30088,-0.86396,224.99,0.66291,-0.5546,-0.50296,59.311
+> view matrix models
+> #1,-0.60522,-0.79563,-0.026037,564.5,-0.4515,0.37002,-0.81194,209.77,0.65563,-0.47965,-0.58317,61.313
+> view matrix models
+> #1,-0.51594,-0.8087,-0.28251,600.78,-0.65671,0.58517,-0.47573,138.81,0.55003,-0.059923,-0.83299,45.531
+> view matrix models
+> #1,-0.75431,-0.62553,0.19933,513.87,-0.20404,-0.065216,-0.97679,283.54,0.62401,-0.77747,-0.078442,28.164
+> view matrix models
+> #1,0.75405,0.27605,-0.59599,163.26,0.6559,-0.26853,0.70547,-200.8,0.034703,-0.92287,-0.38355,247.17
+> view matrix models
+> #1,0.73033,0.35167,-0.58562,150.07,0.68309,-0.37214,0.62842,-168.74,0.0030683,-0.85898,-0.51201,266.6
+> view matrix models
+> #1,0.72602,0.36576,-0.58233,147.32,0.68766,-0.39043,0.61212,-162.48,-0.0034657,-0.84486,-0.53498,269.69
+> select subtract #1
+Nothing selected
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> select add #177
+atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
+> ui mousemode right "translate selected models"
+> view matrix models
+> #177,0.46578,-0.098371,0.87942,92.221,0.51629,0.83733,-0.17979,-43.763,-0.71868,0.53777,0.4408,171.47
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #177,-0.49891,-0.69823,-0.51339,651.92,-0.83168,0.55231,0.057061,237.03,0.24371,0.45544,-0.85626,230.01
+> view matrix models
+> #177,0.26698,-0.55614,-0.78704,521.35,-0.5875,0.55345,-0.59037,305.23,0.76392,0.62,-0.17897,-27.896
+> ui mousemode right "translate selected models"
+> view matrix models
+> #177,0.26698,-0.55614,-0.78704,529.97,-0.5875,0.55345,-0.59037,261.16,0.76392,0.62,-0.17897,-91.066
+> view matrix models
+> #177,0.26698,-0.55614,-0.78704,447.11,-0.5875,0.55345,-0.59037,192.81,0.76392,0.62,-0.17897,-38.287
+> select subtract #177
+Nothing selected
+> ui tool show "Fit in Map"
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> fitmap #177 inMap #236
+Fit molecule 6skl (#177) to map cryosparc_P17_J544_007_volume_map_zflip.mrc
+(#236) using 118220 atoms
+average map value = 0.2679, steps = 436
+shifted from previous position = 21.5
+rotated from previous position = 40.5 degrees
+atoms outside contour = 24734, contour level = 0.17324
+Position of 6skl (#177) relative to
+cryosparc_P17_J544_007_volume_map_zflip.mrc (#236) coordinates:
+Matrix rotation and translation
+-0.51563097 -0.12952906 -0.84696336 558.27691744
+-0.84526058 -0.08486257 0.52757265 364.76426350
+-0.14021148 0.98793753 -0.06572804 118.82779302
+Axis 0.41616323 -0.63889353 -0.64701099
+Axis point 390.84775709 -13.99098898 0.00000000
+Rotation angle (degrees) 146.41962992
+Shift along axis -77.59409021
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!234 models
+> show #!234 models
+> show #!232 models
+> hide #!234 models
+> show #!233 models
+> hide #!236 models
+> ui mousemode right zoom
+> ui tool show Matchmaker
+> matchmaker #1/E to #177/E pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain E (#177) with 8xgc, chain E (#1), sequence alignment
+score = 3091.5
+RMSD between 562 pruned atom pairs is 0.577 angstroms; (across all 562 pairs:
+.577)
+> hide #!233 models
+> hide #!232 models
+> select add #177
+atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
+> cartoon style (#!177 & sel) modeHelix tube sides 20
+> select subtract #177
+Nothing selected
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> matchmaker #!1 to #177
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain X (#177) with 8xgc, chain I (#1), sequence alignment
+score = 5322.6
+RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
+.839)
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> matchmaker #1/I to #177/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain X (#177) with 8xgc, chain I (#1), sequence alignment
+score = 5322.6
+RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
+.839)
+> hide #!177 models
+> show #!177 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #237 models
+> hide #237 models
+> show #243 models
+> hide #243 models
+> show #243 models
+> hide #243 models
+> show #237 models
+> show #!234 models
+> hide #!234 models
+> show #243 models
+> hide #243 models
+> show #243 models
+> hide #243 models
+> combine #237
+> hide #237 models
+> show #243 models
+> hide #243 models
+> show #243 models
+> hide #243 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> hide #2 models
+> show #2 models
+> ui tool show Matchmaker
+> hide #2 models
+> close #2
+> open /Users/cvetkom/Documents/AlphaFold/yCsm3_Tof1_Oliver/yCsm3Tof1_AF.pdb
+Chain information for yCsm3Tof1_AF.pdb #2
+---
+Chain | Description
+A | No description available
+B | No description available
+> select add #2
+atoms, 25142 bonds, 1555 residues, 1 model selected
+> view sel
+> select clear
+> matchmaker #2/A to #177/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain X (#177) with yCsm3Tof1_AF.pdb, chain A (#2), sequence
+alignment score = 5355
+RMSD between 517 pruned atom pairs is 1.040 angstroms; (across all 665 pairs:
+.956)
+> hide #2 models
+> show #2 models
+> hide #2 models
+> show #2 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #2/A
+Alignment identifier is 2/A
+> select #2/A:612
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #2/A:612-643
+atoms, 528 bonds, 32 residues, 1 model selected
+> select #2/A:612-613
+atoms, 34 bonds, 2 residues, 1 model selected
+> select #2/A:613-657
+atoms, 731 bonds, 45 residues, 1 model selected
+> color sel blue
+> color sel orange red
+> select clear
+> hide #2 models
+> show #2 models
+> hide #2 models
+> show #2 models
+> show #!236 models
+> hide #!236 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc
+Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc as #3, grid size
+,440,440, pixel 0.95, shown at level 0.0283, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1206_003_volume_map_EMReady.mrc
+Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc as #4, grid size
+,440,440, pixel 0.95, shown at level 0.00374, step 2, values float32
+> open /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1207_map_sharp.mrc
+Opened cryosparc_P17_J1207_map_sharp.mrc as #5, grid size 440,440,440, pixel
+.95, shown at level 2.63e-06, step 2, values float32
+> open /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1210_map_sharp.mrc
+Opened cryosparc_P17_J1210_map_sharp.mrc as #6, grid size 440,440,440, pixel
+.95, shown at level 0.000291, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1268_002_volume_map_sharp.mrc
+Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #7, grid size
+,440,440, pixel 0.95, shown at level 0.0259, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1163_006_volume_map.mrc
+Opened cryosparc_P17_J1163_006_volume_map.mrc as #8, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 4, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J864_007_volume_map_zflip.mrc
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #9, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 4, values float32
+> hide #!9 models
+> hide #!8 models
+> hide #!7 models
+> hide #!6 models
+> hide #!5 models
+> hide #!4 models
+> hide #!3 models
+> hide #2 models
+> show #!236 models
+> show #!9 models
+> volume #9 step 1
+> select add #9
+models selected
+> ui mousemode right "translate selected models"
+> view matrix models #9,1,0,0,44.079,0,1,0,-129.91,0,0,1,33.561
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #9,-0.89241,-0.2853,-0.34957,745.33,-0.22047,0.95166,-0.21387,0.58537,0.39369,-0.11379,-0.91217,447.06
+> view matrix models
+> #9,-0.86115,-0.40726,-0.30424,765.4,-0.37668,0.9131,-0.15612,41.487,0.34138,-0.019841,-0.93972,437.48
+> ui mousemode right "translate selected models"
+> view matrix models
+> #9,-0.86115,-0.40726,-0.30424,699.37,-0.37668,0.9131,-0.15612,-44.304,0.34138,-0.019841,-0.93972,339.64
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #9,-0.93636,-0.11772,-0.33072,631.45,-0.22073,0.93,0.2939,-206.54,0.27297,0.34819,-0.8968,226.48
+> ui mousemode right zoom
+> fitmap #9 inMap #236
+Fit map cryosparc_P17_J864_007_volume_map_zflip.mrc in map
+cryosparc_P17_J544_007_volume_map_zflip.mrc using 2028136 points
+correlation = 0.9937, correlation about mean = 0.9426, overlap = 1.458e+05
+steps = 468, shift = 23.6, angle = 33.5 degrees
+Position of cryosparc_P17_J864_007_volume_map_zflip.mrc (#9) relative to
+cryosparc_P17_J544_007_volume_map_zflip.mrc (#236) coordinates:
+Matrix rotation and translation
+-0.96823974 -0.24332681 -0.05747924 633.07873275
+.10233189 -0.59543288 0.79686125 204.91238326
+-0.22812274 0.76567078 0.60142188 -52.82098481
+Axis -0.08064861 0.44122957 0.89376298
+Axis point 302.77781545 150.02897929 0.00000000
+Rotation angle (degrees) 168.85032375
+Shift along axis -7.85295761
+> select subtract #9
+Nothing selected
+> show #!8 models
+> volume #8 step 1
+> select add #8
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #8,0.83981,0.16349,-0.51768,159.04,-0.33783,0.90383,-0.26259,201.97,0.42496,0.39542,0.81428,-171.03
+> view matrix models
+> #8,-0.088093,0.71527,-0.69328,321.17,0.1227,0.69847,0.70504,-168.1,0.98853,-0.022959,-0.1493,82.529
+> view matrix models
+> #8,0.18202,-0.63889,-0.74746,635.26,0.31514,-0.68216,0.65981,172.32,-0.93143,-0.35565,0.077172,642.94
+> ui mousemode right "translate selected models"
+> view matrix models
+> #8,0.18202,-0.63889,-0.74746,569.25,0.31514,-0.68216,0.65981,-13.259,-0.93143,-0.35565,0.077172,525.18
+> view matrix models
+> #8,0.18202,-0.63889,-0.74746,562.71,0.31514,-0.68216,0.65981,-14.599,-0.93143,-0.35565,0.077172,487.95
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #8,0.49045,-0.55087,-0.67528,429.78,0.60915,-0.33743,0.71769,-209.84,-0.62321,-0.76334,0.17007,485.31
+> ui mousemode right "translate selected models"
+> view matrix models
+> #8,0.49045,-0.55087,-0.67528,444.24,0.60915,-0.33743,0.71769,-178.89,-0.62321,-0.76334,0.17007,497.07
+> fitmap #8 inMap #236
+Fit map cryosparc_P17_J1163_006_volume_map.mrc in map
+cryosparc_P17_J544_007_volume_map_zflip.mrc using 2031120 points
+correlation = 0.9907, correlation about mean = 0.9161, overlap = 1.477e+05
+steps = 368, shift = 21.9, angle = 21.5 degrees
+Position of cryosparc_P17_J1163_006_volume_map.mrc (#8) relative to
+cryosparc_P17_J544_007_volume_map_zflip.mrc (#236) coordinates:
+Matrix rotation and translation
+.99949009 -0.03184645 0.00231562 7.34723952
+.03147411 0.99482700 0.09658474 -35.10247418
+-0.00537952 -0.09646261 0.99532207 32.64947374
+Axis -0.94951030 0.03784884 0.31144447
+Axis point 0.00000000 313.97495420 380.98360453
+Rotation angle (degrees) 5.83455364
+Shift along axis 1.86363064
+> select add #8
+models selected
+> select subtract #8
+Nothing selected
+> lighting soft
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> color #8 silver models
+> hide #!8 models
+> show #!9 models
+> hide #!9 models
+> show #!8 models
+> hide #!8 models
+> show #!9 models
+> hide #!9 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J959_008_volume_map_zflip.mrc
+Opened cryosparc_P17_J959_008_volume_map_zflip.mrc as #10, grid size
+,588,588, pixel 0.95, shown at level 0.148, step 4, values float32
+> select add #10
+models selected
+> view matrix models #10,1,0,0,23.505,0,1,0,-15.929,0,0,1,-23.739
+> lighting simple
+> view matrix models #10,1,0,0,124.8,0,1,0,-99.812,0,0,1,-122.71
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #10,-0.42765,0.3857,-0.81752,672.45,0.75258,-0.34906,-0.55837,194.61,-0.50073,-0.85404,-0.141,572.88
+> view matrix models
+> #10,-0.5836,0.78463,0.2092,308.37,-0.51615,-0.15955,-0.84151,586.63,-0.62689,-0.59908,0.4981,352.72
+> view matrix models
+> #10,-0.66506,0.6951,0.273,334.38,-0.54368,-0.20005,-0.8151,596.53,-0.51196,-0.69052,0.51096,339.61
+> view matrix models
+> #10,-0.87025,-0.14082,0.47205,540.96,-0.24214,-0.71221,-0.65888,593.45,0.42898,-0.68769,0.58571,53.595
+> view matrix models
+> #10,-0.51532,-0.60142,0.61052,515.4,0.36144,-0.79846,-0.48148,393.16,0.77704,-0.027449,0.62885,-221.63
+> view matrix models
+> #10,-0.57269,-0.31806,0.75556,417.1,0.29571,-0.93976,-0.17146,353.87,0.76458,0.12523,0.63225,-257.33
+> ui mousemode right "translate selected models"
+> view matrix models
+> #10,-0.57269,-0.31806,0.75556,316.03,0.29571,-0.93976,-0.17146,301.69,0.76458,0.12523,0.63225,-291.73
+> view matrix models
+> #10,-0.57269,-0.31806,0.75556,307.58,0.29571,-0.93976,-0.17146,309.28,0.76458,0.12523,0.63225,-267.22
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #10,-0.69988,-0.20741,0.68348,337.07,0.084924,-0.97429,-0.2087,387.97,0.70919,-0.088019,0.6995,-218.61
+> ui mousemode right "translate selected models"
+> view matrix models
+> #10,-0.69988,-0.20741,0.68348,322.79,0.084924,-0.97429,-0.2087,374.73,0.70919,-0.088019,0.6995,-205.24
+> volume #10 step 1
+> fitmap #10 inMap #236
+Fit map cryosparc_P17_J959_008_volume_map_zflip.mrc in map
+cryosparc_P17_J544_007_volume_map_zflip.mrc using 2028921 points
+correlation = 0.9436, correlation about mean = 0.7528, overlap = 1.329e+05
+steps = 224, shift = 12.9, angle = 13.2 degrees
+Position of cryosparc_P17_J959_008_volume_map_zflip.mrc (#10) relative to
+cryosparc_P17_J544_007_volume_map_zflip.mrc (#236) coordinates:
+Matrix rotation and translation
+-0.96431898 -0.25440259 0.07326822 606.33395084
+-0.22036646 0.61794867 -0.75470396 377.39307444
+.14672264 -0.74392121 -0.65196143 620.81486733
+Axis 0.13202542 -0.89938569 0.41674293
+Axis point 323.81378637 0.00000000 404.72898510
+Rotation angle (degrees) 177.65962530
+Shift along axis -0.65022839
+> select add #10
+models selected
+> select subtract #10
+Nothing selected
+> color #10 #945200ff models
+> color #10 #941100ff models
+> color #10 #945200ff models
+> color #10 #ff9300ff models
+> color #10 #ff2600ff models
+> color #10 #ff7e79ff models
+> color #10 #fffc79ff models
+> color #10 #d4fb79ff models
+> color #10 #fffc79ff models
+> color #10 #d4fb79ff models
+> volume #10 level 0.1697
+> volume #10 level 0.1731
+> ui mousemode right zoom
+> lighting soft
+> hide #!10 models
+> show #!10 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job802_run_class001.mrc
+Opened Ref3D_job802_run_class001.mrc as #11, grid size 588,588,588, pixel
+.95, shown at level 0.00416, step 4, values float32
+> lighting simple
+> select add #11
+models selected
+> ui mousemode right "translate selected models"
+> view matrix models #11,1,0,0,-51.74,0,1,0,-84.314,0,0,1,-73.541
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #11,0.0036933,-0.45538,0.89029,72.314,-0.79632,0.53717,0.27807,170.48,-0.60486,-0.70998,-0.36065,684.31
+> view matrix models
+> #11,-0.90602,-0.026747,0.4224,361.01,-0.42311,0.032534,-0.90549,549.65,0.010478,-0.99911,-0.040793,487.81
+> view matrix models
+> #11,-0.90163,0.38295,-0.20102,445.5,0.0063584,-0.453,-0.89149,546.69,-0.43245,-0.80508,0.406,428.35
+> view matrix models
+> #11,-0.68901,-0.48447,0.53903,379.58,0.2377,-0.85366,-0.46343,452.94,0.68467,-0.19118,0.70333,-127.8
+> view matrix models
+> #11,-0.70406,-0.10147,0.70285,238.48,-0.37448,-0.78789,-0.48887,615.54,0.60338,-0.60739,0.51673,55.46
+> view matrix models
+> #11,-0.76623,0.05272,0.6404,236.16,-0.49162,-0.68984,-0.53144,636.65,0.41376,-0.72204,0.5545,125.83
+> ui mousemode right "translate selected models"
+> view matrix models
+> #11,-0.76623,0.05272,0.6404,261.62,-0.49162,-0.68984,-0.53144,557.66,0.41376,-0.72204,0.5545,116.13
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #11,-0.60221,0.45689,0.65467,110.25,-0.62773,-0.77766,-0.034707,467.75,0.49325,-0.43186,0.75511,-39.317
+> view matrix models
+> #11,-0.68577,0.26569,0.67759,174.57,-0.57475,-0.76886,-0.28021,524.85,0.44652,-0.58161,0.67996,33.93
+> volume #11 step 1
+> fitmap #11 inMap #236
+Fit map Ref3D_job802_run_class001.mrc in map
+cryosparc_P17_J544_007_volume_map_zflip.mrc using 2030281 points
+correlation = 0.9571, correlation about mean = 0.8205, overlap = 3535
+steps = 488, shift = 19.8, angle = 32.9 degrees
+Position of Ref3D_job802_run_class001.mrc (#11) relative to
+cryosparc_P17_J544_007_volume_map_zflip.mrc (#236) coordinates:
+Matrix rotation and translation
+-0.96450343 -0.25313673 0.07519943 605.61171904
+-0.21928378 0.60909585 -0.76217904 383.34466562
+.14713185 -0.75161431 -0.64298380 621.67767309
+Axis 0.13173116 -0.89692214 0.42211086
+Axis point 323.99781428 0.00000000 407.81801536
+Rotation angle (degrees) 177.70184669
+Shift along axis -1.63548244
+> hide #!10 models
+> select add #11
+models selected
+> select subtract #11
+Nothing selected
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> hide #!11 models
+> show #!7 models
+> hide #!7 models
+> show #!233 models
+> show #!3 models
+> volume #3 step 1
+> volume #3 level 0.2689
+> hide #!3 models
+> show #!3 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> fitmap #3 inMap #233
+Fit map cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc in map
+cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc using 171797 points
+correlation = 0.9986, correlation about mean = 0.9835, overlap = 1.873e+05
+steps = 64, shift = 2.32, angle = 0.05 degrees
+Position of cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) relative
+to cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc (#233) coordinates:
+Matrix rotation and translation
+.99999969 -0.00055856 -0.00055446 0.28221116
+.00055877 0.99999977 0.00037517 -0.20830704
+.00055425 -0.00037548 0.99999978 -2.35151229
+Axis -0.43044636 -0.63576954 0.64071291
+Axis point 2074.34448759 -648.53479123 0.00000000
+Rotation angle (degrees) 0.04995831
+Shift along axis -1.49568576
+> volume #3 level 0.25
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!234 models
+> hide #!236 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> show #!232 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> hide #!232 models
+> show #!232 models
+> show #!234 models
+> select add #232
+atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
+> select add #234
+atoms, 19000 bonds, 223 pseudobonds, 1946 residues, 5 models selected
+> view matrix models
+> #232,-0.019001,-0.99844,0.052579,192.68,-0.84729,0.043998,0.5293,242.41,-0.53078,-0.034493,-0.84681,167.29,#234,-0.045299,-0.99887,-0.014131,189.08,-0.79838,0.027697,0.60152,244.8,-0.60045,0.03853,-0.79874,172.18
+> ui mousemode right "translate selected models"
+> view matrix models
+> #232,-0.019001,-0.99844,0.052579,192.71,-0.84729,0.043998,0.5293,242.76,-0.53078,-0.034493,-0.84681,167.34,#234,-0.045299,-0.99887,-0.014131,189.11,-0.79838,0.027697,0.60152,245.15,-0.60045,0.03853,-0.79874,172.22
+> select subtract #234
+atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
+> select subtract #232
+Nothing selected
+> hide #!234 models
+> show #!234 models
+> hide #!232 models
+> hide #!234 models
+> volume flip #4,5,6
+Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip as #12, grid size
+,440,440, pixel 0.95, shown at step 1, values float32
+Opened cryosparc_P17_J1207_map_sharp.mrc z flip as #13, grid size 440,440,440,
+pixel 0.95, shown at step 1, values float32
+Opened cryosparc_P17_J1210_map_sharp.mrc z flip as #14, grid size 440,440,440,
+pixel 0.95, shown at step 1, values float32
+> hide #!13 models
+> volume #12 level 0.6868
+> hide #!14 models
+> volume #12 level 1.994
+> volume #12 level 2.112
+> hide #!12 models
+> show #!13 models
+> volume #13 level 0.04456
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!13 models
+> show #!14 models
+> volume #14 level 0.06454
+> volume #14 level 0.1669
+> hide #!14 models
+> show #!14 models
+> volume #14 level 0.2071
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> show #!7 models
+> volume #7 level 0.1489
+> volume #7 step 1
+> volume #7 level 0.2483
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> select add #7
+models selected
+> show #!3 models
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #7,0.95557,0.0046513,-0.29472,69.933,0.27535,0.34272,0.89818,-107.26,0.10519,-0.93943,0.32621,316.27
+> view matrix models
+> #7,0.91915,0.11688,-0.37617,70.997,0.39267,-0.1961,0.89853,-18.651,0.031252,-0.97359,-0.22614,454.39
+> view matrix models
+> #7,0.91426,0.13556,-0.38178,69.268,0.40482,-0.26848,0.87409,-0.87336,0.015992,-0.9537,-0.30034,468.92
+> view matrix models
+> #7,0.95579,-0.038803,-0.29149,78.32,0.26406,-0.32299,0.90882,32.378,-0.12941,-0.94561,-0.29846,496.89
+> view matrix models
+> #7,0.94972,0.029908,-0.31167,69.398,0.30564,-0.30453,0.90213,21.312,-0.067931,-0.95203,-0.29836,485.5
+> view matrix models
+> #7,0.9488,-0.094559,-0.30141,93.528,0.2555,-0.33137,0.90825,36.024,-0.18576,-0.93875,-0.29025,505.38
+> view matrix models
+> #7,0.95015,-0.094376,-0.29717,92.323,0.25152,-0.33129,0.90939,36.591,-0.18427,-0.9388,-0.29104,505.25
+> view matrix models
+> #7,0.95804,-0.094732,-0.27054,85.191,0.22599,-0.33099,0.91617,40.384,-0.17634,-0.93887,-0.29569,504.6
+> view matrix models
+> #7,0.9581,-0.19453,-0.21025,93.469,0.13432,-0.34319,0.92961,59.077,-0.25299,-0.9189,-0.30268,517.72
+> view matrix models
+> #7,0.95765,-0.21305,-0.19368,93.974,0.11202,-0.34399,0.93227,63.299,-0.26525,-0.91448,-0.30556,519.93
+> hide #!3 models
+> show #!3 models
+> view matrix models
+> #7,0.95696,-0.21706,-0.19263,94.734,0.10944,-0.34484,0.93226,64.012,-0.26878,-0.91322,-0.30625,520.54
+> view matrix models
+> #7,0.94815,-0.27392,-0.1612,101.89,0.14424,-0.081125,0.98621,-9.7554,-0.28322,-0.95833,-0.03741,476.68
+> view matrix models
+> #7,0.95414,-0.24037,-0.17843,97.229,0.16379,-0.079738,0.98327,-13.471,-0.25057,-0.9674,-0.036713,471.68
+> ui mousemode right "translate selected models"
+> view matrix models
+> #7,0.95414,-0.24037,-0.17843,96.447,0.16379,-0.079738,0.98327,-14.654,-0.25057,-0.9674,-0.036713,467.78
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #7,0.99024,-0.071411,-0.11966,41.263,0.11264,-0.095331,0.98905,-2.0232,-0.082036,-0.99288,-0.086357,448.67
+> view matrix models
+> #7,0.99499,-0.013505,-0.099097,23.84,0.096797,-0.11921,0.98814,6.4479,-0.025158,-0.99278,-0.1173,443.37
+> view matrix models
+> #7,0.996,0.01454,-0.088107,15.449,0.089245,-0.12802,0.98775,9.9368,0.0030827,-0.99167,-0.1288,439.71
+> view matrix models
+> #7,0.99258,0.11362,-0.043338,-13.986,0.055935,-0.11014,0.99234,12.115,0.10798,-0.9874,-0.11568,414.38
+> view matrix models
+> #7,0.99638,0.054238,-0.065393,2.2931,0.06993,-0.086471,0.9938,3.9549,0.048247,-0.99478,-0.089951,422.89
+> select subtract #7
+Nothing selected
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> fitmap #7 inMap #3
+Fit map cryosparc_P17_J1268_002_volume_map_sharp.mrc in map
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc using 184853 points
+correlation = 0.8964, correlation about mean = 0.4436, overlap = 2.415e+04
+steps = 140, shift = 3.54, angle = 8.85 degrees
+Position of cryosparc_P17_J1268_002_volume_map_sharp.mrc (#7) relative to
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) coordinates:
+Matrix rotation and translation
+.99817702 -0.04588002 0.03921297 3.35030958
+-0.04066443 -0.03114210 0.99868743 12.39857491
+-0.04459863 -0.99846141 -0.03295101 431.82063884
+Axis -0.99911720 0.04192858 0.00260921
+Axis point 0.00000000 215.36415158 209.87663468
+Rotation angle (degrees) 91.88869867
+Shift along axis -1.70078525
+> fitmap #7 inMap #3
+Fit map cryosparc_P17_J1268_002_volume_map_sharp.mrc in map
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc using 184853 points
+correlation = 0.8964, correlation about mean = 0.4436, overlap = 2.415e+04
+steps = 52, shift = 0.00236, angle = 0.00447 degrees
+Position of cryosparc_P17_J1268_002_volume_map_sharp.mrc (#7) relative to
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) coordinates:
+Matrix rotation and translation
+.99817611 -0.04587745 0.03923922 3.34208981
+-0.04068728 -0.03106753 0.99868882 12.38761501
+-0.04459824 -0.99846385 -0.03287749 431.80589646
+Axis -0.99911670 0.04194141 0.00259649
+Axis point 0.00000000 215.36687767 209.87412872
+Rotation angle (degrees) 91.88448023
+Shift along axis -1.69840331
+> hide #!7 models
+> show #!7 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> lighting soft
+> lighting full
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!3 models
+> volume #7 level 0.22
+> lighting simple
+> show #!5 models
+> hide #!5 models
+> show #!3 models
+> hide #!3 models
+> hide #!7 models
+> show #!3 models
+> close #144-146,148-154
+> show #!162 models
+> hide #!162 models
+> close #162-165
+> close #169-171
+> show #!12 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!13 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> volume #13 level 0.04
+> volume #13 level 0.02
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> hide #!13 models
+> show #!13 models
+> show #!14 models
+> hide #!13 models
+> volume #14 level 0.25
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!14 models
+> hide #!11 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> show #2 models
+> hide #2 models
+> show #!1 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #1/I
+Alignment identifier is 1/I
+> select #1/I:613
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/I:613-657
+atoms, 362 bonds, 45 residues, 1 model selected
+> color sel red
+> select add #1
+atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
+> select subtract #1
+Nothing selected
+> show #2 models
+> hide #!1 models
+> show #!1 models
+> hide #2 models
+> show #2 models
+> hide #!1 models
+> hide #2 models
+> show #2 models
+> hide #2 models
+> show #!19 models
+> hide #!19 models
+> close
+> #19-21,76-84,91-97,136-140,142-143,155-156,158-159,161,166-168,172-173,175-176
+> show #!178 models
+> hide #!178 models
+> show #!232 models
+> hide #!232 models
+> show #!234 models
+> hide #!234 models
+> show #!232 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!232 models
+> hide #!234 models
+> show #!233 models
+> hide #!233 models
+> close #180-231
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!1 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> color #9 #d6d6d6ff models
+> color #9 silver models
+> color #9 darkgrey models
+> color #9 #919191ff models
+> show #!8 models
+> hide #!9 models
+> show #!9 models
+> hide #!8 models
+> show #!8 models
+> hide #!9 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> show #2 models
+> hide #!8 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!8 models
+> show #!3 models
+> select add #8
+models selected
+> select subtract #8
+Nothing selected
+> select add #8
+models selected
+> ui tool show "Color Actions"
+> color sel light sea green
+> select subtract #8
+Nothing selected
+> hide #!8 models
+> show #!9 models
+> select add #9
+models selected
+> color sel steel blue
+> select subtract #9
+Nothing selected
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!9 models
+> hide #!3 models
+> show #!4 models
+> hide #!4 models
+> show #!12 models
+> hide #!12 models
+> show #!13 models
+> show #!14 models
+> hide #!13 models
+> show #!13 models
+> hide #!14 models
+> show #!12 models
+> hide #!12 models
+> show #!3 models
+> fitmap #13 inMap #3
+Fit map cryosparc_P17_J1207_map_sharp.mrc z flip in map
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc using 135754 points
+correlation = 0.8195, correlation about mean = 0.6657, overlap = 1.259e+04
+steps = 52, shift = 2.26, angle = 0.101 degrees
+Position of cryosparc_P17_J1207_map_sharp.mrc z flip (#13) relative to
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) coordinates:
+Matrix rotation and translation
+.99999956 -0.00066700 -0.00066264 0.29074301
+.00066701 0.99999978 0.00001245 -0.17783395
+.00066263 -0.00001289 0.99999978 -0.07194977
+Axis -0.01347599 -0.70471591 0.70936161
+Axis point 192.41646705 437.19131956 0.00000000
+Rotation angle (degrees) 0.05387447
+Shift along axis 0.07036596
+> hide #!13 models
+> show #!12 models
+> fitmap #12 inMap #3
+Fit map cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip in map
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc using 178682 points
+correlation = 0.9651, correlation about mean = 0.6584, overlap = 2.725e+05
+steps = 56, shift = 2.37, angle = 0.0731 degrees
+Position of cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip (#12)
+relative to cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3)
+coordinates:
+Matrix rotation and translation
+.99999939 0.00102607 0.00041428 -0.30090785
+-0.00102640 0.99999915 0.00080313 0.12472239
+-0.00041345 -0.00080355 0.99999959 0.19980920
+Axis -0.58749376 0.30266385 -0.75049695
+Axis point 102.26087289 256.35146195 0.00000000
+Rotation angle (degrees) 0.07834647
+Shift along axis 0.06457425
+> hide #!12 models
+> fitmap #14 inMap #3
+Fit map cryosparc_P17_J1210_map_sharp.mrc z flip in map
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc using 113255 points
+correlation = 0.9486, correlation about mean = 0.6387, overlap = 2.633e+04
+steps = 52, shift = 2.43, angle = 0.0525 degrees
+Position of cryosparc_P17_J1210_map_sharp.mrc z flip (#14) relative to
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) coordinates:
+Matrix rotation and translation
+.99999995 0.00019277 -0.00024648 0.02840578
+-0.00019280 0.99999997 -0.00012225 0.02141418
+.00024646 0.00012230 0.99999996 -0.18912634
+Axis 0.36395622 -0.73365042 -0.57384051
+Axis point 527.18097402 0.00000000 -37.18039835
+Rotation angle (degrees) 0.01924876
+Shift along axis 0.10315629
+> show #!14 models
+> hide #!14 models
+> show #!10 models
+> hide #!10 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!11 models
+> hide #!8 models
+> hide #!11 models
+> hide #2 models
+> hide #!3 models
+> show #!11 models
+> show #!7 models
+> combine #7
+No structures specified
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1268_002_volume_map_sharp.mrc
+Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #15, grid size
+,440,440, pixel 0.95, shown at level 0.0259, step 2, values float32
+> volume #15 step 1
+> volume #15 level 0.22
+> select add #15
+models selected
+> ui mousemode right "translate selected models"
+> view matrix models #15,1,0,0,100.39,0,1,0,-46.513,0,0,1,45.903
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #15,0.80976,-0.45265,0.37335,153.4,0.3286,0.877,0.35057,-163.14,-0.48611,-0.1612,0.8589,208.93
+> view matrix models
+> #15,0.48179,-0.6745,0.5594,227.28,0.3403,0.73229,0.58987,-186.41,-0.80751,-0.093832,0.58234,319.83
+> view matrix models
+> #15,0.11088,-0.79909,0.5909,322.74,0.17639,0.60095,0.77958,-165.65,-0.97805,0.017785,0.20759,411.17
+> ui mousemode right "translate selected models"
+> view matrix models
+> #15,0.11088,-0.79909,0.5909,326.79,0.17639,0.60095,0.77958,-133.13,-0.97805,0.017785,0.20759,331.85
+> view matrix models
+> #15,0.11088,-0.79909,0.5909,305.76,0.17639,0.60095,0.77958,-140.24,-0.97805,0.017785,0.20759,332.58
+> view matrix models
+> #15,0.11088,-0.79909,0.5909,312.36,0.17639,0.60095,0.77958,-53.435,-0.97805,0.017785,0.20759,338.76
+> view matrix models
+> #15,0.11088,-0.79909,0.5909,308.51,0.17639,0.60095,0.77958,-56.402,-0.97805,0.017785,0.20759,338.76
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #15,-0.024164,-0.79613,0.60464,332.95,0.20877,0.58746,0.78186,-60.832,-0.97767,0.14512,0.15201,324.44
+> view matrix models
+> #15,-0.11821,-0.78529,0.60774,349.54,0.18703,0.58347,0.7903,-57.299,-0.97522,0.20709,0.077898,326.9
+> view matrix models
+> #15,-0.105,-0.78677,0.60825,347,0.20205,0.58199,0.78769,-59.555,-0.97373,0.2056,0.097857,322.7
+> view matrix models
+> #15,-0.19293,-0.90299,-0.3839,597.45,0.097707,-0.40698,0.90819,138.04,-0.97633,0.13771,0.16675,322.58
+> view matrix models
+> #15,-0.14742,-0.90868,-0.3906,590.6,0.015659,-0.39701,0.91768,150.99,-0.98895,0.12916,0.072754,346.69
+> view matrix models
+> #15,-0.22245,-0.89505,-0.38653,602.49,0.048703,-0.40617,0.9125,147.11,-0.97373,0.18416,0.13394,319.48
+> view matrix models
+> #15,-0.22402,-0.95714,-0.18358,572.78,0.083751,-0.20657,0.97484,86.116,-0.97098,0.20301,0.12644,316.65
+> ui mousemode right "translate selected models"
+> view matrix models
+> #15,-0.22402,-0.95714,-0.18358,576.09,0.083751,-0.20657,0.97484,-0.31383,-0.97098,0.20301,0.12644,309.91
+> view matrix models
+> #15,-0.22402,-0.95714,-0.18358,576.03,0.083751,-0.20657,0.97484,0.10503,-0.97098,0.20301,0.12644,306.13
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #15,-0.2138,-0.95931,-0.18443,574.53,0.10809,-0.21087,0.97152,-3.3553,-0.97088,0.18777,0.14877,304.52
+> view matrix models
+> #15,-0.23097,-0.97294,-0.0055806,543.26,0.1557,-0.042623,0.98688,-50.688,-0.96042,0.22707,0.16133,291.71
+> ui mousemode right "translate selected models"
+> view matrix models
+> #15,-0.23097,-0.97294,-0.0055806,539.65,0.1557,-0.042623,0.98688,-54.918,-0.96042,0.22707,0.16133,290.53
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #15,-0.28101,-0.95968,0.0065516,544.75,0.21102,-0.055129,0.97593,-61.509,-0.93622,0.27563,0.21801,263.72
+> hide #!15 models
+> show #!15 models
+> select subtract #15
+Nothing selected
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!7 models
+> show #!7 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!7 models
+> show #!7 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> select add #15
+models selected
+> view matrix models
+> #15,-0.25657,-0.95952,-0.11618,565.46,0.1776,-0.16496,0.97018,-31.028,-0.95007,0.22828,0.21274,277.33
+> view matrix models
+> #15,-0.2471,-0.95598,-0.15824,571.63,0.16674,-0.20281,0.96492,-19.967,-0.95454,0.21204,0.20951,282.24
+> select subtract #15
+Nothing selected
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!3 models
+> hide #!11 models
+> show #!177 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> show #243 models
+> hide #243 models
+> close #240-243
+> show #!239 models
+> hide #!239 models
+> close #239
+> close #237-238
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+\u2014\u2014\u2014 End of log from Tue Sep 3 13:30:10 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> hide #!3 models
+> show #!3 models
+> show #!232 models
+> hide #!232 models
+> show #!1 models
+> hide #!177 models
+> hide #!3 models
+> hide #!15 models
+> show #!9 models
+> hide #!9 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> color #8 #20b2aa8f models
+> set bgColor white
+> color #8 #20b2aaa3 models
+> color #8 #20b2aaab models
+> color #8 #20b2aaae models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> color #8 #20b2aa8a models
+> show #!232 models
+> hide #!8 models
+> show #!8 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #1/L
+Alignment identifier is 1/L
+> select clear
+> select #1/L:905-996
+atoms, 638 bonds, 1 pseudobond, 88 residues, 2 models selected
+> hide #!8 models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> hide #!1 models
+> show #!1 models
+> show #!8 models
+> hide #!232 models
+> lighting soft
+> lighting full
+> lighting simple
+> hide #!1 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J535_003_volume_map_zflip.mrc
+Opened cryosparc_P17_J535_003_volume_map_zflip.mrc as #16, grid size
+,588,588, pixel 0.95, shown at level 0.0831, step 4, values float32
+> select add #8
+atoms, 638 bonds, 1 pseudobond, 88 residues, 6 models selected
+> cofr sel
+> select subtract #8
+atoms, 638 bonds, 1 pseudobond, 88 residues, 2 models selected
+> select add #8
+atoms, 638 bonds, 1 pseudobond, 88 residues, 6 models selected
+> view sel
+> select subtract #8
+atoms, 638 bonds, 1 pseudobond, 88 residues, 2 models selected
+> volume #16 step 1
+> volume #16 level 0.2325
+> select add #16
+atoms, 638 bonds, 1 pseudobond, 88 residues, 5 models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #1,-0.25096,-0.5068,-0.82472,635.54,0.24628,-0.85738,0.45193,125.51,-0.93614,-0.089699,0.33999,418.44,#16,0.38885,-0.060579,0.91931,48.211,-0.26865,0.94702,0.17604,66.153,-0.88126,-0.31542,0.35197,458.59
+> view matrix models
+> #1,-0.22215,-0.94943,-0.22187,455.62,0.42836,-0.29946,0.85254,-75.15,-0.87587,0.094354,0.47323,351.85,#16,-0.088966,0.51185,0.85446,2.4214,-0.38273,0.77443,-0.50376,264.06,-0.91957,-0.37184,0.127,524.01
+> view matrix models
+> #1,-0.38537,-0.9141,-0.12615,489.05,0.83574,-0.40371,0.37223,-86.716,-0.39118,0.038019,0.91953,35.134,#16,-0.26392,0.43198,0.8624,77.602,0.2312,0.89637,-0.37824,28.981,-0.93643,0.099556,-0.33645,444.31
+> view matrix models
+> #1,-0.1356,-0.57517,-0.80671,587.5,0.91613,-0.38283,0.11895,-42.958,-0.37725,-0.72292,0.57884,147.36,#16,0.44409,0.060297,0.89395,-3.9514,0.47456,0.83047,-0.29176,-31.753,-0.75999,0.5538,0.34018,134.84
+> view matrix models
+> #1,0.26845,-0.68107,-0.68124,397.8,0.89856,-0.077833,0.4319,-135.6,-0.34718,-0.72807,0.59108,132.33,#16,0.6063,0.40624,0.68364,-132.59,0.26507,0.70727,-0.65536,126.61,-0.74976,0.57856,0.32114,126.66
+> view matrix models
+> #1,0.38233,-0.62566,-0.67998,352.57,0.87609,0.011513,0.48201,-143.78,-0.29374,-0.78001,0.55254,124.4,#16,0.68689,0.42691,0.58816,-147.27,0.22309,0.64636,-0.72969,170.71,-0.69167,0.63243,0.34874,87.742
+> ui mousemode right "translate selected models"
+> view matrix models
+> #1,0.38233,-0.62566,-0.67998,380.63,0.87609,0.011513,0.48201,-254.96,-0.29374,-0.78001,0.55254,165.63,#16,0.68689,0.42691,0.58816,-119.21,0.22309,0.64636,-0.72969,59.535,-0.69167,0.63243,0.34874,128.97
+> view matrix models
+> #1,0.38233,-0.62566,-0.67998,289.1,0.87609,0.011513,0.48201,-274.53,-0.29374,-0.78001,0.55254,190.38,#16,0.68689,0.42691,0.58816,-210.74,0.22309,0.64636,-0.72969,39.961,-0.69167,0.63243,0.34874,153.72
+> view matrix models
+> #1,0.38233,-0.62566,-0.67998,298.14,0.87609,0.011513,0.48201,-272.93,-0.29374,-0.78001,0.55254,167.18,#16,0.68689,0.42691,0.58816,-201.7,0.22309,0.64636,-0.72969,41.57,-0.69167,0.63243,0.34874,130.51
+> view matrix models
+> #1,0.38233,-0.62566,-0.67998,282.73,0.87609,0.011513,0.48201,-276.94,-0.29374,-0.78001,0.55254,170.84,#16,0.68689,0.42691,0.58816,-217.11,0.22309,0.64636,-0.72969,37.554,-0.69167,0.63243,0.34874,134.18
+> view matrix models
+> #1,0.38233,-0.62566,-0.67998,281.94,0.87609,0.011513,0.48201,-275.2,-0.29374,-0.78001,0.55254,167.66,#16,0.68689,0.42691,0.58816,-217.9,0.22309,0.64636,-0.72969,39.291,-0.69167,0.63243,0.34874,130.99
+> select subtract #16
+atoms, 638 bonds, 1 pseudobond, 88 residues, 2 models selected
+> ui tool show "Fit in Map"
+> select add #1
+atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
+> select subtract #1
+Nothing selected
+> fitmap #16 inMap #8
+Fit map cryosparc_P17_J535_003_volume_map_zflip.mrc in map
+cryosparc_P17_J1163_006_volume_map.mrc using 276739 points
+correlation = 0.9612, correlation about mean = 0.5525, overlap = 1.969e+04
+steps = 164, shift = 2.78, angle = 15.9 degrees
+Position of cryosparc_P17_J535_003_volume_map_zflip.mrc (#16) relative to
+cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
+Matrix rotation and translation
+.99998050 -0.00425494 -0.00457199 0.73851682
+-0.00391421 -0.99738877 0.07211322 540.07003803
+-0.00486689 -0.07209391 -0.99738598 573.94195717
+Axis -0.99999512 0.00204496 0.00236281
+Axis point 0.00000000 280.39509902 277.22388946
+Rotation angle (degrees) 175.86516180
+Shift along axis 1.72202130
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!8 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> fitmap #3 inMap #16
+Fit map cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc in map
+cryosparc_P17_J535_003_volume_map_zflip.mrc using 193604 points
+correlation = 0.9176, correlation about mean = 0.2012, overlap = 2.042e+04
+steps = 124, shift = 8.42, angle = 17.5 degrees
+Position of cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) relative
+to cryosparc_P17_J535_003_volume_map_zflip.mrc (#16) coordinates:
+Matrix rotation and translation
+.58513310 0.56587388 -0.58086660 162.67581615
+.53803292 0.26503049 0.80017461 1.17881883
+.60674527 -0.78073400 -0.14938067 218.34134813
+Axis -0.79945189 -0.60056511 -0.01407893
+Axis point 0.00000000 55.92177713 150.33929755
+Rotation angle (degrees) 98.60424165
+Shift along axis -133.83346040
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> select add #16
+models selected
+> ui tool show "Color Actions"
+> color sel cornflower blue
+> color sel light sea green
+> color sel cornflower blue
+> color sel dark turquoise
+> color sel light sky blue
+[Repeated 1 time(s)]
+> color sel light blue
+> color sel light sky blue
+> color sel light blue
+> color sel light sky blue
+> color sel powder blue
+> color sel light steel blue
+> color sel pale turquoise
+> color sel light blue
+> color sel light sky blue
+> select subtract #16
+Nothing selected
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!8 models
+> show #!8 models
+> hide #!9 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> hide #!3 models
+> show #!8 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J655_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J655_005_volume_map_sharp.mrc as #17, grid size
+,588,588, pixel 0.95, shown at level 0.168, step 4, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J645_010_volume_map_sharp.mrc
+Opened cryosparc_P17_J645_010_volume_map_sharp.mrc as #18, grid size
+,588,588, pixel 0.95, shown at level 0.158, step 4, values float32
+> volume #18 level 0.2742
+> volume #18 step 1
+> volume #18 level 0.4422
+> volume #17 step 1
+> volume #17 level 0.4266
+> select add #17
+models selected
+> view matrix models #17,1,0,0,61.784,0,1,0,-62.478,0,0,1,-102.28
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #17,0.48945,0.25112,-0.83509,356.29,-0.79242,0.52783,-0.30572,377.6,0.36402,0.81137,0.45734,-292.7
+> view matrix models
+> #17,0.15791,0.038191,-0.98672,550.87,-0.45006,0.89221,-0.03749,107.36,0.87893,0.45,0.15807,-262.93
+> view matrix models
+> #17,-0.52223,0.57538,-0.62945,504.75,-0.48515,0.40657,0.77416,41.996,0.70136,0.70967,0.066821,-260.32
+> view matrix models
+> #17,-0.58537,-0.023225,-0.81043,736.95,-0.72536,0.46156,0.5107,164.54,0.3622,0.88681,-0.28703,-119.76
+> ui mousemode right "translate selected models"
+> view matrix models
+> #17,-0.58537,-0.023225,-0.81043,769.33,-0.72536,0.46156,0.5107,134.03,0.3622,0.88681,-0.28703,-184.13
+> view matrix models
+> #17,-0.58537,-0.023225,-0.81043,689.38,-0.72536,0.46156,0.5107,105.15,0.3622,0.88681,-0.28703,-37.942
+> view matrix models
+> #17,-0.58537,-0.023225,-0.81043,631.43,-0.72536,0.46156,0.5107,-28.227,0.3622,0.88681,-0.28703,-100.2
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #17,-0.3388,-0.27569,-0.89956,653.75,-0.79784,0.59094,0.11938,58.328,0.49867,0.75815,-0.42016,-69.159
+> ui mousemode right "translate selected models"
+> view matrix models
+> #17,-0.3388,-0.27569,-0.89956,660.19,-0.79784,0.59094,0.11938,89.728,0.49867,0.75815,-0.42016,-58.912
+> fitmap #17 inMap #8
+Fit map cryosparc_P17_J655_005_volume_map_sharp.mrc in map
+cryosparc_P17_J1163_006_volume_map.mrc using 286513 points
+correlation = 0.8688, correlation about mean = 0.2449, overlap = 8.66e+04
+steps = 256, shift = 11.4, angle = 20.7 degrees
+Position of cryosparc_P17_J655_005_volume_map_sharp.mrc (#17) relative to
+cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
+Matrix rotation and translation
+-0.95262622 -0.30211083 -0.03510445 642.60145687
+.17067519 -0.62654330 0.76046925 202.72382050
+-0.25174046 0.71845148 0.64842440 -51.92560179
+Axis -0.08053233 0.41521020 0.90615398
+Axis point 303.70069952 160.23700769 0.00000000
+Rotation angle (degrees) 164.87800612
+Shift along axis -14.62978716
+> select subtract #17
+Nothing selected
+> hide #!17 models
+> show #!17 models
+> show #!18 models
+> select add #18
+models selected
+> view matrix models #18,1,0,0,64.318,0,1,0,-54.342,0,0,1,-66.309
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #18,-0.21982,0.46975,-0.85499,506.62,-0.95518,0.074469,0.28649,397.56,0.19825,0.87965,0.43233,-216.22
+> view matrix models
+> #18,-0.94049,0.19544,-0.278,639.01,-0.33946,-0.50251,0.79514,246.97,0.015703,0.84219,0.53895,-181.2
+> view matrix models
+> #18,-0.54157,-0.62412,-0.56319,821.43,-0.82771,0.27878,0.487,253.66,-0.14694,0.7299,-0.66757,207.28
+> view matrix models
+> #18,-0.42526,-0.61847,-0.66079,811.74,-0.90422,0.2587,0.3398,319.03,-0.039206,0.742,-0.66925,173.54
+> view matrix models
+> #18,-0.94737,0.13657,-0.28954,659.99,-0.1521,0.60383,0.78247,-104.74,0.2817,0.78533,-0.55128,39.326
+> view matrix models
+> #18,-0.93716,-0.1073,-0.33199,734.43,-0.3217,0.63403,0.70321,-43.906,0.13504,0.76582,-0.62871,106.65
+> ui mousemode right "translate selected models"
+> view matrix models
+> #18,-0.93716,-0.1073,-0.33199,676.58,-0.3217,0.63403,0.70321,-192.92,0.13504,0.76582,-0.62871,39.473
+> view matrix models
+> #18,-0.93716,-0.1073,-0.33199,622.9,-0.3217,0.63403,0.70321,-192.02,0.13504,0.76582,-0.62871,103.22
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #18,-0.79577,-0.00053325,-0.6056,623.89,-0.55271,0.40935,0.72591,-70.483,0.24752,0.91238,-0.32605,-47.021
+> ui mousemode right "translate selected models"
+> view matrix models
+> #18,-0.79577,-0.00053325,-0.6056,629.43,-0.55271,0.40935,0.72591,-66.36,0.24752,0.91238,-0.32605,-58.769
+> fitmap #18 inMap #8
+Fit map cryosparc_P17_J645_010_volume_map_sharp.mrc in map
+cryosparc_P17_J1163_006_volume_map.mrc using 292439 points
+correlation = 0.7365, correlation about mean = 0.04959, overlap = 5.271e+04
+steps = 264, shift = 14.2, angle = 19.7 degrees
+Position of cryosparc_P17_J645_010_volume_map_sharp.mrc (#18) relative to
+cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
+Matrix rotation and translation
+-0.98450205 -0.17536898 0.00119668 603.21178623
+.16771790 -0.93951186 0.29864389 420.47135877
+-0.05124858 0.29421622 0.95436387 -43.01006329
+Axis -0.01275615 0.15109534 0.98843689
+Axis point 282.81965590 240.21101021 0.00000000
+Rotation angle (degrees) 170.00569893
+Shift along axis 13.32387113
+> select subtract #18
+Nothing selected
+> hide #!18 models
+> show #!18 models
+> hide #!17 models
+> select add #18
+models selected
+> view matrix models
+> #18,-0.71292,0.17712,-0.6785,584.31,-0.44227,0.63729,0.63107,-109.78,0.54418,0.74999,-0.37601,-58.453
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #18,-0.60845,0.16613,-0.77601,582.51,-0.56737,0.59263,0.57173,-46.453,0.55487,0.78815,-0.26633,-100.21
+> view matrix models
+> #18,-0.53501,-0.18143,-0.82514,668.78,-0.55166,0.81473,0.17855,-9.9926,0.63987,0.55072,-0.53597,9.6575
+> ui mousemode right "translate selected models"
+> view matrix models
+> #18,-0.53501,-0.18143,-0.82514,676.27,-0.55166,0.81473,0.17855,-55.746,0.63987,0.55072,-0.53597,-8.0105
+> view matrix models
+> #18,-0.53501,-0.18143,-0.82514,686.76,-0.55166,0.81473,0.17855,-55.075,0.63987,0.55072,-0.53597,-10.997
+> view matrix models
+> #18,-0.53501,-0.18143,-0.82514,683.39,-0.55166,0.81473,0.17855,-62.825,0.63987,0.55072,-0.53597,-15.419
+> fitmap #18 inMap #8
+Fit map cryosparc_P17_J645_010_volume_map_sharp.mrc in map
+cryosparc_P17_J1163_006_volume_map.mrc using 292439 points
+correlation = 0.8615, correlation about mean = 0.2577, overlap = 9.246e+04
+steps = 124, shift = 4.79, angle = 8.22 degrees
+Position of cryosparc_P17_J645_010_volume_map_sharp.mrc (#18) relative to
+cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
+Matrix rotation and translation
+-0.95287653 -0.30128223 -0.03543080 642.50639609
+.16990142 -0.62678199 0.76044582 202.97462428
+-0.25131620 0.71859123 0.64843413 -52.01912235
+Axis -0.08049372 0.41518546 0.90616874
+Axis point 303.68746244 160.20985177 0.00000000
+Rotation angle (degrees) 164.93072677
+Shift along axis -14.58371648
+> select subtract #18
+Nothing selected
+> hide #!18 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J842_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #19, grid size
+,588,588, pixel 0.95, shown at level 0.15, step 4, values float32
+> volume #19 step 1
+> volume #19 level 0.3083
+> volume #19 level 0.349
+> ui mousemode right "rotate selected models"
+> select add #19
+models selected
+> view matrix models
+> #19,-0.44408,0.45825,0.76993,46.649,-0.84084,-0.50996,-0.18146,698.91,0.30948,-0.72797,0.61178,228.1
+> view matrix models
+> #19,0.74377,0.47854,0.4667,-198.52,-0.1168,0.7805,-0.61415,275.9,-0.65815,0.40228,0.63641,182.36
+> view matrix models
+> #19,0.63923,-0.27239,0.71916,-40.675,0.75039,0.42547,-0.50585,98.912,-0.16819,0.86301,0.47637,-31.378
+> view matrix models
+> #19,0.48406,-0.45879,0.74511,45.429,0.87025,0.16344,-0.46471,124.56,0.091425,0.87338,0.47838,-107
+> view matrix models
+> #19,0.42748,-0.56077,0.70909,99.683,0.84962,-0.018802,-0.52707,198.53,0.30889,0.82776,0.4684,-152.09
+> view matrix models
+> #19,0.34186,-0.69155,0.63631,180.84,0.90812,0.068905,-0.41301,124.28,0.24177,0.71904,0.65156,-158.63
+> view matrix models
+> #19,0.71424,0.27698,0.64276,-188.14,0.046489,0.89756,-0.43844,146.08,-0.69835,0.34303,0.6282,212.11
+> view matrix models
+> #19,0.62219,0.51419,0.59033,-211.39,-0.24699,0.84448,-0.47524,253.15,-0.74288,0.14988,0.65243,269.79
+> ui mousemode right "translate selected models"
+> view matrix models
+> #19,0.62219,0.51419,0.59033,-152.75,-0.24699,0.84448,-0.47524,157.57,-0.74288,0.14988,0.65243,108.45
+> view matrix models
+> #19,0.62219,0.51419,0.59033,-232.8,-0.24699,0.84448,-0.47524,39.083,-0.74288,0.14988,0.65243,122.29
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #19,0.80455,0.20201,0.55847,-189.06,0.21173,0.78102,-0.58752,-37.641,-0.55486,0.59094,0.58559,-30.003
+> view matrix models
+> #19,0.66658,0.035494,0.74459,-161.06,0.34504,0.87073,-0.3504,-170.05,-0.66077,0.49048,0.56817,31.993
+> view matrix models
+> #19,0.69056,-0.011725,0.72318,-148.48,0.35206,0.87887,-0.32193,-182.74,-0.63181,0.47691,0.61104,14.806
+> ui mousemode right "translate selected models"
+> view matrix models
+> #19,0.69056,-0.011725,0.72318,-139.38,0.35206,0.87887,-0.32193,-182.11,-0.63181,0.47691,0.61104,39.587
+> fitmap #19 inMap #8
+Fit map cryosparc_P17_J842_005_volume_map_sharp.mrc in map
+cryosparc_P17_J1163_006_volume_map.mrc using 437476 points
+correlation = 0.926, correlation about mean = 0.3771, overlap = 9.23e+04
+steps = 76, shift = 5.07, angle = 2.91 degrees
+Position of cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) relative to
+cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
+Matrix rotation and translation
+.99898029 -0.04235492 0.01563476 10.76195054
+-0.02350758 -0.78361084 -0.62080710 683.98076137
+.03854581 0.61980652 -0.78380744 301.98502466
+Axis 0.99971420 -0.01846223 0.01518761
+Axis point 0.00000000 289.57241421 269.88486029
+Rotation angle (degrees) 141.64850238
+Shift along axis 2.71749516
+> select subtract #19
+Nothing selected
+> hide #!8 models
+> show #!17 models
+> hide #!19 models
+> show #!19 models
+> hide #!17 models
+> show #!18 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!18 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J845_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #20, grid size
+,588,588, pixel 0.95, shown at level 0.142, step 4, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J846_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #21, grid size
+,588,588, pixel 0.95, shown at level 0.14, step 4, values float32
+> volume #20 step 1
+> volume #20 level 0.1747
+> volume #20 level 0.2443
+> volume #21 step 1
+> volume #21 level 0.2884
+> select add #19
+models selected
+> select subtract #19
+Nothing selected
+> select add #20
+models selected
+> select add #21
+models selected
+> view matrix models
+> #20,1,0,0,0.47841,0,1,0,-12.3,0,0,1,-3.7669,#21,1,0,0,0.47841,0,1,0,-12.3,0,0,1,-3.7669
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #20,0.63928,-0.35722,0.68096,33.855,0.40184,0.91021,0.10024,-135.3,-0.65562,0.20956,0.72543,208.01,#21,0.63928,-0.35722,0.68096,33.855,0.40184,0.91021,0.10024,-135.3,-0.65562,0.20956,0.72543,208.01
+> view matrix models
+> #20,0.44179,-0.40839,0.79877,77.732,0.52263,0.84084,0.14085,-162.96,-0.72916,0.35524,0.58491,225.7,#21,0.44179,-0.40839,0.79877,77.732,0.52263,0.84084,0.14085,-162.96,-0.72916,0.35524,0.58491,225.7
+> view matrix models
+> #20,0.33252,-0.42236,0.84324,103.34,0.57932,0.79701,0.17076,-175.57,-0.74419,0.43173,0.5097,228.18,#21,0.33252,-0.42236,0.84324,103.34,0.57932,0.79701,0.17076,-175.57,-0.74419,0.43173,0.5097,228.18
+> view matrix models
+> #20,0.46255,-0.082779,0.88272,-43.162,0.6141,0.74804,-0.25164,-61.782,-0.63948,0.65847,0.39684,161.31,#21,0.46255,-0.082779,0.88272,-43.162,0.6141,0.74804,-0.25164,-61.782,-0.63948,0.65847,0.39684,161.31
+> ui mousemode right "translate selected models"
+> view matrix models
+> #20,0.46255,-0.082779,0.88272,-108.16,0.6141,0.74804,-0.25164,-245.68,-0.63948,0.65847,0.39684,53.335,#21,0.46255,-0.082779,0.88272,-108.16,0.6141,0.74804,-0.25164,-245.68,-0.63948,0.65847,0.39684,53.335
+> view matrix models
+> #20,0.46255,-0.082779,0.88272,-113.17,0.6141,0.74804,-0.25164,-247,-0.63948,0.65847,0.39684,59.993,#21,0.46255,-0.082779,0.88272,-113.17,0.6141,0.74804,-0.25164,-247,-0.63948,0.65847,0.39684,59.993
+> hide #!19 models
+> show #!8 models
+> fitmap #20 inMap #8
+Fit map cryosparc_P17_J845_005_volume_map_sharp.mrc in map
+cryosparc_P17_J1163_006_volume_map.mrc using 832636 points
+correlation = 0.9229, correlation about mean = 0.5258, overlap = 1.189e+05
+steps = 380, shift = 9.47, angle = 18.4 degrees
+Position of cryosparc_P17_J845_005_volume_map_sharp.mrc (#20) relative to
+cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
+Matrix rotation and translation
+.99901244 -0.04125012 0.01650989 10.10628769
+-0.02203512 -0.78263856 -0.62208628 683.70365274
+.03858241 0.62110813 -0.78277461 301.46889960
+Axis 0.99972305 -0.01774976 0.01545187
+Axis point 0.00000000 289.37571004 269.89498614
+Rotation angle (degrees) 141.55453890
+Shift along axis 2.62616910
+> hide #!21 models
+> show #!21 models
+> fitmap #21 inMap #8
+Fit map cryosparc_P17_J846_005_volume_map_sharp.mrc in map
+cryosparc_P17_J1163_006_volume_map.mrc using 615528 points
+correlation = 0.9307, correlation about mean = 0.4766, overlap = 1.046e+05
+steps = 256, shift = 8.97, angle = 18.4 degrees
+Position of cryosparc_P17_J846_005_volume_map_sharp.mrc (#21) relative to
+cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
+Matrix rotation and translation
+.99901041 -0.04132365 0.01644837 10.15187435
+-0.02212851 -0.78259628 -0.62213616 683.73846275
+.03858136 0.62115652 -0.78273626 301.42350706
+Axis 0.99972248 -0.01779698 0.01543467
+Axis point 0.00000000 289.39631274 269.89032870
+Rotation angle (degrees) 141.55091738
+Shift along axis 2.63294913
+> select subtract #21
+models selected
+> select subtract #20
+Nothing selected
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!19 models
+> hide #!21 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> volume #19 level 0.3
+> volume #20 level 0.3
+> volume #21 level 0.3
+> ui mousemode right zoom
+> lighting soft
+> hide #!20 models
+> hide #!21 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!19 models
+> show #!19 models
+> hide #!20 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!21 models
+> hide #!19 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> hide #!20 models
+> show #!21 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!21 models
+> show #!177 models
+> hide #!19 models
+> show #!19 models
+> fitmap #177 inMap #19
+Fit molecule 6skl (#177) to map cryosparc_P17_J842_005_volume_map_sharp.mrc
+(#19) using 118220 atoms
+average map value = 0.3221, steps = 64
+shifted from previous position = 0.243
+rotated from previous position = 0.297 degrees
+atoms outside contour = 66812, contour level = 0.3
+Position of 6skl (#177) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.52950222 -0.10066174 -0.84231504 552.59666642
+.51811377 0.74784553 -0.41507252 112.80308239
+.67170345 -0.65619683 -0.34383163 339.58429947
+Axis -0.14584759 -0.91577637 0.37427547
+Axis point 163.10260363 0.00000000 350.04343026
+Rotation angle (degrees) 124.24578811
+Shift along axis -56.79921564
+> hide #!19 models
+> select add #177
+atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> select subtract #177
+Nothing selected
+> color #19 #b2b2ff80 models
+> color #19 #b2b2ffb4 models
+> color #19 #b2b2ffbf models
+> color #19 #b2b2ffd8 models
+> color #19 #b2b2ffc6 models
+> color #19 #b2b2ffc7 models
+> set bgColor black
+> set bgColor transparent
+> hide #!177 models
+> show #!177 models
+> color #19 #b2b2ffff models
+> color #19 #b2b2fffb models
+> color #19 #b2b2ffff models
+> hide #!19 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> hide #!177 models
+> show #!19 models
+> show #!1 models
+> hide #!1 models
+> show #!177 models
+> hide #!177 models
+> show #!15 models
+> hide #!15 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!1 models
+> hide #!1 models
+> ui tool show Matchmaker
+> show #!1 models
+> show #!177 models
+> matchmaker #1/I to #177/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain X (#177) with 8xgc, chain I (#1), sequence alignment
+score = 5322.6
+RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
+.839)
+> select #1/8
+atoms, 7098 bonds, 7 pseudobonds, 859 residues, 3 models selected
+> combine #1
+> hide #!22 models
+> delete atoms (#!1 & sel)
+> delete bonds (#!1 & sel)
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> select #1/9
+atoms, 4699 bonds, 3 pseudobonds, 573 residues, 2 models selected
+> delete atoms (#!1 & sel)
+> delete bonds (#!1 & sel)
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> hide #!1 models
+> set bgColor white
+> set bgColor #ffffff00
+> hide #!19 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> hide #!177 models
+> show #!177 models
+> combine #177
+[Repeated 2 time(s)]
+> rename #23 6skl-Mcm2
+> hide #!24 models
+> hide #!25 models
+> hide #!177 models
+> hide #!23 models
+> show #!23 models
+> select #23/2
+atoms, 10708 bonds, 8 pseudobonds, 672 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 108697 bonds, 122 pseudobonds, 6649 residues, 4 models selected
+> delete atoms (#!23 & sel)
+> delete bonds (#!23 & sel)
+> select add #23
+atoms, 10708 bonds, 8 pseudobonds, 672 residues, 3 models selected
+> ui tool show "Color Actions"
+> color sel hot pink
+> show #!19 models
+> color #19 #b2b2ffea models
+> color #19 #b2b2ffde models
+> color #19 #b2b2ffff models
+> color #19 #b2b2ffdd models
+> color #19 #b2b2ffd4 models
+> hide #!19 models
+> show #!19 models
+> color #19 #b2b2ffff models
+> select subtract #23
+Nothing selected
+> hide #!19 models
+> show #!19 models
+> color #19 #b2b2ff7f models
+> color #19 #b2b2ffd4 models
+> lighting soft
+> lighting full
+> lighting soft
+> lighting simple
+> lighting full
+> color #19 #b2b2ff82 models
+> color #19 #b2b2ff90 models
+> hide #!19 models
+> show #!19 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> show #!24 models
+> hide #!24 models
+> show #!24 models
+> hide #!24 models
+> show #!24 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!24 models
+> show #!24 models
+> hide #!24 models
+> show #!24 models
+> hide #!24 models
+> hide #!19 models
+> combine #23
+> ui tool show "Show Sequence Viewer"
+> sequence chain #23/2
+Alignment identifier is 23/2
+> select clear
+[Repeated 1 time(s)]
+> select #23/2:173-442
+atoms, 4320 bonds, 270 residues, 1 model selected
+> select #23/2:458-459
+atoms, 47 bonds, 2 residues, 1 model selected
+> select #23/2:458-459
+atoms, 47 bonds, 2 residues, 1 model selected
+> select #23/2:458
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #23/2:173-458
+atoms, 4577 bonds, 286 residues, 1 model selected
+> select #23/2:466-467
+atoms, 21 bonds, 2 residues, 1 model selected
+> select #23/2:173-467
+atoms, 4697 bonds, 295 residues, 1 model selected
+> select #23/2:465-466
+atoms, 28 bonds, 2 residues, 1 model selected
+> select #23/2:465-466
+atoms, 28 bonds, 2 residues, 1 model selected
+> select #23/2:465
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #23/2:173-465
+atoms, 4675 bonds, 293 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 6033 bonds, 8 pseudobonds, 379 residues, 3 models selected
+> delete atoms (#!23 & sel)
+> delete bonds (#!23 & sel)
+> hide #!26 models
+> rename #23 N-Mcm2_6skl
+> show #!26 models
+> hide #!23 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #26/2
+Alignment identifier is 26/2
+> select #26/2:466
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #26/2:466-868
+atoms, 5986 bonds, 1 pseudobond, 376 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 4722 bonds, 7 pseudobonds, 296 residues, 2 models selected
+> delete atoms (#!26 & sel)
+> delete bonds (#!26 & sel)
+> rename #26 C-Mcm2_6skl
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> hide #!26 models
+> show #!24 models
+> lighting simple
+> show #!26 models
+> hide #!24 models
+> show #!24 models
+> hide #!24 models
+> show #!24 models
+> hide #!26 models
+> hide #!24 models
+> show #!24 models
+> select #25/3
+atoms, 9839 bonds, 7 pseudobonds, 618 residues, 3 models selected
+> select add #25
+atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
+> select subtract #25
+Nothing selected
+> hide #!24 models
+> show #!24 models
+> select #24/3
+atoms, 9839 bonds, 7 pseudobonds, 618 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 109566 bonds, 123 pseudobonds, 6703 residues, 4 models selected
+> delete atoms (#!24 & sel)
+> delete bonds (#!24 & sel)
+> rename #24 Mcm3_6skl
+> combine #24
+> ui tool show "Show Sequence Viewer"
+> sequence chain #24/3
+Alignment identifier is 24/3
+> sequence chain #27/3
+Alignment identifier is 27/3
+> hide #!27 models
+> select #24/3:332
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #24/3:18-332
+atoms, 4476 bonds, 1 pseudobond, 282 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 5363 bonds, 6 pseudobonds, 336 residues, 3 models selected
+> delete atoms (#!24 & sel)
+> delete bonds (#!24 & sel)
+> rename #24 N-Mcm3_6skl
+> show #!27 models
+> hide #!24 models
+> select clear
+> select #27/3:337-675
+atoms, 4351 bonds, 1 pseudobond, 275 residues, 2 models selected
+> select clear
+> select #27/3:337-740
+atoms, 5317 bonds, 2 pseudobonds, 334 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 4522 bonds, 5 pseudobonds, 284 residues, 3 models selected
+> delete atoms (#!27 & sel)
+> delete bonds (#!27 & sel)
+> rename #27 C-Mcm3_6skl
+> show #!24 models
+> select add #27
+atoms, 5317 bonds, 2 pseudobonds, 334 residues, 2 models selected
+> select add #24
+atoms, 9793 bonds, 3 pseudobonds, 616 residues, 4 models selected
+> ui tool show "Color Actions"
+> color sel turquoise
+> color sel cyan
+[Repeated 1 time(s)]
+> color sel turquoise
+[Repeated 1 time(s)]
+> color sel pale turquoise
+[Repeated 4 time(s)]
+> color sel turquoise
+[Repeated 1 time(s)]
+> select subtract #27
+atoms, 4476 bonds, 1 pseudobond, 282 residues, 2 models selected
+> select subtract #24
+Nothing selected
+> hide #!24 models
+> hide #!27 models
+> combine #177
+[Repeated 1 time(s)]
+> hide #!28 models
+> hide #!29 models
+> show #!25 models
+> select #25/4
+atoms, 10952 bonds, 11 pseudobonds, 680 residues, 3 models selected
+> select #25/4
+atoms, 10952 bonds, 11 pseudobonds, 680 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 108453 bonds, 119 pseudobonds, 6641 residues, 4 models selected
+> delete atoms (#!25 & sel)
+> delete bonds (#!25 & sel)
+> rename #25 Mcm4_6skl
+> combine #25
+> ui tool show "Show Sequence Viewer"
+> sequence chain #25/4
+Alignment identifier is 25/4
+> sequence chain #30/4
+Alignment identifier is 30/4
+> hide #!30 models
+> select #25/4:469
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #25/4:174-469
+atoms, 4834 bonds, 296 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 6118 bonds, 11 pseudobonds, 384 residues, 3 models selected
+> delete atoms (#!25 & sel)
+> delete bonds (#!25 & sel)
+> rename #25 N-Mcm4_6skl
+> show #!30 models
+> hide #!25 models
+> select clear
+> select #30/4:505-815
+atoms, 4465 bonds, 4 pseudobonds, 280 residues, 2 models selected
+> select #30/4:505-815
+atoms, 4465 bonds, 4 pseudobonds, 280 residues, 2 models selected
+> select #30/4:505-815
+atoms, 4465 bonds, 4 pseudobonds, 280 residues, 2 models selected
+> select clear
+> select #30/4:505-927
+atoms, 6118 bonds, 6 pseudobonds, 383 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 4834 bonds, 5 pseudobonds, 297 residues, 3 models selected
+> delete atoms (#!30 & sel)
+> delete bonds (#!30 & sel)
+> rename #30 C-Mcm4_6skl
+> show #!25 models
+> select add #25
+atoms, 4834 bonds, 296 residues, 1 model selected
+> select add #30
+atoms, 10952 bonds, 6 pseudobonds, 679 residues, 3 models selected
+> ui tool show "Color Actions"
+> color sel forest green
+> color sel sea green
+> color sel turquoise
+> color sel sea green
+> color sel green
+> color sel forest green
+> color sel sea green
+[Repeated 1 time(s)]
+> select subtract #30
+atoms, 4834 bonds, 296 residues, 1 model selected
+> hide #!30 models
+> select subtract #25
+Nothing selected
+> hide #!25 models
+> show #!28 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> select #28/5
+atoms, 9789 bonds, 11 pseudobonds, 614 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 109616 bonds, 119 pseudobonds, 6707 residues, 4 models selected
+> delete atoms (#!28 & sel)
+> delete bonds (#!28 & sel)
+> rename #28 Mcm5_6skl
+> combine #28
+> select add #28
+atoms, 9789 bonds, 11 pseudobonds, 614 residues, 3 models selected
+> select add #31
+atoms, 19578 bonds, 22 pseudobonds, 1228 residues, 6 models selected
+> ui tool show "Color Actions"
+> color sel yellow
+> select subtract #28
+atoms, 9789 bonds, 11 pseudobonds, 614 residues, 3 models selected
+> select subtract #31
+Nothing selected
+> ui tool show "Show Sequence Viewer"
+> sequence chain #28/5
+Alignment identifier is 28/5
+> sequence chain #31/5
+Alignment identifier is 31/5
+> select #28/5:342
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #28/5:20-342
+atoms, 4202 bonds, 4 pseudobonds, 259 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 5587 bonds, 7 pseudobonds, 355 residues, 2 models selected
+> delete atoms (#!28 & sel)
+> delete bonds (#!28 & sel)
+> hide #!31 models
+> rename #28 N-Mcm5_6skl
+> show #!25 models
+> show #!30 models
+> hide #!30 models
+> hide #!25 models
+> show #!31 models
+> hide #!31 models
+> hide #!28 models
+> show #!31 models
+> select #31/5:343
+atoms, 25 bonds, 1 residue, 1 model selected
+> select #31/5:343-694
+atoms, 5540 bonds, 352 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 4249 bonds, 11 pseudobonds, 262 residues, 3 models selected
+> delete atoms (#!31 & sel)
+> delete bonds (#!31 & sel)
+> rename #31 C-Mcm5_6skl
+> show #!28 models
+> hide #!28 models
+> hide #!31 models
+> combine #177
+> hide #!32 models
+> show #!29 models
+> select #29/6
+atoms, 10126 bonds, 9 pseudobonds, 638 residues, 3 models selected
+> select #29/6
+atoms, 10126 bonds, 9 pseudobonds, 638 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 109279 bonds, 121 pseudobonds, 6683 residues, 4 models selected
+> delete atoms (#!29 & sel)
+> delete bonds (#!29 & sel)
+> rename #29 Mcm6_6skl
+> combine #29
+> select add #29
+atoms, 10126 bonds, 9 pseudobonds, 638 residues, 3 models selected
+> select add #33
+atoms, 20252 bonds, 18 pseudobonds, 1276 residues, 6 models selected
+> ui tool show "Color Actions"
+> color sel orange
+> color sel dark orange
+> color sel orange
+> color sel dark orange
+[Repeated 1 time(s)]
+> color sel goldenrod
+> color sel dark orange
+> color sel sandy brown
+> color sel dark orange
+[Repeated 1 time(s)]
+> select subtract #29
+atoms, 10126 bonds, 9 pseudobonds, 638 residues, 3 models selected
+> select subtract #33
+Nothing selected
+> ui tool show "Show Sequence Viewer"
+> sequence chain #29/6
+Alignment identifier is 29/6
+> sequence chain #33/6
+Alignment identifier is 33/6
+> select #29/6:463
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #29/6:459-463
+atoms, 71 bonds, 5 residues, 1 model selected
+> select
+> #29/6:98-102,105-122,134-147,155-161,164-193,277-284,384-386,407-411,500-521,524-533,540-553,580-592,604-609,626-631,640-650,652-658,694-699,702-707,720-735,747-759,766-784,796-814,820-836
+atoms, 4500 bonds, 275 residues, 1 model selected
+> select clear
+[Repeated 1 time(s)]
+> select #29/6:91-463
+atoms, 4908 bonds, 2 pseudobonds, 305 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 5218 bonds, 7 pseudobonds, 333 residues, 3 models selected
+> delete atoms (#!29 & sel)
+> delete bonds (#!29 & sel)
+> rename #29 N-Mcm6_6skl
+> hide #!29 models
+> show #!29 models
+> hide #!33 models
+> show #!33 models
+> hide #!33 models
+> show #!33 models
+> hide #!33 models
+> show #!33 models
+> hide #!33 models
+> show #!33 models
+> hide #!33 models
+> show #!28 models
+> show #!31 models
+> hide #!31 models
+> hide #!29 models
+> hide #!28 models
+> show #!28 models
+> show #!31 models
+> hide #!28 models
+> show #!28 models
+> hide #!31 models
+> show #!31 models
+> hide #!31 models
+> show #!31 models
+> hide #!31 models
+> show #!31 models
+> hide #!28 models
+> show #!28 models
+> hide #!31 models
+> show #!31 models
+> hide #!28 models
+> show #!28 models
+> hide #!31 models
+> show #!31 models
+> hide #!28 models
+> show #!28 models
+> hide #!31 models
+> hide #!28 models
+> show #!28 models
+> hide #!28 models
+> show #!28 models
+> show #!31 models
+> hide #!28 models
+> show #!28 models
+> hide #!28 models
+> hide #!31 models
+> show #!29 models
+> show #!33 models
+> show #!28 models
+> hide #!28 models
+> hide #!33 models
+> show #!33 models
+> hide #!29 models
+> select clear
+[Repeated 2 time(s)]
+> select #33/6:497-838
+atoms, 5218 bonds, 2 pseudobonds, 332 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 4908 bonds, 7 pseudobonds, 306 residues, 3 models selected
+> delete atoms (#!33 & sel)
+> delete bonds (#!33 & sel)
+> rename #33 C-Mcm6_6skl
+> show #!29 models
+> hide #!29 models
+> hide #!33 models
+> show #!32 models
+> select #32/7
+atoms, 10055 bonds, 11 pseudobonds, 636 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 109350 bonds, 119 pseudobonds, 6685 residues, 4 models selected
+> delete atoms (#!32 & sel)
+> delete bonds (#!32 & sel)
+> select add #32
+atoms, 10055 bonds, 11 pseudobonds, 636 residues, 3 models selected
+> rename #32 Mcm7_6skl
+> ui tool show "Color Actions"
+> color sel deep sky blue
+> color sel cornflower blue
+> color sel dodger blue
+> select subtract #32
+Nothing selected
+> combine #32
+> ui tool show "Show Sequence Viewer"
+> sequence chain #32/7
+Alignment identifier is 32/7
+> sequence chain #34/7
+Alignment identifier is 34/7
+> ui tool show "Show Sequence Viewer"
+> sequence chain #32/7
+Destroying pre-existing alignment with identifier 32/7
+Alignment identifier is 32/7
+> sequence chain #34/7
+Destroying pre-existing alignment with identifier 34/7
+Alignment identifier is 34/7
+> select #32/7:385
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #32/7:4-385
+atoms, 4986 bonds, 3 pseudobonds, 317 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 5069 bonds, 8 pseudobonds, 319 residues, 3 models selected
+> delete atoms (#!32 & sel)
+> delete bonds (#!32 & sel)
+> rename #32 N-Mcm7_6skl
+> select clear
+> select #34/7:396-729
+atoms, 5069 bonds, 3 pseudobonds, 318 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 4986 bonds, 8 pseudobonds, 318 residues, 3 models selected
+> delete atoms (#!34 & sel)
+> delete bonds (#!34 & sel)
+> rename #34 C-Mcm7_6skl
+> hide #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!34 models
+> hide #!34 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> combine #177
+[Repeated 3 time(s)]
+> hide #!36 models
+> hide #!37 models
+> hide #!38 models
+> hide #!35 models
+> show #!23 models
+> show #!24 models
+> show #!25 models
+> show #!26 models
+> show #!27 models
+> show #!28 models
+> show #!29 models
+> show #!30 models
+> show #!31 models
+> show #!32 models
+> show #!33 models
+> show #!34 models
+> hide #!34 models
+> hide #!33 models
+> hide #!32 models
+> hide #!31 models
+> hide #!30 models
+> hide #!29 models
+> hide #!28 models
+> hide #!27 models
+> hide #!26 models
+> hide #!25 models
+> hide #!24 models
+> hide #!23 models
+> show #!35 models
+> select #35/E
+atoms, 9213 bonds, 4 pseudobonds, 564 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 110192 bonds, 126 pseudobonds, 6757 residues, 4 models selected
+> delete atoms (#!35 & sel)
+> delete bonds (#!35 & sel)
+> rename #35 Cdc45_6skl
+> select add #35
+atoms, 9213 bonds, 4 pseudobonds, 564 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel light cyan
+[Repeated 1 time(s)]
+> color sel powder blue
+> color sel light blue
+[Repeated 1 time(s)]
+> color sel light cyan
+> select subtract #35
+Nothing selected
+> lighting soft
+[Repeated 1 time(s)]
+> lighting full
+> hide #!35 models
+> show #!36 models
+> lighting simple
+> select #36/A,B,C,D
+atoms, 13508 bonds, 6 pseudobonds, 810 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 105897 bonds, 124 pseudobonds, 6511 residues, 4 models selected
+> delete atoms (#!36 & sel)
+> delete bonds (#!36 & sel)
+> select add #36
+atoms, 13508 bonds, 6 pseudobonds, 810 residues, 2 models selected
+> rename #36 GINS_6skl
+> ui tool show "Color Actions"
+> color sel silver
+> color sel gray
+> select clear
+> hide #!36 models
+> show #!37 models
+> select #37/F,G,H
+atoms, 20476 bonds, 6 pseudobonds, 1271 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 98929 bonds, 124 pseudobonds, 6050 residues, 4 models selected
+> delete atoms (#!37 & sel)
+> delete bonds (#!37 & sel)
+> select add #37
+atoms, 20476 bonds, 6 pseudobonds, 1271 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel slate blue
+> color sel medium slate blue
+[Repeated 3 time(s)]
+> color sel royal blue
+> color sel dodger blue
+> color sel royal blue
+[Repeated 1 time(s)]
+> color sel dodger blue
+> color sel royal blue
+> select subtract #37
+Nothing selected
+> show #!32 models
+> hide #!32 models
+> hide #!37 models
+> show #!37 models
+> hide #!37 models
+> rename #37 Ctf4_6skl
+> combine #177
+> hide #!39 models
+> show #!38 models
+> select #38/X
+atoms, 11092 bonds, 7 pseudobonds, 665 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 108313 bonds, 123 pseudobonds, 6656 residues, 4 models selected
+> delete atoms (#!38 & sel)
+> delete bonds (#!38 & sel)
+> rename #38 Tof1_6skl
+> select add #38
+atoms, 11092 bonds, 7 pseudobonds, 665 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel slate blue
+> color sel medium slate blue
+> color sel royal blue
+> color sel medium slate blue
+[Repeated 7 time(s)]
+> color sel dark slate blue
+> color sel medium slate blue
+> select subtract #38
+Nothing selected
+> hide #!38 models
+> show #!38 models
+> show #!39 models
+> hide #!38 models
+> select #39/Y
+atoms, 1632 bonds, 94 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 117773 bonds, 130 pseudobonds, 7227 residues, 4 models selected
+> delete atoms (#!39 & sel)
+> delete bonds (#!39 & sel)
+> rename #39 Csm3_6skl
+> select add #39
+atoms, 1632 bonds, 94 residues, 1 model selected
+> hide #!39 models
+> select subtract #39
+Nothing selected
+> show #!39 models
+> show #!38 models
+> show #!37 models
+> show #!36 models
+> show #!35 models
+> show #!34 models
+> show #!33 models
+> show #!32 models
+> show #!31 models
+> show #!30 models
+> show #!29 models
+> show #!28 models
+> show #!27 models
+> show #!26 models
+> show #!25 models
+> show #!24 models
+> show #!23 models
+> select add #39
+atoms, 1632 bonds, 94 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel orchid
+> color sel blue violet
+> color sel deep pink
+> color sel magenta
+> color sel dark magenta
+> color sel purple
+[Repeated 1 time(s)]
+> color sel dark magenta
+> color sel purple
+[Repeated 1 time(s)]
+> color sel medium purple
+> color sel purple
+[Repeated 1 time(s)]
+> select subtract #39
+Nothing selected
+> combine #177
+> hide #!39 models
+> hide #!38 models
+> hide #!37 models
+> hide #!36 models
+> hide #!35 models
+> hide #!34 models
+> show #!35 models
+> hide #!35 models
+> show #!35 models
+> hide #!35 models
+> show #!34 models
+> hide #!33 models
+> hide #!40 models
+> show #!35 models
+> hide #!35 models
+> hide #!34 models
+> hide #!32 models
+> hide #!31 models
+> hide #!30 models
+> hide #!29 models
+> hide #!28 models
+> hide #!27 models
+> hide #!26 models
+> hide #!25 models
+> hide #!24 models
+> hide #!23 models
+> show #!40 models
+> select #40/I,J
+atoms, 2015 bonds, 50 pseudobonds, 59 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 117390 bonds, 80 pseudobonds, 7262 residues, 3 models selected
+> delete atoms (#!40 & sel)
+> delete bonds (#!40 & sel)
+> rename #40 DNA_6skl
+> select #40/I
+atoms, 1279 bonds, 37 residues, 1 model selected
+> color sel black
+> select #40/J
+atoms, 736 bonds, 22 residues, 1 model selected
+> color sel dim gray
+> select clear
+> hide #!40 models
+> show #!19 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!19 models
+> show #!24 models
+> show #!25 models
+> hide #!25 models
+> hide #!24 models
+> hide #!23 models
+> show #!23 models
+> show #!19 models
+> fitmap #23 inMap #19
+Fit molecule N-Mcm2_6skl (#23) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4631 atoms
+average map value = 0.4542, steps = 52
+shifted from previous position = 1.09
+rotated from previous position = 3.28 degrees
+atoms outside contour = 1773, contour level = 0.3
+Position of N-Mcm2_6skl (#23) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.48619287 -0.07981194 -0.87019915 544.75612919
+.53368692 0.76140981 -0.36801274 98.39251819
+.69194998 -0.64333907 -0.32759742 329.31388927
+Axis -0.16188679 -0.91851479 0.36072599
+Axis point 157.28465121 0.00000000 346.27079505
+Rotation angle (degrees) 121.74840423
+Shift along axis -59.77172713
+> fitmap #23 inMap #19
+Fit molecule N-Mcm2_6skl (#23) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4631 atoms
+average map value = 0.4542, steps = 36
+shifted from previous position = 0.0153
+rotated from previous position = 0.0153 degrees
+atoms outside contour = 1772, contour level = 0.3
+Position of N-Mcm2_6skl (#23) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.48612668 -0.08005636 -0.87021368 544.79200838
+.53355946 0.76145094 -0.36811244 98.44034714
+.69209476 -0.64326002 -0.32744679 329.22783276
+Axis -0.16176651 -0.91852227 0.36076090
+Axis point 157.31175798 0.00000000 346.27934228
+Rotation angle (degrees) 121.73971426
+Shift along axis -59.77622153
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!24 models
+> fitmap #24 inMap #19
+Fit molecule N-Mcm3_6skl (#24) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4424 atoms
+average map value = 0.4899, steps = 72
+shifted from previous position = 1.7
+rotated from previous position = 1.03 degrees
+atoms outside contour = 1496, contour level = 0.3
+Position of N-Mcm3_6skl (#24) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.51684057 -0.09904554 -0.85033277 552.53192555
+.53049272 0.74253315 -0.40892786 109.84096466
+.67190275 -0.66244585 -0.33122832 337.40029650
+Axis -0.15211044 -0.91333918 0.37772207
+Axis point 161.67410853 0.00000000 351.20284420
+Rotation angle (degrees) 123.55710836
+Shift along axis -56.92439016
+> hide #!24 models
+> show #!25 models
+> fitmap #25 inMap #19
+Fit molecule N-Mcm4_6skl (#25) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4793 atoms
+average map value = 0.4529, steps = 52
+shifted from previous position = 2.33
+rotated from previous position = 1.94 degrees
+atoms outside contour = 1614, contour level = 0.3
+Position of N-Mcm4_6skl (#25) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.51485483 -0.08657680 -0.85289447 549.29032703
+.51292450 0.76605243 -0.38739145 104.77742894
+.68690099 -0.63692082 -0.34999843 331.94917409
+Axis -0.14931878 -0.92141613 0.35874256
+Axis point 162.77097442 0.00000000 344.51466083
+Rotation angle (degrees) 123.32588851
+Shift along axis -59.47868024
+> hide #!25 models
+> show #!28 models
+> fitmap #28 inMap #19
+Fit molecule N-Mcm5_6skl (#28) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4172 atoms
+average map value = 0.5001, steps = 48
+shifted from previous position = 0.477
+rotated from previous position = 0.518 degrees
+atoms outside contour = 1491, contour level = 0.3
+Position of N-Mcm5_6skl (#28) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.52208241 -0.10009271 -0.84700143 552.10007852
+.52281543 0.74707399 -0.41054169 110.98680483
+.67386497 -0.65716201 -0.33770418 337.87117097
+Axis -0.14839770 -0.91514390 0.37481963
+Axis point 162.27606171 0.00000000 350.25308806
+Rotation angle (degrees) 123.80418376
+Shift along axis -56.85853328
+> hide #!28 models
+> show #!29 models
+> fitmap #29 inMap #19
+Fit molecule N-Mcm6_6skl (#29) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4862 atoms
+average map value = 0.4386, steps = 64
+shifted from previous position = 1.82
+rotated from previous position = 1.81 degrees
+atoms outside contour = 1794, contour level = 0.3
+Position of N-Mcm6_6skl (#29) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.50972104 -0.08434926 -0.85619488 547.63107126
+.52443527 0.75845239 -0.38693363 104.75971281
+.68202061 -0.64624700 -0.34236341 333.92722557
+Axis -0.15485966 -0.91860876 0.36356077
+Axis point 160.21705818 0.00000000 346.31455571
+Rotation angle (degrees) 123.14885220
+Shift along axis -59.63631555
+> hide #!29 models
+> show #!32 models
+> fitmap #32 inMap #19
+Fit molecule N-Mcm7_6skl (#32) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4942 atoms
+average map value = 0.4432, steps = 72
+shifted from previous position = 2.55
+rotated from previous position = 2 degrees
+atoms outside contour = 1716, contour level = 0.3
+Position of N-Mcm7_6skl (#32) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.50209844 -0.09646270 -0.85941382 551.56164113
+.52217420 0.75834411 -0.39019012 105.12547600
+.68937019 -0.64467757 -0.33039306 330.21496061
+Axis -0.15084576 -0.91803150 0.36669294
+Axis point 162.01873803 0.00000000 348.31963616
+Rotation angle (degrees) 122.48465413
+Shift along axis -58.62173799
+> hide #!32 models
+> show #!26 models
+> hide #!26 models
+> show #!27 models
+> fitmap #27 inMap #19
+Fit molecule C-Mcm3_6skl (#27) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5283 atoms
+average map value = 0.2453, steps = 68
+shifted from previous position = 2.23
+rotated from previous position = 2.57 degrees
+atoms outside contour = 3746, contour level = 0.3
+Position of C-Mcm3_6skl (#27) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.49125191 -0.10951013 -0.86410596 552.71575277
+.52980778 0.74986873 -0.39623302 105.24621685
+.69135757 -0.65246028 -0.31035512 328.13372850
+Axis -0.15062172 -0.91437023 0.37581934
+Axis point 161.23471230 0.00000000 351.59387631
+Rotation angle (degrees) 121.72677225
+Shift along axis -56.16600219
+> hide #!27 models
+> show #!26 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> fitmap #26 inMap #19
+Fit molecule C-Mcm2_6skl (#26) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5941 atoms
+average map value = 0.2499, steps = 120
+shifted from previous position = 7.11
+rotated from previous position = 16.9 degrees
+atoms outside contour = 4089, contour level = 0.3
+Position of C-Mcm2_6skl (#26) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.72499338 -0.17926092 -0.66501889 564.61757623
+.30570305 0.78146839 -0.54392354 172.58562424
+.61719547 -0.59763926 -0.51175880 374.68531048
+Axis -0.03915385 -0.93461689 0.35349433
+Axis point 195.27960459 0.00000000 339.48855257
+Rotation angle (degrees) 136.68906839
+Shift along axis -50.95925582
+> hide #!26 models
+> show #!27 models
+> hide #!27 models
+> show #!30 models
+> hide #!30 models
+> show #!31 models
+> fitmap #31 inMap #19
+Fit molecule C-Mcm5_6skl (#31) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5504 atoms
+average map value = 0.2192, steps = 72
+shifted from previous position = 1.38
+rotated from previous position = 0.644 degrees
+atoms outside contour = 4241, contour level = 0.3
+Position of C-Mcm5_6skl (#31) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.52798995 -0.11167009 -0.84187672 553.62723896
+.51297984 0.74809912 -0.42095058 113.66344352
+.67681482 -0.65412346 -0.33770431 336.54923223
+Axis -0.14058346 -0.91564213 0.37661090
+Axis point 164.28052383 0.00000000 350.23415639
+Rotation angle (degrees) 123.97268209
+Shift along axis -55.15775830
+> hide #!31 models
+> show #!32 models
+> hide #!32 models
+> show #!33 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> fitmap #33 inMap #19
+Fit molecule C-Mcm6_6skl (#33) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5182 atoms
+average map value = 0.2506, steps = 100
+shifted from previous position = 2.49
+rotated from previous position = 3.08 degrees
+atoms outside contour = 3615, contour level = 0.3
+Position of C-Mcm6_6skl (#33) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.56822296 -0.11833571 -0.81432140 555.66185955
+.48213507 0.75407081 -0.44600784 124.85237619
+.66683465 -0.64604479 -0.37142655 342.86696321
+Axis -0.12419139 -0.91956426 0.37279763
+Axis point 169.39701035 0.00000000 347.59627562
+Rotation angle (degrees) 126.35519939
+Shift along axis -55.99821082
+> hide #!33 models
+> show #!34 models
+> fitmap #34 inMap #19
+Fit molecule C-Mcm7_6skl (#34) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5038 atoms
+average map value = 0.2488, steps = 84
+shifted from previous position = 3.58
+rotated from previous position = 6.44 degrees
+atoms outside contour = 3687, contour level = 0.3
+Position of C-Mcm7_6skl (#34) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.60810284 -0.04397762 -0.79263921 541.80870758
+.49024443 0.76452307 -0.41852703 112.51289532
+.62439678 -0.64309443 -0.44334887 361.42999934
+Axis -0.14668479 -0.92559125 0.34894756
+Axis point 166.00281620 0.00000000 336.12434083
+Rotation angle (degrees) 130.05063287
+Shift along axis -57.49592849
+> hide #!34 models
+> show #!26 models
+> fitmap #26 inMap #19
+Fit molecule C-Mcm2_6skl (#26) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5941 atoms
+average map value = 0.2499, steps = 40
+shifted from previous position = 0.00827
+rotated from previous position = 0.0158 degrees
+atoms outside contour = 4089, contour level = 0.3
+Position of C-Mcm2_6skl (#26) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.72508101 -0.17912737 -0.66495934 564.59530186
+.30560205 0.78160601 -0.54378253 172.54320727
+.61714254 -0.59749932 -0.51198599 374.71726789
+Axis -0.03915999 -0.93466297 0.35337179
+Axis point 195.28291115 0.00000000 339.45035239
+Rotation angle (degrees) 136.69646920
+Shift along axis -50.96478166
+> hide #!26 models
+> show #!27 models
+> fitmap #27 inMap #19
+Fit molecule C-Mcm3_6skl (#27) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5283 atoms
+average map value = 0.2453, steps = 48
+shifted from previous position = 0.00561
+rotated from previous position = 0.0144 degrees
+atoms outside contour = 3745, contour level = 0.3
+Position of C-Mcm3_6skl (#27) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.49119447 -0.10962931 -0.86412349 552.72708725
+.52963562 0.75000136 -0.39621215 105.24134461
+.69153026 -0.65228780 -0.31033293 328.08057761
+Axis -0.15052098 -0.91441153 0.37575921
+Axis point 161.25504150 0.00000000 351.58454506
+Rotation angle (degrees) 121.71962364
+Shift along axis -56.15162171
+> fitmap #27 inMap #19
+Fit molecule C-Mcm3_6skl (#27) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5283 atoms
+average map value = 0.2453, steps = 44
+shifted from previous position = 0.00644
+rotated from previous position = 0.00323 degrees
+atoms outside contour = 3747, contour level = 0.3
+Position of C-Mcm3_6skl (#27) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.49121423 -0.10960226 -0.86411569 552.72290598
+.52966978 0.74997300 -0.39622018 105.24674287
+.69149006 -0.65232495 -0.31034441 328.08956470
+Axis -0.15054136 -0.91440312 0.37577152
+Axis point 161.25087455 0.00000000 351.58379235
+Rotation angle (degrees) 121.72163061
+Shift along axis -56.15889268
+> hide #!27 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> fitmap #34 inMap #19
+Fit molecule C-Mcm7_6skl (#34) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5038 atoms
+average map value = 0.2488, steps = 40
+shifted from previous position = 0.021
+rotated from previous position = 0.0237 degrees
+atoms outside contour = 3683, contour level = 0.3
+Position of C-Mcm7_6skl (#34) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.60807905 -0.04366734 -0.79267461 541.74998075
+.49057375 0.76436052 -0.41843804 112.46427092
+.62416126 -0.64330876 -0.44336957 361.50164606
+Axis -0.14689577 -0.92554158 0.34899056
+Axis point 165.95199356 0.00000000 336.12532515
+Rotation angle (degrees) 130.05660056
+Shift along axis -57.51048000
+> hide #!34 models
+> show #!35 models
+> fitmap #35 inMap #19
+Fit molecule Cdc45_6skl (#35) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 9129 atoms
+average map value = 0.4936, steps = 32
+shifted from previous position = 0.989
+rotated from previous position = 0.293 degrees
+atoms outside contour = 3011, contour level = 0.3
+Position of Cdc45_6skl (#35) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.53238330 -0.10222439 -0.84030840 552.34452064
+.51398389 0.74970935 -0.41684104 113.43549525
+.67259838 -0.65382418 -0.34659105 340.11300103
+Axis -0.14356656 -0.91653277 0.37330461
+Axis point 163.36596759 0.00000000 349.77928908
+Rotation angle (degrees) 124.37677529
+Shift along axis -56.29979678
+> hide #!35 models
+> show #!36 models
+> fitmap #36 inMap #19
+Fit molecule GINS_6skl (#36) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 13385 atoms
+average map value = 0.5009, steps = 64
+shifted from previous position = 1.25
+rotated from previous position = 0.693 degrees
+atoms outside contour = 4520, contour level = 0.3
+Position of GINS_6skl (#36) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.53440728 -0.10575367 -0.83858514 554.21323619
+.51997798 0.74104668 -0.42482082 114.22988038
+.66635709 -0.66307314 -0.34103116 341.67599231
+Axis -0.14464380 -0.91365555 0.37988381
+Axis point 163.82286606 0.00000000 351.69409164
+Rotation angle (degrees) 124.55491640
+Shift along axis -54.73309110
+> hide #!36 models
+> show #!37 models
+> fitmap #37 inMap #19
+Fit molecule Ctf4_6skl (#37) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 20221 atoms
+average map value = 0.3967, steps = 68
+shifted from previous position = 1.75
+rotated from previous position = 0.685 degrees
+atoms outside contour = 7725, contour level = 0.3
+Position of Ctf4_6skl (#37) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.53679956 -0.10566869 -0.83706653 554.09013415
+.51701361 0.74282869 -0.42532631 116.11912844
+.66674070 -0.66108976 -0.34411796 343.05037030
+Axis -0.14335492 -0.91438332 0.37861921
+Axis point 163.58631600 0.00000000 352.06583111
+Rotation angle (degrees) 124.68361653
+Shift along axis -55.72348034
+> hide #!37 models
+> show #!38 models
+> fitmap #38 inMap #19
+Fit molecule Tof1_6skl (#38) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 10990 atoms
+average map value = 0.3486, steps = 52
+shifted from previous position = 2.71
+rotated from previous position = 2.1 degrees
+atoms outside contour = 4840, contour level = 0.3
+Position of Tof1_6skl (#38) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.50884095 -0.07790103 -0.85732860 546.87430545
+.52700003 0.75928729 -0.38177714 104.30156172
+.68069954 -0.64607604 -0.34530262 334.50800166
+Axis -0.15791244 -0.91893600 0.36141430
+Axis point 159.52485154 0.00000000 345.83620169
+Rotation angle (degrees) 123.19075103
+Shift along axis -61.30873983
+> hide #!38 models
+> show #!39 models
+> fitmap #39 inMap #19
+Fit molecule Csm3_6skl (#39) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 1616 atoms
+average map value = 0.3779, steps = 60
+shifted from previous position = 2.5
+rotated from previous position = 1.9 degrees
+atoms outside contour = 645, contour level = 0.3
+Position of Csm3_6skl (#39) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.51530602 -0.07349129 -0.85384937 547.02376900
+.53880358 0.74699785 -0.38946748 106.53379719
+.66644611 -0.66075203 -0.34533512 340.04339220
+Axis -0.16330007 -0.91514372 0.36857164
+Axis point 158.27460801 0.00000000 348.00938205
+Rotation angle (degrees) 123.83627701
+Shift along axis -61.49240111
+> hide #!39 models
+> show #!40 models
+> fitmap #40 inMap #19
+Fit molecule DNA_6skl (#40) to map cryosparc_P17_J842_005_volume_map_sharp.mrc
+(#19) using 1878 atoms
+average map value = 0.3403, steps = 80
+shifted from previous position = 1.35
+rotated from previous position = 3.78 degrees
+atoms outside contour = 831, contour level = 0.3
+Position of DNA_6skl (#40) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.47993510 -0.10126507 -0.87144001 550.20291579
+.51412450 0.77241029 -0.37290528 101.33591686
+.71087151 -0.62699899 -0.31864396 321.37532285
+Axis -0.14801492 -0.92172967 0.35847734
+Axis point 161.49135847 0.00000000 346.98780116
+Rotation angle (degrees) 120.86949809
+Shift along axis -59.63678931
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> combine #23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40
+Remapping chain ID '2' in C-Mcm2_6skl #26 to '5'
+Remapping chain ID '3' in C-Mcm3_6skl #27 to '6'
+Remapping chain ID '5' in N-Mcm5_6skl #28 to '7'
+Remapping chain ID '6' in N-Mcm6_6skl #29 to '8'
+Remapping chain ID '4' in C-Mcm4_6skl #30 to '9'
+Remapping chain ID '5' in C-Mcm5_6skl #31 to '0'
+Remapping chain ID '7' in N-Mcm7_6skl #32 to 'AA'
+Remapping chain ID '6' in C-Mcm6_6skl #33 to 'AB'
+Remapping chain ID '7' in C-Mcm7_6skl #34 to 'AC'
+> hide #!19 models
+> select add #41
+atoms, 119265 bonds, 97 pseudobonds, 7310 residues, 3 models selected
+> cartoon style (#!41 & sel) xsection oval modeHelix default
+> cartoon style (#!41 & sel) xsection rectangle modeHelix default
+> cartoon style (#!41 & sel & coil) xsection oval
+> cartoon style (#!41 & sel) xsection barbell modeHelix default
+> cartoon style (#!41 & sel) xsection oval modeHelix default
+> cartoon hide (#!41 & sel)
+> show (#!41 & sel) target ab
+> ui tool show "Color Zone"
+> select subtract #41
+Nothing selected
+> hide #!41 models
+> show #!19 models
+> color #19 #b2b2ffff models
+> volume copy #19
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc copy as #42, grid size
+,588,588, pixel 0.95, shown at step 1, values float32
+> hide #!42 models
+> show #!42 models
+> show #!41 models
+> hide #!41 models
+> ui tool show "Hide Dust"
+> surface dust #42 size 5.7
+> surface dust #42 size 5.67
+> surface dust #42 size 6.93
+> surface dust #42 size 7.1
+> surface dust #42 size 5.86
+> surface dust #42 size 5.91
+> surface dust #42 size 6.71
+> show #!41 models
+> color zone #42 near #41 distance 5.7
+> hide #!41 models
+> lighting soft
+> lighting simple
+> graphics silhouettes true
+> color zone #42 near #41 distance 5.8
+> color zone #42 near #41 distance 5.9
+> show #!41 models
+> color zone #42 near #41 distance 5.9
+> color zone #42 near #41 distance 6.2
+> color zone #42 near #41 distance 7.58
+> color zone #42 near #41 distance 6.79
+> color zone #42 near #41 distance 10.77
+> color zone #42 near #41 distance 11.05
+> color zone #42 near #41 distance 8.88
+> color zone #42 near #41 distance 10.95
+> color zone #42 near #41 distance 9.58
+> hide #!42 models
+> show #!42 models
+> color zone #42 near #41 distance 9.68
+> color zone #42 near #41 distance 9.6
+> color zone #42 near #41 distance 9
+> color zone #42 near #41 distance 9.9
+> color zone #42 near #41 distance 9.99
+> color zone #42 near #41 distance 10.42
+> color zone #42 near #41 distance 11.42
+> hide #!42 models
+> show #!42 models
+> lighting soft
+> hide #!41 models
+> hide #!42 models
+> show #!42 models
+> lighting simple
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+[Repeated 1 time(s)]
+\u2014\u2014\u2014 End of log from Wed Sep 4 05:32:36 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> show #!3 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> lighting full
+> lighting soft
+> lighting simple
+> show #2 models
+> hide #2 models
+> show #2 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!22 models
+> hide #!22 models
+> show #!1 models
+> ui tool show Matchmaker
+> matchmaker #1/I to #38/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker Tof1_6skl, chain X (#38) with 8xgc, chain I (#1), sequence
+alignment score = 5308.2
+RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
+.839)
+> hide #!3 models
+> show #!3 models
+> combine #1
+> hide #!1 models
+> show #!22 models
+> hide #!22 models
+> rename #22 8xgc_with_polE
+> hide #!43 models
+> show #!43 models
+> hide #!43 models
+> show #!43 models
+> select #43/L,M,P,Q,N,R,O,S
+atoms, 9480 bonds, 10 pseudobonds, 1379 residues, 2 models selected
+> hide (#!43 & sel) target a
+> cartoon hide (#!43 & sel)
+> hide #2 models
+> show #2 models
+> hide #2 models
+> cartoon (#!43 & sel)
+> delete atoms (#!43 & sel)
+> delete bonds (#!43 & sel)
+> hide #!43 models
+> show #!43 models
+> select #43/2,I
+atoms, 12460 bonds, 7 pseudobonds, 1525 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 50669 bonds, 146 pseudobonds, 6085 residues, 4 models selected
+> select #43/2,I,X,Y
+atoms, 14513 bonds, 93 pseudobonds, 1615 residues, 4 models selected
+> select ~sel & ##selected
+atoms, 48616 bonds, 60 pseudobonds, 5995 residues, 3 models selected
+> delete atoms (#!43 & sel)
+> delete bonds (#!43 & sel)
+> hide #!43 models
+> show #!43 models
+> rename #43 Tof1_Mcm2_DNA_8xgc
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> hide #!43 models
+> show #!43 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> ui tool show "Fit in Map"
+> hide #!3 models
+> show #!3 models
+> hide #!8 models
+> show #!8 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> fitmap #3 inMap #8
+Fit map cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc in map
+cryosparc_P17_J1163_006_volume_map.mrc using 193604 points
+correlation = 0.9192, correlation about mean = 0.0445, overlap = 1.418e+04
+steps = 72, shift = 2.72, angle = 2.42 degrees
+Position of cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) relative
+to cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
+Matrix rotation and translation
+.59052855 0.53373057 -0.60531621 170.37442141
+-0.50876033 -0.33602858 -0.79262080 554.64399601
+-0.62644949 0.77602608 0.07310647 351.56427577
+Axis 0.83279921 0.01121972 -0.55346146
+Axis point 0.00000000 138.28597245 467.32476580
+Rotation angle (degrees) 109.64532984
+Shift along axis -46.46664408
+> hide #!8 models
+> show #!232 models
+> hide #!232 models
+> show #!234 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> hide #!234 models
+> show #!234 models
+> hide #!3 models
+> show #!3 models
+> fitmap #234 inMap #3
+Fit molecule copy of 1id3 (#234) to map
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) using 6114 atoms
+average map value = 0.2545, steps = 96
+shifted from previous position = 4.78
+rotated from previous position = 8.84 degrees
+atoms outside contour = 2956, contour level = 0.25
+Position of copy of 1id3 (#234) relative to
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) coordinates:
+Matrix rotation and translation
+-0.05320350 -0.99827136 0.02497348 191.32301696
+-0.66299192 0.05401395 0.74667544 251.48569117
+-0.74673362 0.02316853 -0.66471958 182.33677195
+Axis -0.65199157 0.69542739 0.30213861
+Axis point 246.33178982 0.00000000 -20.06616176
+Rotation angle (degrees) 146.30004573
+Shift along axis 105.24002362
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> hide #!234 models
+> show #!177 models
+> hide #!177 models
+> show #!232 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> select #43/x
+atoms, 1159 bonds, 51 residues, 1 model selected
+> color sel black
+> select #43/y
+atoms, 894 bonds, 39 residues, 1 model selected
+> color sel gray
+> select clear
+> select #232/J
+atoms, 3354 bonds, 6 pseudobonds, 160 residues, 2 models selected
+> color (#!232 & sel) black
+> select #232/I
+atoms, 3354 bonds, 3 pseudobonds, 162 residues, 2 models selected
+> color (#!232 & sel) gray
+> select clear
+> select #232/A#232/E#234/A#234/E
+atoms, 3252 bonds, 410 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel khaki
+[Repeated 4 time(s)]
+> color sel peach puff
+> color sel moccasin
+[Repeated 1 time(s)]
+> color sel khaki
+[Repeated 4 time(s)]
+> select #232/B#232/F#234/B#234/F
+atoms, 2652 bonds, 346 residues, 2 models selected
+> color sel khaki
+[Repeated 1 time(s)]
+> select #232/C#232/G#234/C#234/G
+atoms, 3400 bonds, 4 pseudobonds, 462 residues, 4 models selected
+> color sel plum
+[Repeated 2 time(s)]
+> select #232/D#232/H#234/D#234/H
+atoms, 2988 bonds, 2 pseudobonds, 406 residues, 4 models selected
+> color sel plum
+> select clear
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> volume copy #3
+Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy as #44, grid
+size 440,440,440, pixel 0.95, shown at step 1, values float32
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!43 models
+> hide #!42 models
+> hide #!44 models
+> show #!44 models
+> hide #!232 models
+> show #!232 models
+> ui tool show "Color Zone"
+> hide #!44 models
+> show #!44 models
+> color zone #44 near #232 distance 5.7
+> hide #!232 models
+> lighting soft
+> show #!42 models
+> lighting soft
+> lighting full
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!43 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> select #43/2
+atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
+> color sel hot pink
+> select clear
+> ui tool show "Show Sequence Viewer"
+> sequence chain #43/I
+Alignment identifier is 43/I
+> select #43/2
+atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
+> cartoon hide (#!43 & sel)
+> lighting simple
+> lighting soft
+> show #!8 models
+> color #8 #d6d6d6ff models
+> color #8 #ebebebff models
+> color #8 #ebebeb80 models
+> color #8 silver models
+[Repeated 1 time(s)]
+> color #8 #c0c0c080 models
+> color #8 #c0c0c08b models
+> color #8 #c0c0c09e models
+> color #8 #c0c0c0f5 models
+> color #8 #c0c0c0f1 models
+> color #8 #c0c0c0ad models
+> color #8 #c0c0c0a1 models
+> color #8 #c0c0c0ab models
+> color #8 #c0c0c0ad models
+> color #8 #c0c0c0b4 models
+> color #8 #c0c0c0b6 models
+> color #8 #c0c0c0b9 models
+> color #8 #c0c0c0bd models
+> color #8 #c0c0c0c1 models
+> color #8 #c0c0c0bf models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> select #43/I:641
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #43/I:641-642
+atoms, 18 bonds, 2 residues, 1 model selected
+> select #43/I:649
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #43/I:649-650
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #43/I:630
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #43/I:630-631
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #43/I:618
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #43/I:618-619
+atoms, 21 bonds, 2 residues, 1 model selected
+> select #43/I:621
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:621-622
+atoms, 17 bonds, 2 residues, 1 model selected
+> select #43/I:616
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:616
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I
+atoms, 6171 bonds, 2 pseudobonds, 745 residues, 2 models selected
+> color sel slate blue
+[Repeated 1 time(s)]
+> color sel medium slate blue
+> color sel slate blue
+[Repeated 6 time(s)]
+> color sel medium slate blue
+> color sel medium orchid
+> color sel dark orchid
+> color sel magenta
+> color sel dark slate blue
+> color sel slate blue
+> color sel violet
+> color sel slate blue
+> color sel medium slate blue
+[Repeated 1 time(s)]
+> select clear
+> select #43/I:613
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #43/I:613-657
+atoms, 362 bonds, 45 residues, 1 model selected
+> color sel light coral
+> show #!8 models
+> hide #!8 models
+> select clear
+> select #43/I:613-657
+atoms, 362 bonds, 45 residues, 1 model selected
+> select #43/I:616
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:616
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:618
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #43/I:618-619
+atoms, 21 bonds, 2 residues, 1 model selected
+> select #43/I:616
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:616
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:616,618-619
+atoms, 29 bonds, 3 residues, 1 model selected
+> select #43/I:616,618-619,621-622
+atoms, 46 bonds, 5 residues, 1 model selected
+> show sel target ab
+> style sel ball
+Changed 49 atom styles
+> color sel dodger blue
+> color sel royal blue
+> color sel deep sky blue
+> style sel ball
+Changed 49 atom styles
+> style sel sphere
+Changed 49 atom styles
+> style sel stick
+Changed 49 atom styles
+> style sel ball
+Changed 49 atom styles
+> select clear
+> select #43/I:616,618-619,621-622,629
+atoms, 53 bonds, 6 residues, 1 model selected
+> select #43/I:616,618-619,621-622,629
+atoms, 53 bonds, 6 residues, 1 model selected
+> select
+> #43/I:12-31,51-65,72-80,82-109,117-136,146-170,173-188,195-215,244-271,278-295,298-303,330-353,379-395,407-412,430-461,468-493,497-523,526-550,556-565,568-576,584-606,626-638,640-653,658-680,686-702,712-724,733-756,758-763,773-780
+atoms, 4319 bonds, 523 residues, 1 model selected
+> select clear
+> select
+> #43/I:12-31,51-65,72-80,82-109,117-136,146-170,173-188,195-215,244-271,278-295,298-303,330-353,379-395,407-412,430-461,468-493,497-523,526-550,556-565,568-576,584-606,626-638,640-653,658-680,686-702,712-724,733-756,758-763,773-780
+atoms, 4319 bonds, 523 residues, 1 model selected
+> select clear
+> select #43/I:629
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #43/I:629
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #43/I:629,635-637
+atoms, 33 bonds, 4 residues, 1 model selected
+> select #43/I:629,635-637,640
+atoms, 40 bonds, 5 residues, 1 model selected
+> select #43/I:629,635-637,640,642-643
+atoms, 56 bonds, 7 residues, 1 model selected
+> select #43/I:629,635-637,640,642-643,646
+atoms, 63 bonds, 8 residues, 1 model selected
+> show sel target ab
+> color sel crimson
+> style sel ball
+Changed 68 atom styles
+> select clear
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> color #8 #00fdffff models
+> color #8 #73fdffff models
+> color #8 #009193ff models
+> color #8 #00fdffff models
+> color #8 #76d6ffff models
+> color #8 #00fdffff models
+> color #8 #76d6ffff models
+> color #8 #76d6ffd2 models
+> color #8 #76d6ff85 models
+> color #8 #76d6ff86 models
+> color #8 #76d6ffa6 models
+> color #8 #76d6ff80 models
+> lighting full
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> lighting soft
+> lighting full
+> lighting soft
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side.png
+> supersample 6 width 2000 transparentBackground true
+> lighting full
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side2.png
+> supersample 6 width 2000 transparentBackground true
+> hide #!43 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side2.png
+> supersample 6 width 2000 transparentBackground true
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting soft
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side.png
+> supersample 6 width 2000 transparentBackground true
+> hide #!42 models
+> hide #!44 models
+> show #!8 models
+> color #8 #76d6ffff models
+> lighting soft
+> lighting full
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side_single_map.png
+> supersample 6 width 2000 transparentBackground true
+> ui tool show "Hide Dust"
+> surface dust #8 size 5.7
+> surface dust #8 size 5.94
+> surface dust #8 size 8.07
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side_single_map.png
+> supersample 6 width 2000 transparentBackground true
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc
+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #45, grid size
+,588,588, pixel 0.95, shown at level 0.957, step 4, values float32
+> hide #!8 models
+> volume #45 step 1
+> show #!8 models
+> lighting simple
+> select add #8
+models selected
+> view sel
+> select subtract #8
+Nothing selected
+> hide #!8 models
+> show #!42 models
+> show #!44 models
+> show #!43 models
+> lighting soft
+> lighting full
+> lighting soft
+> lighting full
+> hide #!44 models
+> hide #!43 models
+> hide #!42 models
+> show #!45 models
+> hide #!45 models
+> show #!8 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_bottom-
+> up_single_map.png supersample 6 width 2000 transparentBackground true
+> hide #!8 models
+> show #!42 models
+> show #!44 models
+> show #!45 models
+> hide #!45 models
+> show #!43 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_bottom-
+> up_composite_map.png supersample 6 width 2000 transparentBackground true
+> hide #!44 models
+> hide #!43 models
+> hide #!42 models
+> show #!44 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> select add #232
+atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
+> ui mousemode right "rotate selected models"
+> select subtract #232
+Nothing selected
+> select add #232
+atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
+> view matrix models
+> #232,-0.029351,-0.99871,0.041463,192.22,-0.84724,0.046867,0.52914,242.8,-0.5304,-0.019599,-0.84752,167.58
+> view matrix models
+> #232,-0.020898,-0.996,0.086876,194.54,-0.84044,0.064565,0.53805,243.54,-0.54151,-0.06177,-0.83842,167.34
+> view matrix models
+> #232,-0.042506,-0.99356,0.10504,195.69,-0.86935,0.088592,0.48619,241.57,-0.49236,-0.070649,-0.86752,165.27
+> view matrix models
+> #232,-0.053907,-0.99204,0.11378,196.27,-0.88276,0.1006,0.45894,240.51,-0.46673,-0.0757,-0.88115,164.26
+> ui mousemode right "translate selected models"
+> view matrix models
+> #232,-0.053907,-0.99204,0.11378,197.1,-0.88276,0.1006,0.45894,241.87,-0.46673,-0.0757,-0.88115,162.33
+> view matrix models
+> #232,-0.053907,-0.99204,0.11378,197.14,-0.88276,0.1006,0.45894,241.9,-0.46673,-0.0757,-0.88115,162.25
+> select subtract #232
+Nothing selected
+> hide #!44 models
+> show #!44 models
+> fitmap #232 inMap #44
+Fit molecule 1id3 (#232) to map
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy (#44) using 12124
+atoms
+average map value = 0.2847, steps = 68
+shifted from previous position = 3.51
+rotated from previous position = 4.37 degrees
+atoms outside contour = 5383, contour level = 0.25
+Position of 1id3 (#232) relative to
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy (#44) coordinates:
+Matrix rotation and translation
+-0.03410625 -0.99613821 0.08090390 194.35377785
+-0.72343655 0.08045913 0.68568644 250.18361614
+-0.68954791 -0.03514264 -0.72338695 177.33095720
+Axis -0.66146232 0.70699818 0.25024222
+Axis point 246.51764404 0.00000000 -9.19791182
+Rotation angle (degrees) 146.98385179
+Shift along axis 92.69735224
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!177 models
+> hide #!177 models
+> show #!232 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+\u2014\u2014\u2014 End of log from Wed Sep 4 08:32:44 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1328_map_sharp_zflip.mrc
+Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
+pixel 0.95, shown at level 0.0365, step 2, values float32
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #46 step 1
+> volume #46 level 0.1209
+> volume #46 level 0.27
+> ui tool show "Fit in Map"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+[Repeated 1 time(s)]
+> fitmap #46 inMap #44
+Fit map cryosparc_P17_J1328_map_sharp_zflip.mrc in map
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy using 183011 points
+correlation = 0.9983, correlation about mean = 0.9843, overlap = 3.392e+04
+steps = 136, shift = 8.18, angle = 15.4 degrees
+Position of cryosparc_P17_J1328_map_sharp_zflip.mrc (#46) relative to
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy (#44) coordinates:
+Matrix rotation and translation
+.99999993 0.00020825 0.00029549 -0.11547030
+-0.00020819 0.99999995 -0.00022028 0.08133560
+-0.00029553 0.00022022 0.99999993 0.01845130
+Axis 0.52030825 0.69808953 -0.49188447
+Axis point 41.74969574 0.00000000 368.99527237
+Rotation angle (degrees) 0.02425404
+Shift along axis -0.01237652
+> ui tool show "Hide Dust"
+> surface dust #46 size 5.7
+> surface dust #46 size 5.88
+> surface dust #46 size 7.58
+> surface undust #46
+> surface dust #46 size 7.58
+> show #!234 models
+> hide #!234 models
+> hide #!232 models
+> show #!42 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1293_003_volume_map.mrc
+Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
+pixel 0.95, shown at level 0.131, step 4, values float32
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #47 step 1
+> volume #47 level 0.2274
+> select add #47
+models selected
+> lighting simple
+> ui mousemode right "translate selected models"
+> view matrix models #47,1,0,0,34.934,0,1,0,115.11,0,0,1,-196.72
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #47,0.80862,0.53112,-0.25306,75.22,-0.548,0.52343,-0.65247,630.75,-0.21408,0.66628,0.71431,-166.12
+> view matrix models
+> #47,-0.052033,0.59696,-0.80058,521.42,-0.88318,-0.4017,-0.24213,761.94,-0.46614,0.69446,0.54813,-35.04
+> view matrix models
+> #47,-0.56463,0.51635,-0.64387,621.88,-0.70577,-0.70651,0.052329,660.64,-0.42788,0.48397,0.76334,-85.832
+> view matrix models
+> #47,-0.64839,0.75691,-0.081716,371.53,-0.75724,-0.63011,0.17189,611.51,0.078617,0.17333,0.98172,-248.96
+> view matrix models
+> #47,-0.77683,0.61612,-0.13012,457.28,-0.62893,-0.76938,0.11179,628.86,-0.031234,0.16868,0.98518,-218.23
+> view matrix models
+> #47,0.12044,0.50172,0.8566,-162.62,-0.47586,-0.72811,0.49337,425.68,0.87123,-0.46705,0.15105,-7.2804
+> view matrix models
+> #47,0.92809,0.13752,0.34603,-111.13,-0.079004,-0.83541,0.54392,316.34,0.36388,-0.53214,-0.76447,512.58
+> view matrix models
+> #47,0.95173,-0.049595,-0.3029,179.09,0.060764,-0.93688,0.34433,377.51,-0.30086,-0.34611,-0.88865,710
+> view matrix models
+> #47,0.74227,-0.056059,-0.66775,384.14,0.082804,-0.98118,0.17442,448.01,-0.66497,-0.18476,-0.72366,713.19
+> view matrix models
+> #47,0.70283,0.024432,-0.71094,395.12,0.12328,-0.98847,0.0879,472.34,-0.7006,-0.14942,-0.69774,705.44
+> view matrix models
+> #47,0.054631,-0.15566,-0.9863,726.27,-0.030531,-0.98757,0.15417,489.48,-0.99804,0.02169,-0.058704,500.1
+> view matrix models
+> #47,0.60463,-0.27385,-0.74795,501.6,0.099908,-0.90554,0.41232,332.8,-0.79021,-0.32403,-0.52016,698.05
+> view matrix models
+> #47,0.52044,-0.22451,-0.82386,544.88,0.38474,-0.79968,0.46097,210.17,-0.76231,-0.55688,-0.32981,664.82
+> ui mousemode right "translate selected models"
+> color #47.1 light gray
+> view matrix models
+> #47,0.52044,-0.22451,-0.82386,558.57,0.38474,-0.79968,0.46097,110.43,-0.76231,-0.55688,-0.32981,702.7
+> view matrix models
+> #47,0.52044,-0.22451,-0.82386,437.12,0.38474,-0.79968,0.46097,87.569,-0.76231,-0.55688,-0.32981,677.12
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #47,0.56523,-0.45015,-0.69129,420.43,0.27696,-0.6858,0.67303,9.7394,-0.77705,-0.57187,-0.26296,658.06
+> ui mousemode right "translate selected models"
+> view matrix models
+> #47,0.56523,-0.45015,-0.69129,423.1,0.27696,-0.6858,0.67303,13.1,-0.77705,-0.57187,-0.26296,647.01
+> hide #!8 models
+> show #!8 models
+> fitmap #47 inMap #8
+Fit map cryosparc_P17_J1293_003_volume_map.mrc in map
+cryosparc_P17_J1163_006_volume_map.mrc using 254592 points
+correlation = 0.9671, correlation about mean = 0.6025, overlap = 1.762e+04
+steps = 160, shift = 4.19, angle = 15.7 degrees
+Position of cryosparc_P17_J1293_003_volume_map.mrc (#47) relative to
+cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
+Matrix rotation and translation
+.99987281 0.00432290 0.01535233 -6.92417661
+-0.00420416 0.99996106 -0.00775858 5.37169883
+-0.01538527 0.00769307 0.99985205 1.46498711
+Axis 0.43594765 0.86722038 -0.24057941
+Axis point 110.65380262 0.00000000 488.49257940
+Rotation angle (degrees) 1.01544392
+Shift along axis 1.28742242
+> select subtract #47
+Nothing selected
+> hide #!46 models
+> show #!18 models
+> hide #!18 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> color #16 #009193ff models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!8 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> fitmap #47 inMap #8
+Fit map cryosparc_P17_J1293_003_volume_map.mrc in map
+cryosparc_P17_J1163_006_volume_map.mrc using 254592 points
+correlation = 0.9671, correlation about mean = 0.6024, overlap = 1.762e+04
+steps = 48, shift = 0.0108, angle = 0.0117 degrees
+Position of cryosparc_P17_J1293_003_volume_map.mrc (#47) relative to
+cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
+Matrix rotation and translation
+.99987335 0.00426622 0.01533290 -6.90697298
+-0.00414464 0.99995979 -0.00795249 5.42282003
+-0.01536621 0.00788795 0.99985082 1.41490067
+Axis 0.44553022 0.86344648 -0.23656498
+Axis point 106.89545515 -0.00000000 488.26292061
+Rotation angle (degrees) 1.01860486
+Shift along axis 1.27033373
+> hide #!8 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!42 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!46 models
+> show #!46 models
+> fitmap #44 inMap #46
+Fit map cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy in map
+cryosparc_P17_J1328_map_sharp_zflip.mrc using 193604 points
+correlation = 0.9979, correlation about mean = 0.9843, overlap = 3.462e+04
+steps = 40, shift = 0.00361, angle = 0.00695 degrees
+Position of cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy (#44)
+relative to cryosparc_P17_J1328_map_sharp_zflip.mrc (#46) coordinates:
+Matrix rotation and translation
+.99999996 -0.00014217 -0.00023873 0.08639737
+.00014220 0.99999998 0.00013580 -0.05048921
+.00023872 -0.00013583 0.99999996 -0.02306461
+Axis -0.43914796 -0.77188188 0.45972540
+Axis point 78.23841730 0.00000000 344.27567005
+Rotation angle (degrees) 0.01772022
+Shift along axis -0.00957291
+> fitmap #44 inMap #46
+Fit map cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy in map
+cryosparc_P17_J1328_map_sharp_zflip.mrc using 193604 points
+correlation = 0.9979, correlation about mean = 0.9843, overlap = 3.462e+04
+steps = 40, shift = 0.000257, angle = 0.000437 degrees
+Position of cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy (#44)
+relative to cryosparc_P17_J1328_map_sharp_zflip.mrc (#46) coordinates:
+Matrix rotation and translation
+.99999996 -0.00014232 -0.00024540 0.08755876
+.00014235 0.99999998 0.00013952 -0.05131539
+.00024538 -0.00013955 0.99999996 -0.02371294
+Axis -0.44137314 -0.77620112 0.45022392
+Axis point 79.27979005 0.00000000 339.72277629
+Rotation angle (degrees) 0.01811329
+Shift along axis -0.00949115
+> hide #!44 models
+> show #!44 models
+> hide #!46 models
+> show #!46 models
+> hide #!44 models
+> show #!232 models
+> show #!234 models
+> hide #!232 models
+> fitmap #234 inMap #46
+Fit molecule copy of 1id3 (#234) to map
+cryosparc_P17_J1328_map_sharp_zflip.mrc (#46) using 6114 atoms
+average map value = 0.2627, steps = 48
+shifted from previous position = 0.184
+rotated from previous position = 0.919 degrees
+atoms outside contour = 3238, contour level = 0.27
+Position of copy of 1id3 (#234) relative to
+cryosparc_P17_J1328_map_sharp_zflip.mrc (#46) coordinates:
+Matrix rotation and translation
+-0.04201562 -0.99848675 0.03548092 191.85732882
+-0.66725181 0.05447399 0.74283754 251.20982793
+-0.74364623 0.00753607 -0.66853085 181.90203052
+Axis -0.65572927 0.69481226 0.29538966
+Axis point 247.93591832 0.00000000 -19.62380013
+Rotation angle (degrees) 145.89753760
+Shift along axis 102.46918037
+> hide #!46 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> show #!232 models
+> hide #!234 models
+> show #!234 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> ui tool show Matchmaker
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> matchmaker #232/A to #234/A pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker copy of 1id3, chain A (#234) with 1id3, chain A (#232), sequence
+alignment score = 617.3
+RMSD between 97 pruned atom pairs is 0.000 angstroms; (across all 97 pairs:
+.000)
+> hide #!234 models
+> show #!234 models
+> hide #!46 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!234 models
+> ui mousemode right zoom
+> select #232/C#232/G#234/C#234/G
+atoms, 3400 bonds, 4 pseudobonds, 462 residues, 4 models selected
+> ui tool show "Color Actions"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> color sel light goldenrod yellow
+> color sel light yellow
+[Repeated 15 time(s)]
+> color sel light goldenrod yellow
+[Repeated 1 time(s)]
+> color sel yellow
+[Repeated 10 time(s)]
+> color sel yellow green
+[Repeated 16 time(s)]
+> color sel lime
+> color sel yellow green
+[Repeated 7 time(s)]
+> select #232/D#232/H#234/D#234/H
+atoms, 2988 bonds, 2 pseudobonds, 406 residues, 4 models selected
+> select #232/D#232/H#234/D#234/H
+atoms, 2988 bonds, 2 pseudobonds, 406 residues, 4 models selected
+> color sel red
+> color sel dark red
+> color sel crimson
+> color sel orange red
+> color sel red
+[Repeated 1 time(s)]
+> color sel crimson
+[Repeated 1 time(s)]
+> color sel fire brick
+[Repeated 4 time(s)]
+> select #232/C#232/G#234/C#234/G
+atoms, 3400 bonds, 4 pseudobonds, 462 residues, 4 models selected
+> color sel gold
+[Repeated 3 time(s)]
+> color sel dark orange
+> color sel gold
+[Repeated 4 time(s)]
+> select #232/A#232/E#234/A#234/E
+atoms, 3252 bonds, 410 residues, 2 models selected
+> color sel dodger blue
+> color sel dark blue
+> color sel medium blue
+> color sel blue
+[Repeated 1 time(s)]
+> color sel deep sky blue
+[Repeated 1 time(s)]
+> color sel cyan
+> color sel deep sky blue
+> color sel light sky blue
+[Repeated 2 time(s)]
+> color sel sky blue
+[Repeated 1 time(s)]
+> color sel light steel blue
+[Repeated 4 time(s)]
+> color sel powder blue
+> color sel light steel blue
+[Repeated 11 time(s)]
+> color sel slate gray
+> color sel light slate gray
+> color sel cadet blue
+> color sel steel blue
+[Repeated 5 time(s)]
+> color sel blue
+[Repeated 3 time(s)]
+> color sel medium blue
+> color sel blue
+[Repeated 3 time(s)]
+> color sel dodger blue
+> color sel steel blue
+[Repeated 4 time(s)]
+> select #232/B#232/F#234/B#234/F
+atoms, 2652 bonds, 346 residues, 2 models selected
+> color sel medium aquamarine
+> color sel dark cyan
+> color sel medium aquamarine
+[Repeated 1 time(s)]
+> color sel dark cyan
+> color sel turquoise
+> color sel medium sea green
+[Repeated 2 time(s)]
+> color sel sea green
+[Repeated 1 time(s)]
+> color sel medium sea green
+[Repeated 1 time(s)]
+> color sel forest green
+> color sel medium sea green
+[Repeated 1 time(s)]
+> color sel forest green
+> color sel medium sea green
+[Repeated 3 time(s)]
+> select clear
+> show #!235 models
+> hide #!235 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!46 models
+> show #!46 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!46 models
+> color #47 #d3d3d381 models
+> color #47 #d6d6d6ff models
+> color #47 silver models
+> color #47 #c0c0c082 models
+> color #47 #c0c0c0c8 models
+> color #47 #c0c0c0c5 models
+> color #47 #c0c0c0c1 models
+> color #47 #c0c0c0be models
+> color #47 #c0c0c0c2 models
+> color #47 #c0c0c0c1 models
+> color #47 #c0c0c0be models
+> color #47 #c0c0c0c0 models
+> color #47 #c0c0c0bf models
+> hide #!232 models
+> show #!232 models
+> hide #!47 models
+> hide #!42 models
+> show #!42 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> show #!47 models
+> hide #!46 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> hide #!47 models
+> show #!47 models
+> hide #!46 models
+> hide #!47 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!232 models
+> show #!232 models
+> hide #!42 models
+> show #!42 models
+> show #!41 models
+> hide #!41 models
+> show #!41 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> hide #!41 models
+> show #!41 models
+> hide #!41 models
+> show #!41 models
+> hide #!41 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> show #!41 models
+> hide #!41 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> hide #!1 models
+> show #!1 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!22 models
+> hide #!22 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> show #!232 models
+> hide #!232 models
+> hide #!177 models
+> show #!41 models
+> hide #!41 models
+> show #!41 models
+> hide #!41 models
+> show #!38 models
+> hide #!38 models
+> show #!38 models
+> hide #!38 models
+> show #!38 models
+> hide #!38 models
+> matchmaker #1/I to #38/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker Tof1_6skl, chain X (#38) with 8xgc, chain I (#1), sequence
+alignment score = 5308.2
+RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
+.839)
+> matchmaker #1/I to #38/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker Tof1_6skl, chain X (#38) with 8xgc, chain I (#1), sequence
+alignment score = 5308.2
+RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
+.839)
+> matchmaker #1/I to #38/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker Tof1_6skl, chain X (#38) with 8xgc, chain I (#1), sequence
+alignment score = 5308.2
+RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
+.839)
+> matchmaker #1/I to #38/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker Tof1_6skl, chain X (#38) with 8xgc, chain I (#1), sequence
+alignment score = 5308.2
+RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
+.839)
+> show #!38 models
+> hide #!1 models
+> show #!1 models
+> hide #!38 models
+> show #!40 models
+> hide #!40 models
+> combine #1
+> hide #!48 models
+> show #!48 models
+> hide #!1 models
+> hide #!48 models
+> show #!48 models
+> select #48/X,Y
+atoms, 2053 bonds, 86 pseudobonds, 90 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 70556 bonds, 77 pseudobonds, 8899 residues, 3 models selected
+> delete atoms (#!48 & sel)
+> delete bonds (#!48 & sel)
+> hide #!48 models
+> show #!48 models
+> rename #48 DNA_8xgc
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> select #48/X
+atoms, 1159 bonds, 51 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel black
+> select #48/Y
+atoms, 894 bonds, 39 residues, 1 model selected
+> color sel gray
+> color sel dark gray
+> color sel dim gray
+> select clear
+> hide #!48 models
+> show #!48 models
+> hide #!48 models
+> show #!48 models
+> hide #!48 models
+> show #!48 models
+> hide #!40 models
+> show #!40 models
+> hide #!48 models
+> show #!48 models
+> hide #!48 models
+> show #!48 models
+> hide #!40 models
+> show #!40 models
+> hide #!48 models
+> hide #!40 models
+> show #!8 models
+> hide #!8 models
+> show #!19 models
+> hide #!19 models
+> show #!42 models
+> show #!48 models
+> fitmap #48 inMap #42
+Fit molecule DNA_8xgc (#48) to map cryosparc_P17_J842_005_volume_map_sharp.mrc
+copy (#42) using 1837 atoms
+average map value = 0.2869, steps = 136
+shifted from previous position = 2.41
+rotated from previous position = 2.94 degrees
+atoms outside contour = 1074, contour level = 0.3
+Position of DNA_8xgc (#48) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc copy (#42) coordinates:
+Matrix rotation and translation
+.97626723 0.21196039 0.04444217 20.25889577
+.20777495 -0.97457455 0.08386920 422.39463428
+.06108915 -0.07264478 -0.99548524 498.45034022
+Axis -0.99403982 -0.10572708 -0.02658227
+Axis point 0.00000000 219.96323566 240.74169709
+Rotation angle (degrees) 175.48464775
+Shift along axis -78.04663897
+> hide #!48 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> show #!234 models
+> hide #!234 models
+> show #!232 models
+> lighting soft
+> lighting full
+> lighting simple
+> lighting full
+> lighting soft
+[Repeated 3 time(s)]
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting full
+> lighting simple
+> lighting soft
+> lighting full
+> lighting soft
+> show #!234 models
+> hide #!232 models
+> hide #!42 models
+> show #!41 models
+> select #41/G
+atoms, 6778 bonds, 2 pseudobonds, 422 residues, 2 models selected
+> select #41/H,G,F
+atoms, 20476 bonds, 6 pseudobonds, 1271 residues, 2 models selected
+> select
+> #1/F#1/G#1/H#22/F#22/G#22/H#37/F#37/G#37/H#41/F#41/G#41/H#177/F#177/G#177/H
+atoms, 82328 bonds, 30 pseudobonds, 6355 residues, 10 models selected
+> color sel royal blue
+[Repeated 2 time(s)]
+> color sel slate gray
+> color sel royal blue
+> color sel deep sky blue
+> color sel royal blue
+> color sel light sky blue
+> color sel light blue
+> color sel powder blue
+> color sel deep sky blue
+[Repeated 2 time(s)]
+> color sel cyan
+> color sel deep sky blue
+[Repeated 2 time(s)]
+> color sel dark turquoise
+> color sel deep sky blue
+> color sel steel blue
+> color sel royal blue
+> color sel dodger blue
+> color sel deep sky blue
+[Repeated 8 time(s)]
+> select #1/I#22/I#38/X#41/X#43/I#177/X
+atoms, 51789 bonds, 27 pseudobonds, 4230 residues, 12 models selected
+> color sel medium slate blue
+[Repeated 1 time(s)]
+> color sel slate blue
+> color sel medium slate blue
+> color sel medium orchid
+> color sel dark slate blue
+> color sel medium slate blue
+> color sel slate blue
+> color sel medium slate blue
+> color sel indigo
+> color sel medium purple
+[Repeated 4 time(s)]
+> color sel medium slate blue
+> color sel medium purple
+> color sel medium slate blue
+[Repeated 1 time(s)]
+> color sel slate blue
+> color sel medium slate blue
+[Repeated 5 time(s)]
+> select clear
+> combine #1
+> hide #!49 models
+> show #!49 models
+> select #49/2
+atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 66320 bonds, 158 pseudobonds, 8209 residues, 4 models selected
+> delete atoms (#!49 & sel)
+> delete bonds (#!49 & sel)
+> rename #49 N-term-Mcm2_8xgc
+> select add #49
+atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
+> color sel hot pink
+> select clear
+> matchmaker #49/2 to #23/2 pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker N-Mcm2_6skl, chain 2 (#23) with N-term-Mcm2_8xgc, chain 2 (#49),
+sequence alignment score = 3482.9
+RMSD between 276 pruned atom pairs is 0.698 angstroms; (across all 293 pairs:
+.967)
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> ui tool show "Show Sequence Viewer"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> sequence chain #49/2
+Alignment identifier is 49/2
+> select #49/2:126
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #49/2:126-152
+atoms, 215 bonds, 27 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 6074 bonds, 5 pseudobonds, 753 residues, 3 models selected
+> delete atoms (#!49 & sel)
+> delete bonds (#!49 & sel)
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+\u2014\u2014\u2014 End of log from Fri Sep 6 16:21:36 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> show #!48 models
+> hide #!48 models
+> hide #!49 models
+> show #!49 models
+> rename #49 N-patch-Mcm2_8xgc
+> show #!43 models
+> hide #!43 models
+> show #!43 models
+> ui tool show Matchmaker
+> matchmaker #43/I to #38/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker Tof1_6skl, chain X (#38) with Tof1_Mcm2_DNA_8xgc, chain I (#43),
+sequence alignment score = 5320.2
+RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
+.839)
+> matchmaker #43/I to #38/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker Tof1_6skl, chain X (#38) with Tof1_Mcm2_DNA_8xgc, chain I (#43),
+sequence alignment score = 5320.2
+RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
+.839)
+> hide #!49 models
+> hide #!43 models
+> hide #!41 models
+> show #!178 models
+> hide #!178 models
+> open /Users/cvetkom/Documents/cryoSPARC/J842_005_volume_map_EMReady.mrc
+Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
+.95, shown at level 0.116, step 4, values float32
+> volume #50 level 3.037
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #50 step 1
+> volume #50 level 2.102
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> show #!9 models
+> hide #!9 models
+> show #!47 models
+> hide #!50 models
+> show #!50 models
+> show #!42 models
+> select add #50
+models selected
+> lighting simple
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> view matrix models #50,1,0,0,-65.632,0,1,0,-229.59,0,0,1,71.364
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #50,0.4343,-0.44532,0.78299,-22.581,0.48395,0.84849,0.21414,-387.73,-0.75972,0.28593,0.58401,330.58
+> ui mousemode right "move picked models"
+> view matrix models
+> #50,0.4343,-0.44532,0.78299,26.602,0.48395,0.84849,0.21414,-312.09,-0.75972,0.28593,0.58401,140.59
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #50,0.61953,-0.0088021,0.78493,-144.45,0.53432,0.73727,-0.41346,-106.79,-0.57506,0.67555,0.46146,19.955
+> ui mousemode right "translate selected models"
+> view matrix models
+> #50,0.61953,-0.0088021,0.78493,-121.97,0.53432,0.73727,-0.41346,-120.25,-0.57506,0.67555,0.46146,29.342
+> view matrix models
+> #50,0.61953,-0.0088021,0.78493,-138.14,0.53432,0.73727,-0.41346,-168.26,-0.57506,0.67555,0.46146,-2.6429
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #50,0.59893,-0.097848,0.7948,-111.13,0.56367,0.7565,-0.33163,-206.33,-0.56881,0.64663,0.50825,-10.607
+> ui mousemode right zoom
+> ui tool show "Fit in Map"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+[Repeated 1 time(s)]
+> select add #47
+models selected
+> select subtract #47
+models selected
+> hide #!47 models
+> show #!47 models
+> select subtract #50
+Nothing selected
+> select add #50
+models selected
+> select subtract #50
+Nothing selected
+> hide #!50 models
+> show #!50 models
+> hide #!42 models
+> show #!42 models
+> fitmap #50 inMap #42
+Fit map J842_005_volume_map_EMReady.mrc in map
+cryosparc_P17_J842_005_volume_map_sharp.mrc copy using 773474 points
+correlation = 0.9586, correlation about mean = 0.8187, overlap = 1.895e+06
+steps = 176, shift = 18.3, angle = 13 degrees
+Position of J842_005_volume_map_EMReady.mrc (#50) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc copy (#42) coordinates:
+Matrix rotation and translation
+.00000000 0.00008926 0.00001426 -0.02716721
+-0.00008926 1.00000000 0.00004509 0.03060850
+-0.00001425 -0.00004509 1.00000000 0.00885891
+Axis -0.44634943 0.14111659 -0.88366187
+Axis point 329.25912566 261.27343201 0.00000000
+Rotation angle (degrees) 0.00578781
+Shift along axis 0.00861716
+> hide #!42 models
+> show #!46 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> volume #47 level 0.3135
+> volume #47 level 0.3842
+> hide #!46 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> volume #47 level 0.3043
+> volume #47 level 0.2735
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!46 models
+> ui mousemode right "map eraser"
+> hide #!47 models
+> show #!47 models
+> hide #!50 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_2.cxs
+> volume erase #47 center 193.29,217.64,214.85 radius 57.536
+Opened cryosparc_P17_J1293_003_volume_map.mrc copy as #52, grid size
+,588,588, pixel 0.95, shown at step 1, values float32
+> hide #!52 models
+> show #!52 models
+> hide #!52 models
+> show #!52 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!46 models
+> show #!42 models
+> hide #!42 models
+> show #!50 models
+> hide #!52 models
+> show #!52 models
+> close #52
+> show #!49 models
+> hide #!49 models
+> show #!49 models
+> hide #!49 models
+> show #!47 models
+> hide #!46 models
+> hide #!50 models
+> volume erase #47 center 179.18,226.56,216.65 radius 57.536
+Opened cryosparc_P17_J1293_003_volume_map.mrc copy as #52, grid size
+,588,588, pixel 0.95, shown at step 1, values float32
+> hide #51 models
+> show #!46 models
+> volume add #46,52
+Opened volume sum as #53, grid size 1018,965,865, pixel 0.95, shown at step 1,
+values float32
+> volume #53 level 0.3701
+> volume #53 level 0.4202
+> volume #53 level 0.4569
+> volume #53 level 0.5103
+> select add #53
+models selected
+> close #53
+> show #51 models
+> hide #51 models
+> show #!50 models
+> show #!48 models
+> hide #!48 models
+> hide #!234 models
+> show #!47 models
+> volume add #47,50
+Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at step 1,
+values float32
+> volume #53 level 0.3458
+> volume #53 level 0.4721
+> volume #53 level 0.3819
+> volume #53 level 0.2374
+> volume #53 level 0.2555
+[Repeated 1 time(s)]
+> show #!47 models
+> hide #!47 models
+> show #!46 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> show #!232 models
+> hide #!234 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+> close #45,236
+> show #!235 models
+> close #235
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!178 models
+> hide #!178 models
+> close #178-179
+> show #!52 models
+> hide #!52 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> hide #!46 models
+> show #!46 models
+> show #!47 models
+> hide #!47 models
+> hide #!46 models
+> show #!46 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> close #44
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!21 models
+> hide #!21 models
+> show #!20 models
+> hide #!20 models
+> close #16-21
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> close #15
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> show #!13 models
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> hide #!13 models
+> show #!13 models
+> hide #!14 models
+> show #!12 models
+> hide #!12 models
+> close #12
+> show #!14 models
+> hide #!14 models
+> hide #!46 models
+> hide #!53 models
+> hide #!232 models
+> show #!234 models
+> hide #!234 models
+> show #!232 models
+> color #13 #b2ffff7e models
+> color #13 #b2ffffb3 models
+> color #13 #b2ffffc2 models
+> close #23-40
+> show #!22 models
+> close #22
+> show #!1 models
+> hide #!1 models
+> show #2 models
+> select add #2
+atoms, 25142 bonds, 1555 residues, 1 model selected
+> close #2
+> show #!11 models
+> hide #!11 models
+> close #11
+> show #!10 models
+> close #10
+> show #!9 models
+> hide #!9 models
+> close #9
+> show #!8 models
+> show #!7 models
+> hide #!8 models
+> close #7
+> show #!6 models
+> close #6
+> show #!5 models
+> close #5
+> show #!4 models
+> close #4
+> show #!8 models
+> hide #!8 models
+> show #!3 models
+> close #3
+> show #!1 models
+> hide #!1 models
+> show #!8 models
+> hide #!8 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!232 models
+> rename #234 histones
+> show #!233 models
+> hide #!234 models
+> show #!46 models
+> hide #!233 models
+> show #!233 models
+> hide #!13 models
+> hide #!233 models
+> show #!233 models
+> hide #!46 models
+> show #!46 models
+> hide #!233 models
+> show #!233 models
+> hide #!46 models
+> color #233 #b2b2b27c models
+> show #!232 models
+> color #233 #b2b2b27d models
+> show #!41 models
+> hide #!41 models
+> show #!14 models
+> hide #!233 models
+> hide #!14 models
+> show #!13 models
+> close #14
+> show #!8 models
+> hide #!13 models
+> hide #!8 models
+> rename #1 Zhai
+> show #!8 models
+> rename #8 consensus_extended.mrc
+> show #!13 models
+> hide #!8 models
+> rename #13 "deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z
+> flip"
+> show #!41 models
+> hide #!13 models
+> hide #!41 models
+> show #!41 models
+> rename #41 fitted_replisome
+> show #!42 models
+> hide #!41 models
+> rename #42 "sharpened_replisome.mrc copy"
+> show #!43 models
+> hide #!42 models
+> hide #!232 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> show #!233 models
+> hide #!46 models
+> show #!13 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!233 models
+> hide #!232 models
+> show #!232 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> show #!41 models
+> hide #!41 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> rename #233 hetero_ref_good_nucleosome.mrc
+> hide #!232 models
+> show #!232 models
+> rename #232 full_nucleosome
+> show #!177 models
+> hide #!232 models
+> hide #!233 models
+> rename #177 Baretic
+> show #!53 models
+> hide #!177 models
+> show #!52 models
+> hide #!53 models
+> hide #!52 models
+> show #!52 models
+> hide #!52 models
+> show #!52 models
+> hide #!46 models
+> hide #!43 models
+> hide #!13 models
+> rename #52 bad_nucleosome
+> show #!50 models
+> volume add #47,50
+Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at step 1,
+values float32
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+> hide #!53 models
+> hide #!52 models
+> close #51
+> show #!50 models
+> hide #!2 models
+> show #!49 models
+> hide #!50 models
+> ui mousemode right zoom
+> close #3
+> show #!41 models
+> combine #41 #49
+Remapping chain ID '2' in N-patch-Mcm2_8xgc #49 to 'AD'
+> close #41
+> close #49
+> hide #!3 models
+> show #!3 models
+> rename #3 full_replisome
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> close #4
+> show #!233 models
+> select ~sel & ##selected
+Nothing selected
+> select ~sel & ##selected
+Nothing selected
+> select ~sel & ##selected
+Nothing selected
+> select ~sel & ##selected
+Nothing selected
+> select ~sel & ##selected
+Nothing selected
+> color #233 #b2b2b2ff models
+> hide #!2 models
+> hide #!3 models
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> hide #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!8 models
+> hide #!8 models
+> show #!13 models
+> hide #!233 models
+> show #!2 models
+> show #!232 models
+> combine #232
+> rename #4 trimmed_nucleosome
+> hide #!2 models
+> select #13
+models selected
+> view sel
+> select #232/I:21
+atoms, 21 bonds, 1 residue, 1 model selected
+> ui tool show "Show Sequence Viewer"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> sequence chain #232/I
+Alignment identifier is 232/I
+> sequence chain #232/J
+Alignment identifier is 232/J
+> select #232/I:21
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #232/I:1-21
+atoms, 472 bonds, 21 residues, 1 model selected
+> hide #!4 models
+> show #!4 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> delete atoms sel
+> delete bonds sel
+> select #232/J:292
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #232/J:255-292
+atoms, 882 bonds, 38 residues, 1 model selected
+> hide #!232 models
+> hide #!4 models
+> show #!4 models
+> rename #4 full_nucleosome
+> rename #232 trimmed_nucleosome
+> show #!232 models
+> hide #!4 models
+> combine #232/I,J
+> hide sel atoms
+> hide sel cartoons
+[Repeated 1 time(s)]
+> show #232/I,J
+> undo
+> select ~sel & ##selected
+atoms, 11499 bonds, 188 pseudobonds, 1075 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 882 bonds, 38 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 11499 bonds, 188 pseudobonds, 1075 residues, 3 models selected
+> select #232/I,J
+atoms, 6235 bonds, 185 pseudobonds, 301 residues, 3 models selected
+> hide sel cartoons
+> show sel atoms
+> hide sel atoms
+> show sel cartoons
+> show sel atoms
+> style sel ball
+Changed 5588 atom styles
+> select #232/J:162
+atoms, 20 bonds, 1 residue, 1 model selected
+> select #232/J:162
+atoms, 20 bonds, 1 residue, 1 model selected
+> select #232/J:147-162
+atoms, 355 bonds, 16 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> close #5
+> show #!4 models
+> hide #!4 models
+> undo
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> undo
+[Repeated 5 time(s)]
+> close #232
+> show #!4 models
+> combine #4
+> rename #5 trimmedfull_nucleosome
+> rename #5 trimmed_nucleosome
+> show #!13 models
+> select #4/I,J
+atoms, 6708 bonds, 217 pseudobonds, 322 residues, 3 models selected
+> show sel atoms
+> style sel ball
+Changed 6010 atom styles
+> select clear
+> select #4/I:20@O4
+atom, 1 residue, 1 model selected
+> select clear
+> select #4/I:20@C7
+atom, 1 residue, 1 model selected
+> select add #4/J:274@O2
+atoms, 2 residues, 1 model selected
+> ui tool show "Show Sequence Viewer"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> sequence chain #5/I
+Alignment identifier is 5/I
+> sequence chain #5/J
+Alignment identifier is 5/J
+> hide #!4 models
+> select #5/I,J
+atoms, 6708 bonds, 217 pseudobonds, 322 residues, 3 models selected
+> show sel atoms
+> style sel ball
+Changed 6010 atom styles
+> select #5/I:20@C7
+atom, 1 residue, 1 model selected
+> select add #5/J:274@C7
+atoms, 2 residues, 1 model selected
+> select #5/J:274
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #5/J:274-292
+atoms, 441 bonds, 19 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select #5/I:21
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #5/I:1-21
+atoms, 472 bonds, 21 residues, 1 model selected
+> select #5/I:20
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #5/I:1-20
+atoms, 450 bonds, 20 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> show #!1 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> color #2 white models
+> color #2 #ffffff83 models
+> color #2 #ffffff82 models
+> show #!48 models
+> hide #!1 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> select add #48
+atoms, 2053 bonds, 86 pseudobonds, 90 residues, 2 models selected
+> show sel atoms
+> style sel ball
+Changed 1837 atom styles
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!2 models
+> select #48/X:25
+atoms, 23 bonds, 1 residue, 1 model selected
+> select add #5/I:93
+atoms, 44 bonds, 2 residues, 2 models selected
+> select add #48/X:14
+atoms, 65 bonds, 3 residues, 2 models selected
+> select add #48/Y:37
+atoms, 86 bonds, 4 residues, 2 models selected
+> select add #48/Y:48
+atoms, 109 bonds, 5 residues, 2 models selected
+> combine #48
+> rename #6 Zhai_DNA_trimmed
+> ui tool show "Show Sequence Viewer"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> sequence chain #6/X
+Alignment identifier is 6/X
+> sequence chain #6/Y
+Alignment identifier is 6/Y
+> rename #6 Zhai_DNA
+> rename #48 Zhai_DNA_trimmed
+> ui tool show "Show Sequence Viewer"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> sequence chain #48/X
+Alignment identifier is 48/X
+> sequence chain #48/Y
+Alignment identifier is 48/Y
+> select #48/X:14
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #48/X:14-25
+atoms, 273 bonds, 12 residues, 1 model selected
+> select #48/X:13
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #48/X:9-13
+atoms, 115 bonds, 5 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select #48/X:26
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #48/X:26-59
+atoms, 769 bonds, 34 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select #48/Y:32
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #48/Y:15-32
+atoms, 410 bonds, 18 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select #48/Y:49
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #48/Y:49-53
+atoms, 113 bonds, 5 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> hide #!6 models
+> ui tool show "Fit in Map"
+> show #!2 models
+> ui tool show "Fit in Map"
+> fitmap #48 inMap #2
+Fit molecule Zhai_DNA_trimmed (#48) to map volume sum (#2) using 574 atoms
+average map value = 4.031, steps = 592
+shifted from previous position = 14.2
+rotated from previous position = 167 degrees
+atoms outside contour = 5, contour level = 0.27354
+Position of Zhai_DNA_trimmed (#48) relative to volume sum (#2) coordinates:
+Matrix rotation and translation
+-0.91975243 -0.27575503 0.27931101 510.33728112
+-0.23429189 -0.18521113 -0.95436061 602.17741898
+.31490125 -0.94321578 0.10574123 368.51075021
+Axis 0.19984288 -0.63818439 0.74349412
+Axis point 200.04559281 464.04730525 0.00000000
+Rotation angle (degrees) 178.40215888
+Shift along axis -8.32738387
+> volume #52 level 0.3197
+> volume #2 level 0.9596
+> volume #2 level 1.05
+> hide #!2 models
+> ui tool show Matchmaker
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> matchmaker #48/X to #1/6 pairing ss
+Match chain (Zhai_DNA_trimmed (#48) chain X) not compatible with BLOSUM-62
+similarity matrix
+> close #48
+> show #!6 models
+> combine #6
+> hide #!3 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> select add #3
+atoms, 119480 bonds, 97 pseudobonds, 7337 residues, 3 models selected
+> select add #5
+atoms, 131441 bonds, 284 pseudobonds, 8432 residues, 6 models selected
+> ui tool show "Color Zone"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> color zone #2 near #3 distance 2.68
+> select clear
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> select add #5
+atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 3 models selected
+> select add #2
+atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 5 models selected
+> color zone #2 near sel distance 2.68
+[Repeated 1 time(s)]
+> hide #!3 models
+> hide #!5 models
+> show #!5 models
+> hide #!2 models
+> show #!2 models
+> show #!3 models
+> hide #!52 models
+> hide #!13 models
+> select subtract #5
+models selected
+> select add #5
+atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 5 models selected
+> select subtract #2
+atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 3 models selected
+> select add #2
+atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 5 models selected
+> select subtract #2
+atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 3 models selected
+> select add #2
+atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 5 models selected
+> select subtract #2
+atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 3 models selected
+> select add #3
+atoms, 131441 bonds, 284 pseudobonds, 8432 residues, 6 models selected
+> color zone #2 near sel distance 2.68
+> hide #!5 models
+> hide #!3 models
+> volume #233 level 2.785
+> volume #2 level 1.357
+> volume #2 level 0.8512
+> volume #2 level 0.4721
+> volume #2 level 0.3096
+> color zone #2 near sel distance 5
+> color zone #2 near sel distance 3
+> color zone #2 near sel distance 3.5
+> color zone #2 near sel distance 4
+[Repeated 1 time(s)]
+> volume splitbyzone #2
+Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 1 as #9.2, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 2 as #9.3, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 3 as #9.4, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 4 as #9.5, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 5 as #9.6, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 6 as #9.7, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 7 as #9.8, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 8 as #9.9, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 9 as #9.10, grid size 636,840,859, pixel 0.95, shown at
+level 0.31, step 1, values float32
+Opened volume sum 10 as #9.11, grid size 636,840,859, pixel 0.95, shown at
+level 0.31, step 1, values float32
+Opened volume sum 11 as #9.12, grid size 636,840,859, pixel 0.95, shown at
+level 0.31, step 1, values float32
+Opened volume sum 12 as #9.13, grid size 636,840,859, pixel 0.95, shown at
+level 0.31, step 1, values float32
+Opened volume sum 13 as #9.14, grid size 636,840,859, pixel 0.95, shown at
+level 0.31, step 1, values float32
+Opened volume sum 14 as #9.15, grid size 636,840,859, pixel 0.95, shown at
+level 0.31, step 1, values float32
+Opened volume sum 15 as #9.16, grid size 636,840,859, pixel 0.95, shown at
+level 0.31, step 1, values float32
+Opened volume sum 16 as #9.17, grid size 636,840,859, pixel 0.95, shown at
+level 0.31, step 1, values float32
+Opened volume sum 17 as #9.18, grid size 636,840,859, pixel 0.95, shown at
+level 0.31, step 1, values float32
+> close #9.2-18
+> show #!3 models
+> hide #!3 models
+> show #!5 models
+> hide #!5 models
+> show #!3 models
+> hide #!9.1 models
+> hide #!9 models
+> select #6/X:25
+atoms, 23 bonds, 1 residue, 1 model selected
+> select add #6/Y:37@C3'
+atoms, 23 bonds, 2 residues, 1 model selected
+> select add #6/Y:38
+atoms, 43 bonds, 3 residues, 1 model selected
+> select subtract #6/Y:37
+atoms, 43 bonds, 2 residues, 1 model selected
+> hide #!7 models
+> show #!7 models
+> hide #!6 models
+> show #!6 models
+> hide #!7 models
+> ui tool show "Show Sequence Viewer"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> sequence chain #6/X
+Alignment identifier is 6/X
+> sequence chain #6/Y
+Alignment identifier is 6/Y
+> select #6/X:26
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #6/X:26-59
+atoms, 769 bonds, 34 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select #6/Y:34
+atoms, 20 bonds, 1 residue, 1 model selected
+> select #6/Y:34-53
+atoms, 461 bonds, 20 residues, 1 model selected
+> select #6/Y:36
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #6/Y:36-53
+atoms, 415 bonds, 18 residues, 1 model selected
+> select #6/Y:39
+atoms, 24 bonds, 1 residue, 1 model selected
+> select #6/Y:39-53
+atoms, 348 bonds, 15 residues, 1 model selected
+> show #!7 models
+> hide #!6 models
+> hide #!7 models
+> show #!6 models
+> show #!7 models
+> hide #!7 models
+> select #6/Y:38
+atoms, 20 bonds, 1 residue, 1 model selected
+> select #6/Y:15-38
+atoms, 545 bonds, 24 residues, 1 model selected
+> hide #!3 models
+> select #6/Y:36
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #6/Y:15-36
+atoms, 502 bonds, 22 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> show #!9.1 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> select #6/X:15
+atoms, 21 bonds, 1 residue, 1 model selected
+> select clear
+> select #6/X:14
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #6/X:13
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #6/X:9-13
+atoms, 115 bonds, 5 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select #6/Y:53
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #6/Y:49-53
+atoms, 113 bonds, 5 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> ui tool show "Fit in Map"
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> fitmap #6 inMap #9.1
+Fit molecule Zhai_DNA (#6) to map volume sum 0 (#9.1) using 492 atoms
+average map value = 2.428, steps = 112
+shifted from previous position = 2.38
+rotated from previous position = 20.2 degrees
+atoms outside contour = 57, contour level = 0.30965
+Position of Zhai_DNA (#6) relative to volume sum 0 (#9.1) coordinates:
+Matrix rotation and translation
+.84252921 0.47835125 0.24763810 -39.97421560
+-0.52899667 0.64815172 0.54777905 144.67789487
+.10152374 -0.59251958 0.79913296 198.24507755
+Axis -0.74601377 0.09559191 -0.65903387
+Axis point 0.00000000 273.04359310 -103.91847500
+Rotation angle (degrees) 49.84130149
+Shift along axis -86.99886895
+> show #!3 models
+> show #!5 models
+> select #5/I
+atoms, 2903 bonds, 3 pseudobonds, 142 residues, 2 models selected
+> color (#!5 & sel) black
+> select #5/J
+atoms, 2912 bonds, 5 pseudobonds, 141 residues, 2 models selected
+> color (#!5 & sel) dim gray
+> select clear
+> show #!1 models
+> hide #!1 models
+> hide #!3 models
+> show #!3 models
+> select add #3
+atoms, 119480 bonds, 97 pseudobonds, 7337 residues, 3 models selected
+> hide sel atoms
+> show sel cartoons
+> select clear
+> hide #!9.1 models
+> hide #!9 models
+> show #!2 models
+> show #!13 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> combine #3 #6 #5
+Remapping chain ID 'X' in Zhai_DNA #6 to 'Z'
+Remapping chain ID 'Y' in Zhai_DNA #6 to 'a'
+Remapping chain ID 'A' in trimmed_nucleosome #5 to 'K'
+Remapping chain ID 'B' in trimmed_nucleosome #5 to 'L'
+Remapping chain ID 'C' in trimmed_nucleosome #5 to 'M'
+Remapping chain ID 'D' in trimmed_nucleosome #5 to 'N'
+Remapping chain ID 'E' in trimmed_nucleosome #5 to 'O'
+Remapping chain ID 'F' in trimmed_nucleosome #5 to 'P'
+Remapping chain ID 'G' in trimmed_nucleosome #5 to 'Q'
+Remapping chain ID 'H' in trimmed_nucleosome #5 to 'R'
+Remapping chain ID 'I' in trimmed_nucleosome #5 to 'S'
+Remapping chain ID 'J' in trimmed_nucleosome #5 to 'T'
+> hide #!10 models
+> show #!10 models
+> hide #!2 models
+> hide #!3 models
+> hide #!5 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> show #!2 models
+> close #6-7
+> rename #10 extended_structure
+> hide #!10 models
+> show #!10 models
+> select add #10
+atoms, 131991 bonds, 312 pseudobonds, 8456 residues, 4 models selected
+> color zone #2 near sel distance 4.25
+> color zone #2 near sel distance 53.56
+[Repeated 1 time(s)]
+> select clear
+> volume #2 level 0.1833
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+> show #!43 models
+> hide #!43 models
+> show #!43 models
+> hide #!43 models
+> show #!43 models
+> hide #!13 models
+> hide #!10 models
+> hide #!2 models
+Drag select of 6 atoms, 7 residues, 5 bonds
+Drag select of 1 atoms, 4 residues, 1 bonds
+Drag select of 48 atoms, 44 residues, 38 bonds
+Drag select of 66 atoms, 50 residues, 55 bonds
+> select #43/X,Y
+atoms, 2053 bonds, 86 pseudobonds, 90 residues, 2 models selected
+> delete atoms (#!43 & sel)
+> delete bonds (#!43 & sel)
+> show #!2 models
+> hide #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> select #43/I:606
+atoms, 5 bonds, 1 residue, 1 model selected
+> select add #43/I:657
+atoms, 11 bonds, 2 residues, 1 model selected
+> hide #!3 models
+> select clear
+Drag select of 35 atoms, 28 residues, 30 bonds
+Drag select of 14 atoms, 18 residues, 11 bonds
+Drag select of 8 residues
+> select ~sel & ##selected
+atoms, 12085 bonds, 7 pseudobonds, 1480 residues, 3 models selected
+> cartoon hide (#!43 & sel)
+> cartoon (#!43 & sel)
+> ui tool show "Show Sequence Viewer"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> sequence chain #43/I
+Alignment identifier is 43/I
+> select #43/I:605-606
+atoms, 18 bonds, 2 residues, 1 model selected
+> select #43/I:11-606
+atoms, 4671 bonds, 2 pseudobonds, 570 residues, 2 models selected
+> cartoon hide (#!43 & sel)
+> delete atoms (#!43 & sel)
+> delete bonds (#!43 & sel)
+> select #43/I:658
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #43/I:658-781
+atoms, 1089 bonds, 124 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select add #43
+atoms, 6698 bonds, 5 pseudobonds, 831 residues, 3 models selected
+> select #43/2
+atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
+> delete atoms (#!43 & sel)
+> delete bonds (#!43 & sel)
+Drag select of 78 atoms, 55 residues, 65 bonds
+> color sel red
+> combine #43,3
+Remapping chain ID 'I' in full_replisome #3 to 'K'
+> hide #!6 models
+> show #!6 models
+> close #3
+> rename #6 full_replisome
+> combine #5,6
+Remapping chain ID 'A' in full_replisome #6 to 'L'
+Remapping chain ID 'B' in full_replisome #6 to 'M'
+Remapping chain ID 'C' in full_replisome #6 to 'N'
+Remapping chain ID 'D' in full_replisome #6 to 'O'
+Remapping chain ID 'E' in full_replisome #6 to 'P'
+Remapping chain ID 'F' in full_replisome #6 to 'Q'
+Remapping chain ID 'G' in full_replisome #6 to 'R'
+Remapping chain ID 'H' in full_replisome #6 to 'S'
+Remapping chain ID 'I' in full_replisome #6 to 'T'
+Remapping chain ID 'J' in full_replisome #6 to 'U'
+> close #10
+> rename #3 extended_structure
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_2.cxs
+\u2014\u2014\u2014 End of log from Fri Sep 6 19:04:03 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> open /Users/cvetkom/Desktop/extended_structure_old.pdb
+Chain information for extended_structure_old.pdb #7
+---
+Chain | Description
+7 | No description available
+5 AD | No description available
+6 | No description available
+9 | No description available
+AB | No description available
+A | No description available
+AA AC | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F G H | No description available
+I | No description available
+J | No description available
+K O | No description available
+L P | No description available
+M Q | No description available
+N R | No description available
+S T | No description available
+X | No description available
+Y | No description available
+Z | No description available
+a | No description available
+> ui tool show Matchmaker
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> matchmaker #7/2 to #3/2 pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain 2 (#3) with extended_structure_old.pdb,
+chain 2 (#7), sequence alignment score = 3554.3
+RMSD between 293 pruned atom pairs is 0.000 angstroms; (across all 293 pairs:
+.000)
+> select #7/a,Z
+atoms, 550 bonds, 24 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 131441 bonds, 58 pseudobonds, 8432 residues, 3 models selected
+> delete atoms (#!7 & sel)
+> delete bonds (#!7 & sel)
+> select #7/a
+atoms, 277 bonds, 12 residues, 1 model selected
+> color sel dim gray
+> select #7/Z
+atoms, 273 bonds, 12 residues, 1 model selected
+> color sel black
+> combine #3,7
+> hide #!10 models
+> show #!10 models
+> hide #!3 models
+> hide #!7 models
+> close #3,7
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!43 models
+> hide #!6 models
+> hide #!10 models
+> show #!10 models
+> rename #10 extended_structure
+> select #10,T
+Expected an objects specifier or a keyword
+> select #10/T
+atoms, 409 bonds, 51 residues, 1 model selected
+> ui tool show "Color Actions"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> color sel medium slate blue
+> color sel slate blue
+> color sel medium slate blue
+[Repeated 2 time(s)]
+> select clear
+> show #!2 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+> select add #10
+atoms, 132400 bonds, 284 pseudobonds, 8507 residues, 4 models selected
+> ui tool show "Color Zone"
+> color zone #2 near #10 distance 1
+> color zone #2 near #10 distance 10
+> color zone #2 near #10 distance 1
+> color zone #2 near #10 distance 15
+> color zone #2 near #10 distance 2
+> color zone #2 near #10 distance 20
+[Repeated 1 time(s)]
+> select clear
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+> volume splitbyzone #2
+Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+> volume #3.4 level 0.2577
+> volume #3.4 level 0.1585
+> volume #3.5 level 0.2148
+> volume #3.4 level 0.183
+> volume #3.5 level 0.183
+> volume #3.9 level 0.9634
+> volume #3.9 level 2.784
+> volume #3.10 level 2.78
+> volume #3.11 level 2.78
+> volume #3.13 level 2.78
+> volume #3.14 level 2.78
+> volume #3.16 level 2.78
+> volume #3.17 level 2.78
+> volume #3.18 level 2.78
+> volume #3.15 level 2.78
+> volume #3.12 level 2.78
+> volume copy #3.8
+Opened volume sum 7 copy as #7, grid size 636,840,859, pixel 0.95, shown at
+step 1, values float32
+> volume #3.8 level 2.78
+> volume #7 color #7b68ee7c
+> volume #7 color #7b68ee33
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+[Repeated 1 time(s)]
+> hide #!7 models
+> select #10/T
+atoms, 409 bonds, 51 residues, 1 model selected
+> color zone #7 near sel distance 5.7
+> show #!7 models
+> volume #7 color #ff2600
+> ui tool show "Color Actions"
+> color sel medium slate blue
+> select #7
+models selected
+> color sel medium slate blue
+> volume #7 color #ff260081
+> color sel medium slate blue
+> select #10/T
+atoms, 409 bonds, 51 residues, 1 model selected
+> color sel purple
+> color sel magenta
+> color zone #7 near sel distance 5.7
+> volume splitbyzone #7
+Opened volume sum 7 copy 0 as #11.1, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+> close #11.1
+> show #!7 models
+> hide #!3.4 models
+> hide #!3.5 models
+> hide #!3.6 models
+> hide #!3.7 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> show #!5 models
+> select add #5
+atoms, 12370 bonds, 187 pseudobonds, 1146 residues, 4 models selected
+> color zone #13 near sel distance 5.7
+> color zone #13 near sel distance 6.18
+> color zone #13 near sel distance 11.5
+> select clear
+> ui tool show "Hide Dust"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> surface dust #3.3 size 5.7
+> surface dust #3.3 size 5.66
+> surface dust #3.3 size 33
+> surface dust #3.3 size 33.37
+> surface dust #3.3 size 14.12
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+\u2014\u2014\u2014 End of log from Fri Sep 6 19:48:00 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> hide #!11.2 models
+> show #!11.2 models
+> hide #!11 models
+> show #!11 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> rename #7 Tof1_lower_level
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> hide #!11.2 models
+> show #!11.2 models
+> hide #!11.2 models
+> show #!11.2 models
+> hide #!11.2 models
+> show #!11.2 models
+> hide #!11.2 models
+> show #!11.2 models
+> hide #!11.2 models
+> show #!11.2 models
+> hide #!11.2 models
+> show #!11.2 models
+> hide #!11.2 models
+> show #!11.2 models
+> hide #!11.2 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> show #!11.2 models
+> hide #!11.2 models
+> show #!11.2 models
+> hide #!11 models
+> show #!11 models
+> rename #11 Tof1_HTH_lower_level
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> ui tool show "Hide Dust"
+> hide #!13 models
+> show #!13 models
+> hide #!11 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> surface dust #13 size 5.7
+[Repeated 1 time(s)]
+> surface undust #13
+> surface dust #13 size 5.7
+> show #!3 models
+> hide #!3 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3.2 models
+> show #!3.2 models
+> hide #!3.2 models
+> show #!3.2 models
+> hide #!3.2 models
+> show #!3.2 models
+> hide #!3.2 models
+> show #!3.2 models
+> hide #!3.3 models
+> show #!3.3 models
+> show #!3.1 models
+> hide #!3.1 models
+> surface dust #3.2 size 5.7
+> surface dust #3.2 size 5.68
+> surface dust #3.2 size 13.68
+> surface undust #3.2
+> surface dust #3.2 size 13.68
+> surface dust #3.2 size 14.86
+[Repeated 1 time(s)]
+> surface dust #3.4 size 5.7
+> surface dust #3.3 size 14.12
+> surface dust #3.3 size 14.38
+> surface dust #3.3 size 6.94
+> hide #!3.3 models
+> show #!3.3 models
+> hide #!3.2 models
+> show #!3.2 models
+> hide #!3.2 models
+> hide #!3.3 models
+> show #!3.3 models
+> hide #!3.8 models
+> hide #!3.9 models
+> hide #!3.10 models
+> hide #!3.11 models
+> hide #!3.12 models
+> hide #!3.13 models
+> hide #!3.14 models
+> hide #!3.15 models
+> hide #!3.16 models
+> hide #!3.17 models
+> hide #!3.18 models
+> hide #!13 models
+> surface dust #3.3 size 13.23
+> surface undust #3.3
+> surface dust #3.3 size 13.23
+> ui tool show "Map Eraser"
+> volume erase #3.3 center 191.19,155.01,168.45 radius 10.807
+> show #!3.2 models
+> show #!3.4 models
+> show #!3.5 models
+> show #!3.6 models
+> show #!3.7 models
+> show #!3.8 models
+> show #!3.9 models
+> show #!3.10 models
+> show #!3.11 models
+> show #!3.12 models
+> show #!3.13 models
+> show #!3.14 models
+> show #!3.15 models
+> show #!3.16 models
+> show #!3.17 models
+> show #!3.18 models
+> show #!5 models
+> hide #!5 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> surface dust #3.4 size 5.7
+> surface undust #3.4
+> surface dust #3.4 size 7.66
+> surface dust #3.5 size 5.7
+> surface dust #3.5 size 6.18
+> surface dust #3.5 size 8.89
+> surface dust #3.6 size 5.7
+> surface dust #3.6 size 5.97
+> surface dust #3.6 size 6.94
+> surface dust #3.8 size 7.05
+> surface dust #3.8 size 7.54
+> surface dust #3.8 size 5.15
+> surface dust #3.7 size 5.7
+> surface undust #3.9
+> surface dust #3.9 size 5.7
+> surface undust #3.8
+> surface dust #3.8 size 5.15
+> surface dust #3.9 size 5.7
+> hide #!3.5 models
+> show #!3.5 models
+> surface undust #3.5
+> surface dust #3.5 size 8.89
+> lighting soft
+> hide #!3 models
+> show #!3 models
+> select add #3
+models selected
+> view sel
+> select subtract #3
+Nothing selected
+> lighting soft
+> graphics silhouettes false
+> graphics silhouettes true
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_side.png
+> supersample 6 width 2000 transparentBackground true
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_side_back.png
+> supersample 6 width 2000 transparentBackground true
+> show #!1 models
+> hide #!1 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> surface dust #7 size 5.7
+> surface dust #7 size 6.07
+> surface dust #7 size 11.59
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!3 models
+> hide #!2 models
+> show #!2 models
+> surface dust #2 size 5.7
+> surface dust #2 size 5.97
+> surface dust #2 size 35.17
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!7 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+> hide #!2 models
+> show #!2 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> hide #!2 models
+> show #!2 models
+> show #!8 models
+> hide #!8 models
+> show #!10 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> show #!42 models
+> hide #!2 models
+> show #!2 models
+> hide #!42 models
+> hide #!10 models
+> show #!10 models
+> hide #!2 models
+> show #!2 models
+> ui tool show "Color Zone"
+> color zone #2 near #10 distance 19.41
+> color zone #2 near #10 distance 13.26
+> color zone #2 near #10 distance 1
+> color zone #2 near #10 distance 16
+> color zone #2 near #10 distance 1
+> color zone #2 near #10 distance 18
+> color zone #2 near #10 distance 1
+> color zone #2 near #10 distance 2
+> color zone #2 near #10 distance 20
+> hide #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!2 models
+> show #!13 models
+> hide #!10 models
+> lighting soft
+> lighting simple
+> lighting soft
+> ui tool show "Side View"
+> color zone #2 near #10 distance 2
+> color zone #2 near #10 distance 22
+> color zone #2 near #10 distance 2
+> color zone #2 near #10 distance 24
+> hide #!2 models
+> hide #!13 models
+> show #!8 models
+> hide #!8 models
+> show #!10 models
+> hide #!10 models
+> show #!7 models
+> hide #!7 models
+> show #!2 models
+> hide #!2 models
+> show #!3 models
+> show #!10 models
+> hide #!10 models
+> show #!13 models
+> show #!43 models
+> hide #!43 models
+> show #!10 models
+> show #!43 models
+> hide #!43 models
+> show #!43 models
+> hide #!43 models
+> show #!43 models
+> hide #!43 models
+> select #43/I
+atoms, 409 bonds, 51 residues, 1 model selected
+> show #!43 models
+> hide #!10 models
+> hide #!43 models
+> show #!43 models
+> hide #!3 models
+> show #!3 models
+> show #!8 models
+> hide #!8 models
+> show #!10 models
+> hide #!10 models
+> select #43/I
+atoms, 409 bonds, 51 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel magenta
+> hide sel target a
+> select subtract #43
+Nothing selected
+> hide #!43 models
+> hide #!3 models
+> show #!3 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!3 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_low_level.png
+> supersample 6 width 2000 transparentBackground true
+> hide #!2 models
+> show #!2 models
+> show #!3 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!43 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level.png
+> supersample 6 width 2000 transparentBackground true
+> graphics silhouettes false
+> graphics silhouettes true
+> show #!1 models
+> hide #!3 models
+> hide #!13 models
+> hide #!43 models
+> show #!43 models
+> hide #!43 models
+> show #!2 models
+> hide #!2 models
+> show #!3 models
+> hide #!1 models
+> show #!4 models
+> hide #!4 models
+> show #!5 models
+> hide #!5 models
+> show #!6 models
+> hide #!6 models
+> show #!7 models
+> hide #!7 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #7.1 models
+> show #7.1 models
+> show #!13 models
+> show #!43 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #7.1 models
+> show #7.1 models
+> hide #7.1 models
+> hide #!43 models
+> show #!43 models
+> show #!11 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> show #7.1 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> hide #!11 models
+> show #!11 models
+> show #!7 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> color #7 #7b68ee80 models
+> color #7 #7b68ee9e models
+> color #7 #7b68eea0 models
+> color #7 #7b68ee32 models
+> color #7 #7b68ee29 models
+> color #7 #7b68eeab models
+> color #7 #7b68ee89 models
+> color #7 #7b68ee8a models
+> hide #!43 models
+> show #!43 models
+> hide #!43 models
+> hide #!7 models
+> show #!7 models
+> show #!43 models
+> lighting simple
+> lighting full
+> lighting soft
+> hide #!43 models
+> show #!43 models
+> hide #!13 models
+> show #!13 models
+> hide #!7 models
+> hide #!13 models
+> hide #!3 models
+> show #!3 models
+> hide #!3.3 models
+> show #!3.3 models
+> hide #!3.4 models
+> hide #!3.5 models
+> hide #!3.6 models
+> hide #!3.7 models
+> hide #!3.2 models
+> show #!3.2 models
+> hide #!3.3 models
+> show #!3.3 models
+> volume copy #3.2
+Opened volume sum 1 copy as #12, grid size 636,840,859, pixel 0.95, shown at
+step 1, values float32
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> rename #12 leading_strand_vol_3p2
+> volume copy #3.3
+Opened volume sum 2 copy as #14, grid size 636,840,859, pixel 0.95, shown at
+step 1, values float32
+> hide #!14 models
+> show #!14 models
+> rename #14 lagging_strand_vol_3p3
+> hide #!14 models
+> hide #!12 models
+> show #!3.2 models
+> show #!3.3 models
+> hide #!3.3 models
+> hide #!3.2 models
+> show #!12 models
+> show #!11 models
+> hide #!11 models
+> show #!14 models
+> surface dust #12 size 5.7
+> surface dust #12 size 5.59
+> surface dust #12 size 9.82
+> surface dust #12 size 5.68
+[Repeated 1 time(s)]
+> surface undust #12
+> surface dust #12 size 5.68
+> surface dust #14 size 5.7
+> surface dust #14 size 6.18
+> surface dust #14 size 21.74
+> surface dust #14 size 22.85
+> surface dust #14 size 18.43
+> surface dust #14 size 19.68
+> surface dust #14 size 14.62
+> hide #!12 models
+> hide #!14 models
+> show #!3.2 models
+> show #!3.3 models
+> surface undust #3.2
+> surface dust #3.2 size 14.86
+> hide #!3.3 models
+> hide #!3.2 models
+> show #!12 models
+> show #!14 models
+> ui tool show "Map Eraser"
+Can only have one displayed volume when erasing
+[Repeated 1 time(s)]
+> hide #!14 models
+> hide #15 models
+> show #15 models
+> hide #!43 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> hide #15 models
+> show #15 models
+> volume erase #12 center 219.68,211.59,243.35 radius 53.859
+> show #!3 models
+> show #!3.2 models
+> show #!3.3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> volume erase #12 center 202.99,259.45,180.39 radius 53.859
+> volume erase #12 center 157.95,181.67,182.6 radius 53.859
+> volume erase #12 center 178.35,160.14,212.29 radius 53.859
+> volume erase #12 center 206.83,165.32,136.53 radius 18.769
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> volume erase #14 center 196.99,177.22,211.99 radius 31.01
+> volume erase #14 center 212.15,214.12,242.94 radius 40.802
+> volume erase #14 center 208.55,248.81,191.88 radius 40.802
+> volume erase #14 center 168.65,198.46,168.27 radius 40.802
+> volume erase #14 center 172.72,159.07,188.6 radius 40.802
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!12 models
+> show #!2 models
+> hide #!2 models
+> show #!3 models
+> hide #!3.2 models
+> hide #!3.3 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+> hide #!3 models
+> show #!3 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> show #!43 models
+> show #!3.2 models
+> hide #!3.2 models
+> show #!3.2 models
+> show #!3.3 models
+> hide #!3.3 models
+> show #!3.3 models
+> hide #!3.3 models
+> show #!3.3 models
+> show #!1 models
+> open 8XGC fromDatabase pdb format mmcif
+xgc title:
+Structure of yeast replisome associated with FACT and histone hexamer,
+Composite map [more info...]
+Chain information for 8xgc #15
+---
+Chain | Description | UniProt
+| DNA replication licensing factor MCM2 | A0A6A5Q1S9_YEASX 1-868
+| DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
+| DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
+| Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
+| DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
+| DNA replication licensing factor MCM7 | A0A8H4BTB2_YEASX 1-845
+| DNA polymerase epsilon catalytic subunit A | DPOE_YEAST 1-2222
+| DNA polymerase epsilon subunit B | DPB2_YEAST 1-689
+A | DNA replication complex GINS protein PSF1 | PSF1_YEAST 1-208
+B | DNA replication complex GINS protein PSF2 |
+C | DNA replication complex GINS protein PSF3 | PSF3_YEAST 1-194
+D | DNA replication complex GINS protein SLD5 | SLD5_YEAST 1-294
+E | Cell division control protein 45 | CDC45_YEAST 1-650
+F G H | DNA polymerase alpha-binding protein | CTF4_YEAST 1-927
+I | Topoisomerase 1-associated factor 1 | TOF1_YEAST 1-1238
+J | Chromosome segregation in meiosis protein 3 | CSM3_YEAST 1-317
+K | Mediator of replication checkpoint protein 1 | MRC1_YEAST 1-1096
+L | FACT complex subunit SPT16 | SPT16_YEAST 1-1035
+M | FACT complex subunit POB3 | POB3_YEAST 1-552
+N R | Histone H3 | A0A6A5Q536_YEASX 1-136
+O S | Histone H4 | H4_YEAST 1-103
+P | Histone H2A.1 | H2A1_YEAST 1-132
+Q | Histone H2B.2 | H2B2_YEAST 1-131
+X | DNA (51-MER) |
+Y | DNA (39-MER) |
+Non-standard residues in 8xgc #15
+---
+ADP \u2014 adenosine-5'-diphosphate
+ZN \u2014 zinc ion
+> show #!177 models
+> hide #!177 models
+> ui tool show Matchmaker
+> matchmaker #15/I to #1/I pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker Zhai, chain I (#1) with 8xgc, chain I (#15), sequence alignment
+score = 5609.4
+RMSD between 745 pruned atom pairs is 0.000 angstroms; (across all 745 pairs:
+.000)
+> select add #15
+atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
+> hide (#!15 & sel) target a
+> cartoon (#!15 & sel)
+> select subtract #15
+Nothing selected
+> select add #15
+atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
+> select subtract #15
+Nothing selected
+> hide #!15 models
+> select #1/N#1/R#15/N#15/R
+atoms, 2766 bonds, 334 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel dodger blue
+[Repeated 2 time(s)]
+> color sel cornflower blue
+[Repeated 1 time(s)]
+> color sel dodger blue
+[Repeated 1 time(s)]
+> color sel deep sky blue
+[Repeated 1 time(s)]
+> color sel cyan
+[Repeated 1 time(s)]
+> color sel deep sky blue
+> color sel dodger blue
+> color sel steel blue
+> color sel slate blue
+> color sel royal blue
+> color sel dodger blue
+> select #1/O#1/S#15/O#15/S
+atoms, 2560 bonds, 316 residues, 2 models selected
+> color sel medium spring green
+> color sel medium aquamarine
+> color sel sea green
+> color sel medium sea green
+> color sel light sea green
+[Repeated 1 time(s)]
+> color sel medium spring green
+[Repeated 1 time(s)]
+> select #1/P#15/P
+atoms, 1422 bonds, 182 residues, 2 models selected
+> select #1/P#15/P
+atoms, 1422 bonds, 182 residues, 2 models selected
+> color sel gold
+[Repeated 1 time(s)]
+> select #1/Q#15/Q
+atoms, 1432 bonds, 182 residues, 2 models selected
+> color sel crimson
+> select #1/L#15/L
+atoms, 7044 bonds, 6 pseudobonds, 986 residues, 4 models selected
+> color sel salmon
+[Repeated 2 time(s)]
+> color sel tomato
+> color sel salmon
+> select #1/M#15/M
+atoms, 3736 bonds, 14 pseudobonds, 758 residues, 4 models selected
+> color sel sienna
+> color sel saddle brown
+> color sel brown
+[Repeated 1 time(s)]
+> color sel tomato
+> color sel fire brick
+> color sel orange red
+> color sel brown
+> color sel sienna
+> select clear
+> lighting simple
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> select #1/2
+atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
+> color (#!1 & sel) hot pink
+> hide #!1 models
+> select add #1
+atoms, 72609 bonds, 163 pseudobonds, 8989 residues, 4 models selected
+> select subtract #1
+Nothing selected
+> ui tool show "Show Sequence Viewer"
+> sequence chain #43/I
+Alignment identifier is 43/I
+> show #!1 models
+> hide #!1 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> hide #!14 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!3.2 models
+> show #!3.2 models
+> show #!3.4 models
+> hide #!3.4 models
+> show #!3.4 models
+> hide #!3.4 models
+> show #!3.4 models
+> show #!3.5 models
+> show #!3.6 models
+> show #!3.7 models
+> hide #!13 models
+> show #!13 models
+> show #!12 models
+> hide #!12 models
+> show #!11 models
+> hide #!11 models
+> show #!14 models
+> hide #!14 models
+> show #!12 models
+> hide #!12 models
+> hide #!13 models
+> show #!13 models
+> hide #!3.2 models
+> show #!3.2 models
+> hide #!3.2 models
+> show #!3.2 models
+> color #3.2 #00000081 models
+> color #3.2 #0000009d models
+> color #3.2 #00000099 models
+> color #3.3 #696969a7 models
+> color #3.3 #696969a0 models
+> color #3.3 #6969699a models
+> color #3.3 #69696999 models
+> color #3.4 #4682b49a models
+> color #3.4 #4682b499 models
+> color #3.5 #3cb37193 models
+> color #3.5 #3cb37199 models
+> color #3.6 #ffd7009c models
+> color #3.6 #ffd7009a models
+> color #3.6 #ffd70099 models
+> hide #!13 models
+> show #!13 models
+> color #13 #b2ffffbf models
+[Repeated 1 time(s)]
+> color #13 #b2ffffc5 models
+> color #13 #b2ffffc4 models
+> color #13 #b2ffffb0 models
+> color #13 #b2ffff9f models
+> color #13 #b2ffff9b models
+> color #13 #b2ffff98 models
+> color #13 #b2ffff99 models
+> color zone #13 near #10 distance 5.7
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> color #3.7 #b222229c models
+> color #3.7 #b222229b models
+> color #3.7 #b2222297 models
+> color #3.7 #b2222298 models
+> color #3.7 #b2222299 models
+> hide #!3.8 models
+> show #!3.8 models
+> show #!234 models
+> hide #!234 models
+> hide #!13 models
+> show #!13 models
+> color #13 #b2ffffff models
+> show #!9 models
+> hide #!9 models
+> hide #!3.18 models
+> show #!3.18 models
+> hide #!3.17 models
+> show #!3.17 models
+> hide #!3.8 models
+> show #!3.8 models
+> color #3.7 firebrick models
+> color #3.6 gold models
+> color #3.5 mediumseagreen models
+> color #3.4 steelblue models
+> hide #!3.3 models
+> show #!3.3 models
+> color #3.3 dimgrey models
+> color #3.2 black models
+> hide #!13 models
+> show #!13 models
+> color zone #13 near #10 distance 5.7
+[Repeated 1 time(s)]
+> color zone #13 near #10 distance 5.87
+> color zone #13 near #10 distance 12.76
+> ui tool show "Side View"
+> lighting soft
+> hide #!3.2 models
+> show #!3.2 models
+> hide #!3.2 models
+> show #!3.2 models
+> hide #!3.2 models
+> hide #!3.3 models
+> hide #!3.4 models
+> hide #!3.5 models
+> hide #!3.6 models
+> hide #!3.7 models
+> hide #!13 models
+> show #!12 models
+> show #!11 models
+> hide #!11 models
+> show #!14 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level_wo_nucl.png
+> supersample 6 width 2000 transparentBackground true
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> select #43/I:618
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #43/I:618-619
+atoms, 21 bonds, 2 residues, 1 model selected
+> select #43/I:616
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:616-617
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #43/I:609
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:609
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:609,616
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #43/I:609,616,618-619
+atoms, 37 bonds, 4 residues, 1 model selected
+> select #43/I:609,616,618-619,621-622
+atoms, 54 bonds, 6 residues, 1 model selected
+> select #43/I:609,616,618-619,621-622,632
+atoms, 62 bonds, 7 residues, 1 model selected
+> select #43/I:609,616,618-619,621-622,632
+atoms, 62 bonds, 7 residues, 1 model selected
+> select #43/I:609,616,618-619,621-622,632
+atoms, 62 bonds, 7 residues, 1 model selected
+> select #43/I:632
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:632
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:616,632
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #43/I:616,618-619,632
+atoms, 37 bonds, 4 residues, 1 model selected
+> select #43/I:616,618-619,621-622,632
+atoms, 54 bonds, 6 residues, 1 model selected
+> select #43/I:616,618-619,621-622,632
+atoms, 54 bonds, 6 residues, 1 model selected
+> select #43/I:619
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #43/I:619
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #43/I:616,619
+atoms, 18 bonds, 2 residues, 1 model selected
+> select #43/I:616,618-619
+atoms, 29 bonds, 3 residues, 1 model selected
+> select #43/I:616,618-619,621-622
+atoms, 46 bonds, 5 residues, 1 model selected
+> show sel target ab
+> color sel byhetero
+[Repeated 1 time(s)]
+> style sel sphere
+Changed 49 atom styles
+> hide #!12 models
+> show #!12 models
+> ui tool show "Color Actions"
+> color sel cyan
+[Repeated 2 time(s)]
+> color sel byhetero
+[Repeated 1 time(s)]
+> select #43/I:616,618-619,621-622,635-636
+atoms, 63 bonds, 7 residues, 1 model selected
+> select #43/I:635
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:635-637
+atoms, 26 bonds, 3 residues, 1 model selected
+> select #43/I:627,635-637
+atoms, 34 bonds, 4 residues, 1 model selected
+> select #43/I:627,629,635-637
+atoms, 41 bonds, 5 residues, 1 model selected
+> select #43/I:627,629,635-637,640
+atoms, 48 bonds, 6 residues, 1 model selected
+> select #43/I:627,629,635-637,640,642-643
+atoms, 64 bonds, 8 residues, 1 model selected
+> select #43/I:627,629,635-637,640,642-643,646
+atoms, 71 bonds, 9 residues, 1 model selected
+> color sel orange red
+> show sel target ab
+> color sel byhetero
+> style sel ball
+Changed 77 atom styles
+> style sel sphere
+Changed 77 atom styles
+> color sel orange
+> color sel orange red
+> color sel gold
+> color sel orange
+> color sel byhetero
+> select add #43
+atoms, 409 bonds, 51 residues, 1 model selected
+> select subtract #43
+Nothing selected
+> cartoon style #12,14,43#3.8-18#!3 xsection oval modeHelix default
+> cartoon style #12,14,43#3.8-18#!3 xsection rectangle modeHelix default
+> cartoon style (#12,14,43#3.8-18#!3 & coil) xsection oval
+> cartoon style #12,14,43#3.8-18#!3 xsection barbell modeHelix default
+> cartoon style #12,14,43#3.8-18#!3 modeHelix tube sides 20
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level_wo_nucl_patches.png
+> supersample 6 width 2000 transparentBackground true
+> show #!13 models
+> show #!3.1 models
+> hide #!3.1 models
+> show #!3.2 models
+> show #!3.3 models
+> show #!3.4 models
+> show #!3.5 models
+> show #!3.6 models
+> show #!3.7 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level_wo_nucl_patches_2.png
+> supersample 6 width 2000 transparentBackground true
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level_wo_nucl_patches_3.png
+> supersample 6 width 2000 transparentBackground true
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> select #43/I:607-609
+atoms, 24 bonds, 3 residues, 1 model selected
+> select #43/I
+atoms, 409 bonds, 51 residues, 1 model selected
+> hide sel target a
+> color sel magenta
+> select clear
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level_lighter.png
+> supersample 6 width 2000 transparentBackground true
+> show #!2 models
+> hide #!3 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_low_level_lighter.png
+> supersample 6 width 2000 transparentBackground true
+> hide #!2 models
+> show #!3 models
+> show #!7 models
+> color #7 #7b68ee81 models
+> color #7 #7b68ee80 models
+> color #7 #7b68ee73 models
+> color #7 #7b68ee41 models
+> color #7 #7b68ee96 models
+> color #7 #7b68ee8c models
+> color #7 #7b68ee95 models
+> color #7 #7b68ee9c models
+> color #7 #7b68ee96 models
+> color #7 #7b68ee99 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!11 models
+> color #11.2 #ff00ff83 models
+> color #11.2 #ff00ff3b models
+> color #11.2 #ff00ff4d models
+> color #11.2 #ff00ff68 models
+> color #11.2 #ff00ff77 models
+> color #11.2 #ff00ff87 models
+> color #11.2 #ff00ff9e models
+> color #11.2 #ff00ff9a models
+> hide #!11.2 models
+> color #11.2 #ff00ff99 models
+> show #!11.2 models
+> hide #!11.2 models
+> show #!11.2 models
+> select #43/I:607
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #43/I
+atoms, 409 bonds, 51 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel dark violet
+> color sel blue violet
+[Repeated 2 time(s)]
+> color sel blue
+> color sel dark blue
+> color sel navy
+[Repeated 2 time(s)]
+> select clear
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_transp.png
+> supersample 6 width 2000 transparentBackground true
+> select #43/I:607
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #43/I:607-656
+atoms, 402 bonds, 50 residues, 1 model selected
+> color sel magenta
+> select clear
+> color #11.2 #ff00ff3b models
+> color #11.2 #ff00ff71 models
+> color #11.2 magenta models
+> color #11.2 white models
+> color #11.2 #ffffff72 models
+> color #11.2 #ffffff5f models
+> color #11.2 #ffffff79 models
+> color #11.2 #ffffff4d models
+> color #11.2 #ffffff5e models
+> color #11.2 #ff40ffff models
+> select clear
+[Repeated 1 time(s)]
+> hide #!11.2 models
+> hide #!11 models
+> hide #!43 models
+> lighting flat
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting shadows true intensity 0.5
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_flat.png
+> supersample 6 width 2000 transparentBackground true
+> lighting soft
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_background.png
+> supersample 6 width 2000 transparentBackground true
+> show #!43 models
+> show #!1 models
+> hide #!3 models
+> hide #!12 models
+> hide #!13 models
+> hide #!14 models
+> hide #!43 models
+> show #!43 models
+> hide #!43 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!3 models
+> color #3.2 black models
+> color #3.3 dimgrey models
+> color #3.4 steelblue models
+> color #3.5 mediumseagreen models
+> color #3.6 #ffd700fd models
+> color #3.6 gold models
+> color #3.7 firebrick models
+> hide #!3 models
+> show #!3 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!43 models
+> hide #!43 models
+> show #!43 models
+> hide #!43 models
+> show #!43 models
+> hide #!43 models
+> show #!12 models
+> hide #!12 models
+> show #!14 models
+> hide #!14 models
+> select #1/L,M
+atoms, 5390 bonds, 10 pseudobonds, 872 residues, 2 models selected
+> cartoon hide (#!1 & sel)
+> show #!43 models
+> hide #!43 models
+> show #!43 models
+> hide #!43 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_wo_FACT.png
+> supersample 6 width 2000 transparentBackground true
+> select add #12
+atoms, 5390 bonds, 10 pseudobonds, 872 residues, 4 models selected
+> select add #14
+atoms, 5390 bonds, 10 pseudobonds, 872 residues, 6 models selected
+> select subtract #14
+atoms, 5390 bonds, 10 pseudobonds, 872 residues, 4 models selected
+> select subtract #12
+atoms, 5390 bonds, 10 pseudobonds, 872 residues, 2 models selected
+> cartoon (#!1 & sel)
+> select clear
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_with_FACT.png
+> supersample 6 width 2000 transparentBackground true
+> show #!12 models
+> show #!14 models
+> hide #!13 models
+> hide #!3.2 models
+> hide #!3.3 models
+> show #!3.3 models
+> hide #!3.3 models
+> hide #!3.4 models
+> hide #!3.5 models
+> hide #!3.6 models
+> hide #!3.7 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai.png
+> supersample 6 width 2000 transparentBackground true
+> select #1/L,M
+atoms, 5390 bonds, 10 pseudobonds, 872 residues, 2 models selected
+> cartoon hide (#!1 & sel)
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_wo_FACT.png
+> supersample 6 width 2000 transparentBackground true
+> hide #!12 models
+> hide #!14 models
+> show #!14 models
+> show #!12 models
+> hide #!12 models
+> hide #!14 models
+> show #!3.7 models
+> show #!3.6 models
+> show #!3.5 models
+> show #!3.4 models
+> show #!3.3 models
+> show #!3.2 models
+> show #!13 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_wo_FACT_wo_nucl.png
+> supersample 6 width 2000 transparentBackground true
+> cartoon (#!1 & sel)
+> select clear
+> hide #!1 models
+> show #!43 models
+> combine #1
+> select #16/2
+atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 66320 bonds, 158 pseudobonds, 8209 residues, 4 models selected
+> delete atoms (#!16 & sel)
+> delete bonds (#!16 & sel)
+> show #!7 models
+> hide #!7 models
+> show #!11 models
+> show #!11.2 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> color #11.2 #ff40ffde models
+> color #11.2 #ff40ffce models
+> color #11.2 #ff40ffcc models
+> hide #!11.2 models
+> show #!11.2 models
+> hide #!11.2 models
+> show #!11.2 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_Mcm2_Tof1_HTH_density.png
+> supersample 6 width 2000 transparentBackground true
+> hide #!11 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_Mcm2_Tof1_HTH.png
+> supersample 6 width 2000 transparentBackground true
+> show #!1 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+\u2014\u2014\u2014 End of log from Mon Sep 9 04:24:31 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!16 models
+> show #!16 models
+> hide #!1 models
+> hide #!16 models
+> show #!16 models
+> show #!1 models
+> combine #1
+> hide #!1 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> hide #!17 models
+> show #!17 models
+> hide #!3 models
+> hide #!13 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!17 models
+> show #!17 models
+> select #17/L
+atoms, 3522 bonds, 3 pseudobonds, 493 residues, 2 models selected
+> ui tool show Matchmaker
+> matchmaker #17/Q to #10/D pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain D (#10) with copy of Zhai, chain Q (#17),
+sequence alignment score = 586.9
+RMSD between 88 pruned atom pairs is 0.795 angstroms; (across all 91 pairs:
+.028)
+> hide #!10 models
+> select #17/Q,P,O,N,S,R,L,M
+atoms, 9480 bonds, 10 pseudobonds, 1379 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 63129 bonds, 153 pseudobonds, 7610 residues, 4 models selected
+> delete atoms (#!17 & sel)
+> delete bonds (#!17 & sel)
+> show #!8 models
+> hide #!8 models
+> show #!10 models
+> select add #10
+atoms, 132400 bonds, 284 pseudobonds, 8507 residues, 4 models selected
+> view sel
+> select subtract #10
+Nothing selected
+> select #17/L
+atoms, 3522 bonds, 3 pseudobonds, 493 residues, 2 models selected
+> select clear
+> select #17/L
+atoms, 3522 bonds, 3 pseudobonds, 493 residues, 2 models selected
+> ui tool show "Show Sequence Viewer"
+> sequence chain #17/L
+Alignment identifier is 17/L
+> select clear
+> select #17/L:961-996
+atoms, 197 bonds, 36 residues, 1 model selected
+> select #17/L:956
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #17/L:948-956
+atoms, 67 bonds, 9 residues, 1 model selected
+> select #17/L:948-950
+atoms, 23 bonds, 3 residues, 1 model selected
+> select #17/L:948-996
+atoms, 264 bonds, 1 pseudobond, 45 residues, 2 models selected
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!1 models
+> hide #!1 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> hide #!17 models
+> hide #!43 models
+> combine #15
+> hide #!18 models
+> select add #17
+atoms, 9480 bonds, 10 pseudobonds, 1379 residues, 2 models selected
+> select subtract #17
+Nothing selected
+> show #!18 models
+> hide #!18 models
+> show #!18 models
+> show #!17 models
+> hide #!17 models
+> hide #!18 models
+> show #!1 models
+> hide #!1 models
+> combine #1
+> select #19/Q,P,O,N,S,R,L,M,2
+atoms, 15769 bonds, 15 pseudobonds, 2159 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 56840 bonds, 148 pseudobonds, 6830 residues, 4 models selected
+> hide (#!19 & sel) target a
+> hide #!19 models
+> show #!19 models
+> cartoon hide (#!19 & sel)
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> show #!9 models
+> hide #!9 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!1 models
+> show #!1 models
+> hide #!3 models
+> hide #!1 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> hide #!10 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!17 models
+> hide #!17 models
+> show #!16 models
+> hide #!19 models
+> hide #!16 models
+> show #!16 models
+> show #!19 models
+> hide #!16 models
+> show #!16 models
+> hide #!19 models
+> show #!19 models
+> hide #!16 models
+> hide #!19 models
+> show #!19 models
+> cartoon (#!19 & sel)
+> delete atoms (#!19 & sel)
+> delete bonds (#!19 & sel)
+> show #!17 models
+> hide #!17 models
+> show #!17 models
+> hide #!17 models
+> show #!17 models
+> hide #!19 models
+> show #!19 models
+> hide #!17 models
+> show #!17 models
+> ui tool show Matchmaker
+> matchmaker #19/L to #17/L pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker copy of Zhai, chain L (#17) with copy of Zhai, chain L (#19),
+sequence alignment score = 4482.1
+RMSD between 493 pruned atom pairs is 0.000 angstroms; (across all 493 pairs:
+.000)
+> hide #!19 models
+> show #!19 models
+> hide #!17 models
+> show #!17 models
+> hide #!17 models
+> show #!10 models
+> hide #!19 models
+> show #!19 models
+> select #19/L
+atoms, 3522 bonds, 3 pseudobonds, 493 residues, 2 models selected
+> select #19/2
+atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
+> select add #19
+atoms, 15769 bonds, 15 pseudobonds, 2159 residues, 3 models selected
+> select subtract #19
+Nothing selected
+> hide #!19 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!10 models
+> show #!10 models
+> hide #!1 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+\u2014\u2014\u2014 End of log from Wed Sep 11 12:56:29 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> hide #!10 models
+> show #!10 models
+> show #!19 models
+> hide #!19 models
+> show #!18 models
+> hide #!18 models
+> show #!17 models
+> hide #!17 models
+> show #!17 models
+> hide #!17 models
+> show #!17 models
+> hide #!17 models
+> show #!50 models
+> hide #!50 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J819_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
+,588,588, pixel 0.95, shown at level 0.207, step 4, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J819_005_volume_map.mrc
+Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
+pixel 0.95, shown at level 0.108, step 4, values float32
+> hide #!10 models
+> hide #!20 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!20 models
+> volume #20 step 1
+> volume #20 level 0.6282
+> volume #20 level 0.5581
+> volume #21 step 1
+> volume #21 level 0.3191
+> show #!50 models
+> hide #!20 models
+> show #!10 models
+> hide #!10 models
+> show #!20 models
+> select add #20
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #20,0.99684,0.061516,0.050168,-28.958,-0.064381,0.99626,0.057647,4.4916,-0.046434,-0.060695,0.99708,30.666
+> lighting simple
+> view matrix models
+> #20,0.73598,-0.4705,-0.48679,329.31,0.6768,0.52918,0.51178,-191.97,0.01681,-0.70611,0.7079,265.3
+> view matrix models
+> #20,0.12559,-0.15204,-0.98036,539.99,-0.57343,0.79527,-0.1968,269.08,0.80957,0.58689,0.012694,-138.71
+> view matrix models
+> #20,-0.16726,-0.54653,-0.82057,691.05,-0.96595,-0.075783,0.24736,507.43,-0.19738,0.83401,-0.51525,212.61
+> view matrix models
+> #20,-0.44936,-0.35876,-0.81815,718.23,-0.88005,0.3352,0.33637,346.68,0.15357,0.87116,-0.46636,90.611
+> view matrix models
+> #20,-0.44063,-0.37463,-0.81578,719.55,-0.88716,0.32048,0.33201,353.87,0.13706,0.87003,-0.47357,97.439
+> ui mousemode right "translate selected models"
+> view matrix models
+> #20,-0.44063,-0.37463,-0.81578,705.11,-0.88716,0.32048,0.33201,144.71,0.13706,0.87003,-0.47357,26.598
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #20,-0.33684,-0.44475,-0.8299,698.78,-0.91245,0.37165,0.17118,178.84,0.2323,0.81491,-0.531,29.613
+> ui mousemode right "translate selected models"
+> view matrix models
+> #20,-0.33684,-0.44475,-0.8299,696.83,-0.91245,0.37165,0.17118,160.27,0.2323,0.81491,-0.531,22.667
+> ui tool show "Fit in Map"
+> fitmap #20 inMap #50
+Fit map cryosparc_P17_J819_005_volume_map_sharp.mrc in map
+J842_005_volume_map_EMReady.mrc using 218333 points
+correlation = 0.9383, correlation about mean = 0.6201, overlap = 1.633e+06
+steps = 320, shift = 3.21, angle = 32.8 degrees
+Position of cryosparc_P17_J819_005_volume_map_sharp.mrc (#20) relative to
+J842_005_volume_map_EMReady.mrc (#50) coordinates:
+Matrix rotation and translation
+-0.97651784 -0.21085655 -0.04418632 623.63633661
+-0.20170911 0.96689998 -0.15626218 100.15142454
+.07567265 -0.14368002 -0.98672676 575.82401984
+Axis 0.10410159 -0.99168284 0.07568362
+Axis point 308.30489723 0.00000000 301.22875456
+Rotation angle (degrees) 176.53538416
+Shift along axis 9.18353169
+> select subtract #20
+Nothing selected
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> volume #20 level 0.55
+> volume #20 level 0.52
+> ui mousemode right zoom
+> select add #20
+models selected
+> view sel
+> select subtract #20
+Nothing selected
+> show #!10 models
+> hide #!20 models
+> show #!20 models
+> volume #20 level 0.5
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> ui tool show "Color Zone"
+> color zone #20 near #10 distance 5.7
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!20 models
+> show #!20 models
+> hide #!10 models
+> show #!10 models
+> hide #!20 models
+> show #!20 models
+> open
+> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_13_mrc1_mcm265_cdc45/fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif
+Chain information for fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif #22
+---
+Chain | Description
+A | .
+B | .
+C | .
+D | .
+E | .
+> ui tool show Matchmaker
+> matchmaker #22/B to #10/5 pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain 5 (#10) with
+fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain B (#22), sequence
+alignment score = 3612.5
+RMSD between 349 pruned atom pairs is 0.656 angstroms; (across all 376 pairs:
+.211)
+> select add #22
+atoms, 35428 bonds, 4406 residues, 1 model selected
+> hide sel target a
+> cartoon sel
+> lighting soft
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> select subtract #22
+Nothing selected
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> fitmap #21 inMap #50
+Fit map cryosparc_P17_J819_005_volume_map.mrc in map
+J842_005_volume_map_EMReady.mrc using 385073 points
+correlation = -0.002927, correlation about mean = 0.004409, overlap = -0.0752
+steps = 684, shift = 150, angle = 30.2 degrees
+Position of cryosparc_P17_J819_005_volume_map.mrc (#21) relative to
+J842_005_volume_map_EMReady.mrc (#50) coordinates:
+Matrix rotation and translation
+.57579874 0.59202822 -0.56387799 140.55370059
+.23007257 0.54448263 0.80660106 227.62276282
+.78455237 -0.59417273 0.17730296 170.40181219
+Axis -0.70827102 -0.68180470 -0.18301506
+Axis point 0.00000000 142.99311800 40.24521085
+Rotation angle (degrees) 81.44306259
+Shift along axis -285.93048023
+> hide #!20 models
+> show #!20 models
+> lighting simple
+> select add #21
+models selected
+> ui mousemode right "translate selected models"
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> view matrix models
+> #21,0.97135,-0.052031,-0.23188,161.6,0.15157,0.88715,0.43587,-376.59,0.18303,-0.45853,0.86962,210.47
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #21,0.19048,0.81338,-0.54967,226.48,0.29087,0.48802,0.82294,-405.4,0.93761,-0.31663,-0.14363,216.66
+> view matrix models
+> #21,-0.32552,0.21775,-0.92012,629.77,-0.85556,0.34648,0.38467,69.087,0.40256,0.91244,0.073519,-23.833
+> view matrix models
+> #21,-0.53454,-0.15623,-0.83058,768.38,-0.79246,0.43422,0.42833,16.109,0.29374,0.88715,-0.35592,123.32
+> view matrix models
+> #21,-0.53754,0.14132,-0.83131,687.98,-0.53102,0.70909,0.46391,-142.08,0.65503,0.69082,-0.30612,62.244
+> view matrix models
+> #21,-0.084069,-0.50373,-0.85976,743.6,-0.50818,0.76385,-0.39785,56.165,0.85714,0.40347,-0.3202,87.35
+> ui mousemode right "translate selected models"
+> view matrix models
+> #21,-0.084069,-0.50373,-0.85976,600,-0.50818,0.76385,-0.39785,93.73,0.85714,0.40347,-0.3202,23.425
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #21,-0.11912,-0.5728,-0.81099,616.38,-0.60623,0.68884,-0.39748,141.88,0.78632,0.44429,-0.4293,60.08
+> ui mousemode right "translate selected models"
+> view matrix models
+> #21,-0.11912,-0.5728,-0.81099,641.5,-0.60623,0.68884,-0.39748,134.93,0.78632,0.44429,-0.4293,-49.603
+> select subtract #21
+Nothing selected
+> fitmap #21 inMap #50
+Fit map cryosparc_P17_J819_005_volume_map.mrc in map
+J842_005_volume_map_EMReady.mrc using 385073 points
+correlation = 0.9655, correlation about mean = 0.736, overlap = 1.153e+06
+steps = 428, shift = 23.7, angle = 35.9 degrees
+Position of cryosparc_P17_J819_005_volume_map.mrc (#21) relative to
+J842_005_volume_map_EMReady.mrc (#50) coordinates:
+Matrix rotation and translation
+-0.97650910 -0.21085482 -0.04438713 623.66015597
+-0.20170409 0.96695488 -0.15592857 100.07508728
+.07579864 -0.14331260 -0.98677052 575.69053694
+Axis 0.10409896 -0.99169665 0.07550605
+Axis point 308.29085690 0.00000000 301.17618213
+Rotation angle (degrees) 176.52597465
+Shift along axis 9.14636480
+> ui mousemode right zoom
+> lighting soft
+[Repeated 1 time(s)]
+> lighting simple
+> hide #!20 models
+> color #21 #ffffb2b1 models
+> color #21 #ffffb2c3 models
+> color #21 #ffffb2cd models
+> lighting soft
+> hide #!21 models
+> show #!20 models
+> hide #!10 models
+> hide #!20 models
+> show #!21 models
+> color #21 #ffffb2ff models
+> volume #21 level 0.3
+> show #!10 models
+> hide #22 models
+> hide #!21 models
+> show #!21 models
+> volume #21 color #ffffb2a7
+> volume #21 color #ffffb2c7
+> volume #21 level 0.2436
+> lighting simple
+> volume #21 level 0.1591
+> show #22 models
+> volume #21 level 0.1281
+> volume #21 level 0.1788
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> select #22/1
+Nothing selected
+> hide #22 models
+> show #22 models
+> select #22/A
+atoms, 8850 bonds, 1096 residues, 1 model selected
+> color sel red
+> ui tool show "Color Actions"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> color sel fire brick
+[Repeated 1 time(s)]
+> select clear
+> hide #22 models
+> show #22 models
+> hide #!21 models
+> show #!21 models
+> hide #22 models
+> show #22 models
+> hide #!21 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> matchmaker #22/E to #10/P pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain P (#10) with
+fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain E (#22), sequence
+alignment score = 3080.7
+RMSD between 540 pruned atom pairs is 0.670 angstroms; (across all 564 pairs:
+.017)
+> show #!21 models
+> hide #22 models
+> show #22 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> color #21 #ffffb2bd models
+> color #21 #ffffb2b5 models
+> color #21 #ffffb2b2 models
+> color #21 #ffffb2b3 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> show #!20 models
+> hide #!21 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J842_005_volume_map.mrc
+Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
+pixel 0.95, shown at level 0.12, step 4, values float32
+> select add #23
+models selected
+> lighting simple
+> ui mousemode right "translate selected models"
+> view matrix models #23,1,0,0,-7.0847,0,1,0,-197.97,0,0,1,-109.28
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #23,0.98683,-0.1075,-0.12084,64.211,0.093694,0.98898,-0.11463,-186.41,0.13184,0.1018,0.98603,-171.46
+> view matrix models
+> #23,0.94591,0.31213,-0.088466,-59.663,-0.29926,0.73415,-0.60948,142.32,-0.12529,0.60298,0.78785,-193.05
+> view matrix models
+> #23,0.82112,-0.20887,0.53116,-52.333,0.43246,0.83502,-0.34017,-166.12,-0.37248,0.50903,0.77598,-94.238
+> ui mousemode right "translate selected models"
+> view matrix models
+> #23,0.82112,-0.20887,0.53116,-76.409,0.43246,0.83502,-0.34017,-186.01,-0.37248,0.50903,0.77598,-92.077
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #23,0.83793,-0.011709,0.54565,-144.2,0.24675,0.89989,-0.35961,-149.17,-0.48681,0.43596,0.75693,-33.526
+> ui mousemode right "translate selected models"
+> view matrix models
+> #23,0.83793,-0.011709,0.54565,-128.24,0.24675,0.89989,-0.35961,-146.49,-0.48681,0.43596,0.75693,-40.894
+> fitmap #23 inMap #50
+Fit map cryosparc_P17_J842_005_volume_map.mrc in map
+J842_005_volume_map_EMReady.mrc using 31738 points
+correlation = 0.8988, correlation about mean = 0.8848, overlap = 2.616e+04
+steps = 240, shift = 14.4, angle = 16.1 degrees
+Position of cryosparc_P17_J842_005_volume_map.mrc (#23) relative to
+J842_005_volume_map_EMReady.mrc (#50) coordinates:
+Matrix rotation and translation
+.99999950 -0.00093282 -0.00036048 0.38612693
+.00093288 0.99999955 0.00017577 -0.28600473
+.00036032 -0.00017611 0.99999992 -0.03720041
+Axis -0.17327202 -0.35493124 0.91869507
+Axis point 306.61813627 413.85199204 0.00000000
+Rotation angle (degrees) 0.05817852
+Shift along axis 0.00043119
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #23 step 1
+> select subtract #23
+Nothing selected
+> show #!20 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> show #!21 models
+> hide #!21 models
+> volume #20 level 0.4302
+> volume #20 level 0.3778
+> volume #20 level 0.35
+> color zone #20 near #10 distance 5.7
+> color single #20
+> color #20 #b2b2b2d5 models
+> color #20 #b2b2b2be models
+> color #20 #b2b2b2bf models
+> hide #!10 models
+> show #!10 models
+> hide #22 models
+> show #22 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> fitmap #23 inMap #50
+Fit map cryosparc_P17_J842_005_volume_map.mrc in map
+J842_005_volume_map_EMReady.mrc using 2030930 points
+correlation = 0.8962, correlation about mean = 0.8821, overlap = 1.677e+06
+steps = 40, shift = 0.0507, angle = 0.0557 degrees
+Position of cryosparc_P17_J842_005_volume_map.mrc (#23) relative to
+J842_005_volume_map_EMReady.mrc (#50) coordinates:
+Matrix rotation and translation
+.00000000 -0.00007868 -0.00004863 0.03041624
+.00007868 0.99999998 -0.00016626 0.01451905
+.00004864 0.00016625 0.99999998 -0.05718112
+Axis 0.87385342 -0.25564418 0.41355321
+Axis point 0.00000000 342.00873970 86.09530376
+Rotation angle (degrees) 0.01090079
+Shift along axis -0.00077981
+> volume #23 level 0.2075
+> hide #!23 models
+> show #!23 models
+> show #!21 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!21 models
+> show #!21 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!23 models
+> show #!21 models
+> hide #!23 models
+> hide #!21 models
+> hide #22 models
+> show #22 models
+> select clear
+> hide #22 models
+> show #22 models
+> hide #!21 models
+> show #!21 models
+> hide #22 models
+> show #!20 models
+> hide #!21 models
+> volume #20 level 0.38
+> volume #20 level 0.4
+> volume #20 level 0.45
+> show #22 models
+> hide #22 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> show #22 models
+> hide #22 models
+> hide #!23 models
+> show #!23 models
+> hide #!21 models
+> color #23 #b2ffffcc models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #!23 models
+> show #!23 models
+> show #!21 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!21 models
+> ui mousemode right zoom
+> hide #!23 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J1282_volume_map.mrc
+Opened cryosparc_P17_J1282_volume_map.mrc as #24, grid size 588,588,588, pixel
+.95, shown at level 0.156, step 4, values float32
+> close #24
+> show #22 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #22 models
+> show #22 models
+> matchmaker #22/B to #10/AD pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain AD (#10) with
+fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain B (#22), sequence
+alignment score = 3101.9
+RMSD between 14 pruned atom pairs is 1.061 angstroms; (across all 27 pairs:
+.919)
+> matchmaker #22/C to #10/AD pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain AD (#10) with
+fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain C (#22), sequence
+alignment score = 468.1
+RMSD between 6 pruned atom pairs is 1.308 angstroms; (across all 25 pairs:
+.655)
+> hide #22 models
+> show #22 models
+> matchmaker #22/B to #10/AD pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain AD (#10) with
+fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain B (#22), sequence
+alignment score = 3101.9
+RMSD between 14 pruned atom pairs is 1.061 angstroms; (across all 27 pairs:
+.919)
+> hide #!23 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> matchmaker #22/E to #10/P pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain P (#10) with
+fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain E (#22), sequence
+alignment score = 3080.7
+RMSD between 540 pruned atom pairs is 0.670 angstroms; (across all 564 pairs:
+.017)
+> matchmaker #22/B to #10/2 pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain 2 (#10) with
+fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain B (#22), sequence
+alignment score = 3481.1
+RMSD between 244 pruned atom pairs is 0.690 angstroms; (across all 293 pairs:
+.338)
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> show #!21 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!21 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> volume #23 level 0.18
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #!21 models
+> show #22 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> volume #21 level 0.16
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #22 models
+> show #22 models
+> hide #!21 models
+> hide #!23 models
+> hide #22 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
+> open
+> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif
+Chain information for
+fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif #24
+---
+Chain | Description
+A | .
+B | .
+C | .
+D E | .
+F G | .
+H I J | .
+K | .
+> select add #24
+atoms, 35097 bonds, 4327 residues, 1 model selected
+> hide sel target a
+> cartoon sel
+> select subtract #24
+Nothing selected
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> matchmaker #24/B to #10/P pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain P (#10) with
+fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif, chain B
+(#24), sequence alignment score = 3082.5
+RMSD between 545 pruned atom pairs is 0.663 angstroms; (across all 564 pairs:
+.931)
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> matchmaker #24/C to #10/2 pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain 2 (#10) with
+fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif, chain C
+(#24), sequence alignment score = 3488.9
+RMSD between 245 pruned atom pairs is 0.669 angstroms; (across all 293 pairs:
+.945)
+> select #24/A
+atoms, 1527 bonds, 185 residues, 1 model selected
+> color sel red
+> select #10/M:96
+atoms, 21 bonds, 1 residue, 1 model selected
+> select clear
+> color #10,24 hot pink
+> undo
+> select #24/C
+atoms, 7047 bonds, 868 residues, 1 model selected
+> select clear
+> select #24/C
+atoms, 7047 bonds, 868 residues, 1 model selected
+> color sel hot pink
+> select clear
+> select #24/C
+atoms, 7047 bonds, 868 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel deep pink
+> color sel blue violet
+> color sel orchid
+> color sel deep pink
+> select clear
+> select #24/C
+atoms, 7047 bonds, 868 residues, 1 model selected
+> color sel medium violet red
+> select clear
+> select #24/C
+atoms, 7047 bonds, 868 residues, 1 model selected
+> color sel magenta
+> select clear
+> select #24/C
+atoms, 7047 bonds, 868 residues, 1 model selected
+> color sel dark orchid
+> select clear
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #24 models
+> hide #22 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #!10 models
+> show #!4 models
+> hide #!4 models
+> show #!5 models
+> hide #!5 models
+> show #!4 models
+> hide #!4 models
+> select #24/D,E
+atoms, 2190 bonds, 272 residues, 1 model selected
+> color sel dodger blue
+> color sel steel blue
+> color sel dodger blue
+> select clear
+> show #!10 models
+> select #24/K
+atoms, 6153 bonds, 775 residues, 1 model selected
+> select clear
+> select #24/K
+atoms, 6153 bonds, 775 residues, 1 model selected
+> color sel yellow green
+> color sel orange
+> select clear
+[Repeated 1 time(s)]
+> hide #!10 models
+> show #!8 models
+> hide #!8 models
+> show #!10 models
+> open
+> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_741_925_mcm2_cdc45_ctf4ctdx3_mcm5_model_0.cif
+Chain information for fold_mrc1_741_925_mcm2_cdc45_ctf4ctdx3_mcm5_model_0.cif
+#25
+---
+Chain | Description
+A | .
+B | .
+C | .
+D E F | .
+G | .
+> hide #25 models
+> show #25 models
+> hide #25 models
+> show #25 models
+> select add #25
+atoms, 31289 bonds, 3849 residues, 1 model selected
+> select subtract #25
+Nothing selected
+> select add #25
+atoms, 31289 bonds, 3849 residues, 1 model selected
+> hide sel target a
+> cartoon sel
+> select subtract #25
+Nothing selected
+> matchmaker #25/B to #24/B pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif,
+chain B (#24) with fold_mrc1_741_925_mcm2_cdc45_ctf4ctdx3_mcm5_model_0.cif,
+chain B (#25), sequence alignment score = 3315.9
+RMSD between 585 pruned atom pairs is 0.430 angstroms; (across all 650 pairs:
+.003)
+> hide #!10 models
+> matchmaker #25/C to #24/C pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif,
+chain C (#24) with fold_mrc1_741_925_mcm2_cdc45_ctf4ctdx3_mcm5_model_0.cif,
+chain C (#25), sequence alignment score = 4205.3
+RMSD between 670 pruned atom pairs is 0.557 angstroms; (across all 868 pairs:
+.308)
+> hide #24 models
+> show #24 models
+> hide #24 models
+> select #25/A
+atoms, 1527 bonds, 185 residues, 1 model selected
+> color sel red
+> color sel orange red
+> select clear
+> show #24 models
+> select #25/C
+atoms, 7047 bonds, 868 residues, 1 model selected
+> color sel magenta
+> select clear
+[Repeated 1 time(s)]
+> select #25/G
+atoms, 6153 bonds, 775 residues, 1 model selected
+> color sel coral
+> color sel sienna
+> select clear
+[Repeated 1 time(s)]
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> hide #25 models
+> select #24/H,I,J
+atoms, 11241 bonds, 1371 residues, 1 model selected
+> color sel slate gray
+> color sel cadet blue
+> select add #24
+atoms, 35097 bonds, 4327 residues, 1 model selected
+> select subtract #24
+Nothing selected
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #25 models
+> select #25/D,E,F
+atoms, 11241 bonds, 1371 residues, 1 model selected
+> color sel medium aquamarine
+> color sel cyan
+> select clear
+> show #24 models
+> show #!10 models
+> hide #25 models
+> hide #24 models
+> hide #!10 models
+> show #24 models
+> show #25 models
+> hide #25 models
+> show #25 models
+> hide #24 models
+> show #!10 models
+> hide #!10 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> hide #24 models
+> hide #25 models
+> open
+> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_323_337_tof1_model_0.cif
+Chain information for fold_mrc1_323_337_tof1_model_0.cif #26
+---
+Chain | Description
+A | .
+B | .
+> select #26/B
+atoms, 10133 bonds, 1238 residues, 1 model selected
+> color sel slate blue
+> color sel medium slate blue
+[Repeated 4 time(s)]
+> color sel dark slate blue
+[Repeated 1 time(s)]
+> color sel rebecca purple
+[Repeated 4 time(s)]
+> select clear
+> show #!10 models
+> matchmaker #26/B to #10/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain X (#10) with
+fold_mrc1_323_337_tof1_model_0.cif, chain B (#26), sequence alignment score =
+.8
+RMSD between 514 pruned atom pairs is 0.989 angstroms; (across all 665 pairs:
+.879)
+> open
+> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_469_492_tof1_mcm2_mcm6_model_0.cif
+Chain information for fold_mrc1_469_492_tof1_mcm2_mcm6_model_0.cif #27
+---
+Chain | Description
+A | .
+B | .
+C | .
+D | .
+> matchmaker #27/B to #10/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain X (#10) with
+fold_mrc1_469_492_tof1_mcm2_mcm6_model_0.cif, chain B (#27), sequence
+alignment score = 5344.2
+RMSD between 523 pruned atom pairs is 0.976 angstroms; (across all 665 pairs:
+.339)
+> select #27/B
+atoms, 10133 bonds, 1238 residues, 1 model selected
+> color sel blue violet
+> select #27/A
+atoms, 202 bonds, 24 residues, 1 model selected
+> color sel red
+> select #27/C
+atoms, 7047 bonds, 868 residues, 1 model selected
+> color sel orchid
+> color sel medium orchid
+[Repeated 1 time(s)]
+> color sel dark orchid
+> color sel medium orchid
+> select clear
+> select #27/D
+atoms, 8057 bonds, 1017 residues, 1 model selected
+> color sel light coral
+> select clear
+> hide #26 models
+> open
+> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_385_456_mcm6_model_0.cif
+Chain information for fold_mrc1_385_456_mcm6_model_0.cif #28
+---
+Chain | Description
+A | .
+B | .
+> hide #27 models
+> hide #28 models
+> show #28 models
+> select #28/A
+atoms, 562 bonds, 72 residues, 1 model selected
+> color sel red
+> select clear
+> matchmaker #28/B to #10/AB pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain AB (#10) with
+fold_mrc1_385_456_mcm6_model_0.cif, chain B (#28), sequence alignment score =
+.2
+RMSD between 300 pruned atom pairs is 0.858 angstroms; (across all 332 pairs:
+.385)
+> hide #28 models
+> show #28 models
+> hide #!10 models
+> show #!10 models
+> matchmaker #28/B to #10/8 pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain 8 (#10) with
+fold_mrc1_385_456_mcm6_model_0.cif, chain B (#28), sequence alignment score =
+.4
+RMSD between 253 pruned atom pairs is 0.826 angstroms; (across all 305 pairs:
+.667)
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> select #28/A
+atoms, 562 bonds, 72 residues, 1 model selected
+> color sel dark red
+> select #28/B
+atoms, 8057 bonds, 1017 residues, 1 model selected
+> color sel orange
+> select clear
+> open
+> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_813_865_mcm2_cdc45_model_0.cif
+Chain information for fold_mrc1_813_865_mcm2_cdc45_model_0.cif #29
+---
+Chain | Description
+A | .
+B | .
+C | .
+> select #29/A
+atoms, 451 bonds, 53 residues, 1 model selected
+> color sel red
+> select clear
+> select #29/B
+atoms, 5321 bonds, 650 residues, 1 model selected
+> color sel pale violet red
+> select clear
+> matchmaker #29/B to #10/2 pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain 2 (#10) with
+fold_mrc1_813_865_mcm2_cdc45_model_0.cif, chain B (#29), sequence alignment
+score = 13
+Fewer than 3 residues aligned; cannot match extended_structure, chain 2 with
+fold_mrc1_813_865_mcm2_cdc45_model_0.cif, chain B
+> select #29/B
+atoms, 5321 bonds, 650 residues, 1 model selected
+> select #29/C
+atoms, 7047 bonds, 868 residues, 1 model selected
+> matchmaker #29/C to #10/2 pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain 2 (#10) with
+fold_mrc1_813_865_mcm2_cdc45_model_0.cif, chain C (#29), sequence alignment
+score = 3493.1
+RMSD between 246 pruned atom pairs is 0.605 angstroms; (across all 293 pairs:
+.580)
+> color sel pale violet red
+> select #29/B
+atoms, 5321 bonds, 650 residues, 1 model selected
+> color sel gray
+[Repeated 5 time(s)]
+> color sel light gray
+> color sel gray
+> color sel light yellow
+[Repeated 1 time(s)]
+> color sel old lace
+[Repeated 1 time(s)]
+> color sel antique white
+[Repeated 1 time(s)]
+> color sel ghost white
+> color sel mint cream
+> color sel white smoke
+[Repeated 1 time(s)]
+> color sel beige
+[Repeated 1 time(s)]
+> color sel azure
+> color sel wheat
+[Repeated 1 time(s)]
+> select clear
+> hide #28 models
+> hide #29 models
+> show #29 models
+> hide #29 models
+> show #29 models
+> hide #29 models
+> show #29 models
+> hide #29 models
+> show #29 models
+> hide #29 models
+> open
+> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_908_925_cdc45_model_0.cif
+Chain information for fold_mrc1_908_925_cdc45_model_0.cif #30
+---
+Chain | Description
+A | .
+B | .
+> select #30/B
+atoms, 5321 bonds, 650 residues, 1 model selected
+> color sel lavender
+> color sel gainsboro
+> color sel dim gray
+> color sel gray
+> color sel light gray
+> color sel thistle
+[Repeated 1 time(s)]
+> select #30/A
+atoms, 146 bonds, 18 residues, 1 model selected
+> color sel red
+> select clear
+> matchmaker #30/B to #10/P pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain P (#10) with
+fold_mrc1_908_925_cdc45_model_0.cif, chain B (#30), sequence alignment score =
+.5
+RMSD between 536 pruned atom pairs is 0.657 angstroms; (across all 564 pairs:
+.134)
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
+\u2014\u2014\u2014 End of log from Mon Sep 16 15:36:42 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> open
+> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_0.cif
+Chain information for
+fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_0.cif #31
+---
+Chain | Description
+A | .
+B | .
+C | .
+D | .
+E | .
+F | .
+> open
+> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_1.cif
+Chain information for
+fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_1.cif #32
+---
+Chain | Description
+A | .
+B | .
+C | .
+D | .
+E | .
+F | .
+> open
+> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_2.cif
+Chain information for
+fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_2.cif #33
+---
+Chain | Description
+A | .
+B | .
+C | .
+D | .
+E | .
+F | .
+> hide #30 models
+> hide #32 models
+> hide #33 models
+> hide #31 models
+> show #31 models
+> ui tool show Matchmaker
+> matchmaker #31/A to #10/2 pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain 2 (#10) with
+fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_0.cif, chain A (#31),
+sequence alignment score = 3496.1
+RMSD between 253 pruned atom pairs is 0.662 angstroms; (across all 293 pairs:
+.847)
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> select add #31
+atoms, 38162 bonds, 4714 residues, 1 model selected
+> show #32 models
+> show #33 models
+> select add #32
+atoms, 76324 bonds, 9428 residues, 2 models selected
+> select add #33
+atoms, 114486 bonds, 14142 residues, 3 models selected
+> hide sel target a
+> cartoon sel
+> select subtract #33
+atoms, 76324 bonds, 9428 residues, 2 models selected
+> select subtract #32
+atoms, 38162 bonds, 4714 residues, 1 model selected
+> select subtract #31
+Nothing selected
+> hide #32 models
+> hide #33 models
+> show #32 models
+> show #33 models
+> select #31/A #32/A #33/A
+atoms, 21141 bonds, 2604 residues, 3 models selected
+> color sel hot pink
+> select #31/B #32/B #33/B
+atoms, 7926 bonds, 1002 residues, 3 models selected
+> color sel yellow
+> select #31/C #32/C #33/C
+atoms, 24171 bonds, 3051 residues, 3 models selected
+> color sel orange
+> select #31/D #32/D #33/D
+atoms, 15963 bonds, 1950 residues, 3 models selected
+> color sel light gray
+> select #31/E #32/E #33/E
+atoms, 30399 bonds, 3714 residues, 3 models selected
+> ui tool show "Color Actions"
+> color sel slate blue
+> select #31/F #32/F #33/F
+atoms, 14886 bonds, 1821 residues, 3 models selected
+> color sel red
+> select add #31
+atoms, 48086 bonds, 5928 residues, 3 models selected
+> select add #32
+atoms, 81286 bonds, 10035 residues, 3 models selected
+> select subtract #31
+atoms, 43124 bonds, 5321 residues, 2 models selected
+> select subtract #32
+atoms, 4962 bonds, 607 residues, 1 model selected
+> select add #33
+atoms, 38162 bonds, 4714 residues, 1 model selected
+> select subtract #33
+Nothing selected
+> select clear
+> matchmaker #32/A to #10/2 pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain 2 (#10) with
+fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_1.cif, chain A (#32),
+sequence alignment score = 3505.1
+RMSD between 253 pruned atom pairs is 0.693 angstroms; (across all 293 pairs:
+.550)
+> matchmaker #33/A to #10/2 pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain 2 (#10) with
+fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_2.cif, chain A (#33),
+sequence alignment score = 3502.1
+RMSD between 258 pruned atom pairs is 0.659 angstroms; (across all 293 pairs:
+.500)
+> lighting simple
+> hide #32 models
+> hide #33 models
+> show #33 models
+> hide #33 models
+> show #33 models
+> hide #33 models
+> show #33 models
+> hide #33 models
+> show #32 models
+> hide #32 models
+> show #32 models
+> hide #31 models
+> show #31 models
+> hide #31 models
+> show #31 models
+> hide #31 models
+> show #31 models
+> hide #32 models
+> show #32 models
+> hide #32 models
+> show #32 models
+> hide #32 models
+> show #32 models
+> hide #32 models
+> show #32 models
+> hide #32 models
+> show #32 models
+> hide #32 models
+> hide #!10 models
+> show #!50 models
+> hide #!50 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
+\u2014\u2014\u2014 End of log from Tue Sep 24 13:00:23 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> lighting simple
+> open /Users/cvetkom/Documents/pdb/4c95_Ctf4_Sld5.pdb
+c95_Ctf4_Sld5.pdb title:
+Crystal structure of the carboxy-terminal domain of yeast CTF4 bound to SLD5
+[more info...]
+Chain information for 4c95_Ctf4_Sld5.pdb #34
+---
+Chain | Description
+A B C | No description available
+D E | No description available
+atoms have alternate locations. Control/examine alternate locations with
+Altloc Explorer [start tool...] or the altlocs command.
+> select add #34
+atoms, 9722 bonds, 4 pseudobonds, 1360 residues, 2 models selected
+> hide sel atoms
+> show sel cartoons
+> select subtract #34
+Nothing selected
+> select #34/A
+atoms, 3493 bonds, 2 pseudobonds, 510 residues, 2 models selected
+> select #34/B
+atoms, 3550 bonds, 1 pseudobond, 498 residues, 2 models selected
+> select #34/C
+atoms, 2473 bonds, 1 pseudobond, 326 residues, 2 models selected
+> select #34/D
+atoms, 103 bonds, 13 residues, 1 model selected
+> select #34/E
+atoms, 103 bonds, 13 residues, 1 model selected
+> select #34/D,E
+atoms, 206 bonds, 26 residues, 1 model selected
+> color sel red
+> hide #31 models
+> open
+> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_23_3c_ctf4_mrc1_1081_1096/fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif
+Chain information for fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif #35
+---
+Chain | Description
+A B C | .
+D | .
+> show #!10 models
+> hide #!23 models
+> select clear
+> ui tool show Matchmaker
+> matchmaker #34/B to #10/S pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain S (#10) with 4c95_Ctf4_Sld5.pdb, chain B
+(#34), sequence alignment score = 2232.7
+RMSD between 391 pruned atom pairs is 0.878 angstroms; (across all 424 pairs:
+.248)
+> matchmaker #35/A to #10/S pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain S (#10) with
+fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif, chain A (#35), sequence
+alignment score = 2301.6
+RMSD between 411 pruned atom pairs is 0.645 angstroms; (across all 425 pairs:
+.817)
+> hide #!10 models
+> show #!10 models
+> show #!23 models
+> hide #!23 models
+> show #!42 models
+> color #42 #b2b2ffeb models
+> color #42 #b2b2ffff models
+> color #42 #b2b2ffb7 models
+> color #42 #b2b2ff95 models
+> color #42 #b2b2ff84 models
+> hide #!10 models
+> lighting soft
+> lighting full
+> lighting simple
+> ui tool show "Side View"
+> hide #!42 models
+> show #!42 models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> hide #35 models
+> show #35 models
+> hide #!42 models
+> show #!42 models
+> hide #35 models
+> show #35 models
+> select #35/D
+atoms, 129 bonds, 16 residues, 1 model selected
+> color sel orange
+> color sel orange red
+> color sel orange
+> select clear
+> hide #!34 models
+> show #!34 models
+> ui tool show "Fit in Map"
+> hide #!42 models
+> show #!42 models
+> fitmap #34 inMap #42
+Fit molecule 4c95_Ctf4_Sld5.pdb (#34) to map sharpened_replisome.mrc copy
+(#42) using 9660 atoms
+average map value = 0.381, steps = 128
+shifted from previous position = 2.63
+rotated from previous position = 6.17 degrees
+atoms outside contour = 4354, contour level = 0.3
+Position of 4c95_Ctf4_Sld5.pdb (#34) relative to sharpened_replisome.mrc copy
+(#42) coordinates:
+Matrix rotation and translation
+.28572805 -0.31647925 0.90454429 338.42345045
+-0.43402411 -0.88427381 -0.17228725 294.11719747
+.85439016 -0.34336673 -0.39002146 373.35631167
+Axis -0.80114939 0.23486712 -0.55045172
+Axis point 0.00000000 201.64420355 57.39058667
+Rotation angle (degrees) 173.87077288
+Shift along axis -407.56390486
+> fitmap #35 inMap #42
+Fit molecule fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif (#35) to map
+sharpened_replisome.mrc copy (#42) using 11336 atoms
+average map value = 0.4111, steps = 68
+shifted from previous position = 0.628
+rotated from previous position = 1.83 degrees
+atoms outside contour = 4371, contour level = 0.3
+Position of fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif (#35) relative
+to sharpened_replisome.mrc copy (#42) coordinates:
+Matrix rotation and translation
+-0.98706242 -0.07882972 0.13961966 285.86123137
+.08488406 0.48183004 0.87214363 299.11678968
+-0.13602378 0.87271169 -0.46890494 372.10103280
+Axis 0.00177188 0.85978425 0.51065438
+Axis point 149.35362784 0.00000000 83.84935178
+Rotation angle (degrees) 170.77580491
+Shift along axis 447.69744149
+> hide #35 models
+> hide #!42 models
+> show #!42 models
+> hide #!34 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> hide #!42 models
+> show #!42 models
+> color #42 #b2b2ffff models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> ui tool show "Side View"
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!47 models
+> show #!46 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> hide #!42 models
+> hide #!46 models
+> show #!43 models
+> hide #!43 models
+> show #!34 models
+> show #33 models
+> hide #33 models
+> show #35 models
+> hide #!34 models
+> show #!34 models
+> hide #35 models
+> show #35 models
+> show #!2 models
+> hide #!2 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
+\u2014\u2014\u2014 End of log from Wed Sep 25 19:02:23 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> hide #!34 models
+> hide #35 models
+> show #35 models
+> hide #35 models
+> close #2-3
+> close #7
+> close #11
+> close #9
+> show #!50 models
+> hide #!50 models
+> show #!53 models
+> close #53
+> show #!52 models
+> close #52
+> show #!16 models
+> hide #!16 models
+> show #!17 models
+> hide #!17 models
+> show #!18 models
+> hide #!18 models
+> show #!19 models
+> hide #!19 models
+> show #!10 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
+\u2014\u2014\u2014 End of log from Fri Oct 4 13:17:26 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> hide #!10 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J819_005_volume_map_EMready.mrc
+Opened cryosparc_P17_J819_005_volume_map_EMready.mrc as #2, grid size
+,588,588, pixel 0.95, shown at level 0.0383, step 4, values float32
+> volume #2 step 1
+> volume #2 level 0.9283
+> volume #2 level 1.647
+> ui tool show "Side View"
+> hide #!2 models
+> show #!21 models
+> show #!2 models
+> select add #2
+models selected
+> lighting simple
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #2,0.21372,0.65189,-0.72758,228.01,-0.15215,0.75791,0.63437,-52.313,0.96497,-0.024879,0.26116,-76.828
+> view matrix models
+> #2,-0.22904,0.42092,-0.8777,455.06,-0.48229,0.73415,0.47793,87.401,0.84554,0.53277,0.034859,-139.12
+> view matrix models
+> #2,-0.30253,0.24312,-0.92161,536.06,-0.68897,0.61238,0.38771,202.38,0.65863,0.75225,-0.017761,-133.46
+> view matrix models
+> #2,-0.17917,0.019523,-0.98362,578.75,-0.64564,0.75206,0.13253,216.8,0.74233,0.65881,-0.12214,-104.65
+> view matrix models
+> #2,-0.39996,0.21624,-0.89066,563.08,-0.18128,0.93391,0.30815,-9.3049,0.89843,0.28471,-0.33432,8.6733
+> view matrix models
+> #2,-0.45252,0.485,-0.74833,467.43,0.38691,0.86285,0.32525,-154.48,0.80345,-0.14235,-0.57811,215.56
+> view matrix models
+> #2,-0.19899,0.25008,-0.94756,511.54,0.14679,0.96359,0.22349,-88.484,0.96895,-0.094621,-0.22845,66.354
+> view matrix models
+> #2,-0.40366,0.20697,-0.89119,566.81,-0.0090314,0.97313,0.23009,-48.812,0.91486,0.10093,-0.39095,69.189
+> view matrix models
+> #2,-0.42359,0.12332,-0.89742,597.11,0.0008642,0.99074,0.13574,-32.363,0.90585,0.056721,-0.41978,91.291
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,-0.42359,0.12332,-0.89742,572.5,0.0008642,0.99074,0.13574,-244.94,0.90585,0.056721,-0.41978,20.155
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #2,-0.42268,0.11844,-0.8985,573.87,0.0011522,0.99149,0.13015,-243.8,0.90628,0.053978,-0.41923,20.651
+> view matrix models
+> #2,-0.54332,-0.16268,-0.82361,666.33,-0.42868,0.89727,0.10557,-90.185,0.72182,0.41043,-0.55725,9.6598
+> view matrix models
+> #2,-0.59204,-0.092954,-0.80053,654.96,-0.41205,0.88859,0.20156,-117.01,0.6926,0.44919,-0.56439,9.0402
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,-0.59204,-0.092954,-0.80053,657.43,-0.41205,0.88859,0.20156,-126.64,0.6926,0.44919,-0.56439,12.296
+> view matrix models
+> #2,-0.59204,-0.092954,-0.80053,663.52,-0.41205,0.88859,0.20156,-124.44,0.6926,0.44919,-0.56439,2.3033
+> ui mousemode right zoom
+> ui tool show "Fit in Map"
+> fitmap #2 inMap #21
+Fit map cryosparc_P17_J819_005_volume_map_EMready.mrc in map
+cryosparc_P17_J819_005_volume_map.mrc using 740829 points
+correlation = 0.938, correlation about mean = 0.7691, overlap = 1.576e+06
+steps = 160, shift = 3.85, angle = 10.8 degrees
+Position of cryosparc_P17_J819_005_volume_map_EMready.mrc (#2) relative to
+cryosparc_P17_J819_005_volume_map.mrc (#21) coordinates:
+Matrix rotation and translation
+.99999999 0.00005310 -0.00009395 0.01216343
+-0.00005312 0.99999998 -0.00020453 0.08100750
+.00009394 0.00020453 0.99999998 -0.07859161
+Axis 0.88443714 -0.40622568 -0.22967726
+Axis point 0.00000000 388.90207101 387.88928499
+Rotation angle (degrees) 0.01324986
+Shift along axis -0.00409883
+> select subtract #2
+Nothing selected
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!20 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> hide #!20 models
+> show #!42 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J842_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #3, grid size
+,588,588, pixel 0.95, shown at level 0.15, step 4, values float32
+> volume #3 step 1
+> volume #3 level 0.2175
+> volume #3 level 0.4032
+> select add #3
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #3,0.96087,0.15628,0.2287,-100.29,-0.086083,0.95323,-0.28971,123.99,-0.26328,0.25869,0.92939,24.765
+> view matrix models
+> #3,0.94784,0.022072,0.31799,-87.222,0.026112,0.98887,-0.14647,39.853,-0.31769,0.14713,0.93671,67.954
+> ui mousemode right "translate selected models"
+> view matrix models
+> #3,0.94784,0.022072,0.31799,-188.13,0.026112,0.98887,-0.14647,-129.94,-0.31769,0.14713,0.93671,62.858
+> view matrix models
+> #3,0.94784,0.022072,0.31799,-118.63,0.026112,0.98887,-0.14647,-168.34,-0.31769,0.14713,0.93671,-44.135
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #3,0.79338,0.092061,0.60172,-179.94,0.1255,0.94252,-0.30967,-134.37,-0.59565,0.32121,0.73623,46.771
+> ui mousemode right "translate selected models"
+> view matrix models
+> #3,0.79338,0.092061,0.60172,-166.19,0.1255,0.94252,-0.30967,-142.23,-0.59565,0.32121,0.73623,35.37
+> view matrix models
+> #3,0.79338,0.092061,0.60172,-165.26,0.1255,0.94252,-0.30967,-141.13,-0.59565,0.32121,0.73623,35.671
+> select subtract #3
+Nothing selected
+> fitmap #3 inMap #42
+Fit map cryosparc_P17_J842_005_volume_map_sharp.mrc in map
+sharpened_replisome.mrc copy using 329084 points
+correlation = 1, correlation about mean = 0.9999, overlap = 1.568e+05
+steps = 236, shift = 0.4, angle = 16.9 degrees
+Position of cryosparc_P17_J842_005_volume_map_sharp.mrc (#3) relative to
+sharpened_replisome.mrc copy (#42) coordinates:
+Matrix rotation and translation
+.00000000 -0.00001351 0.00004557 -0.02152036
+.00001352 1.00000000 -0.00003397 0.01017840
+-0.00004557 0.00003397 1.00000000 0.00711885
+Axis 0.58150158 0.77996616 0.23131947
+Axis point 171.08172050 0.00000000 434.91154679
+Rotation angle (degrees) 0.00334730
+Shift along axis -0.00292859
+> hide #!42 models
+> show #!42 models
+> volume #3 level 0.3
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> ui mousemode right zoom
+> ui tool show "Hide Dust"
+> surface undust #42
+> fitmap #3 inMap #42
+Fit map cryosparc_P17_J842_005_volume_map_sharp.mrc in map
+sharpened_replisome.mrc copy using 586182 points
+correlation = 1, correlation about mean = 0.9999, overlap = 1.874e+05
+steps = 28, shift = 0.0238, angle = 0.00733 degrees
+Position of cryosparc_P17_J842_005_volume_map_sharp.mrc (#3) relative to
+sharpened_replisome.mrc copy (#42) coordinates:
+Matrix rotation and translation
+.00000000 0.00000906 -0.00005933 0.02130757
+-0.00000906 1.00000000 0.00003559 -0.01782195
+.00005933 -0.00003559 1.00000000 0.00029158
+Axis -0.51008916 -0.85026779 -0.12982191
+Axis point -14.19118466 0.00000000 395.65343560
+Rotation angle (degrees) 0.00399795
+Shift along axis 0.00424682
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/Jacob_cryosparc_P5_J117_006_volume_map.mrc
+Opened Jacob_cryosparc_P5_J117_006_volume_map.mrc as #7, grid size
+,480,480, pixel 0.95, shown at level 0.152, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc
+Opened Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc as #9, grid size
+,480,480, pixel 0.95, shown at level 0.28, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc
+Opened Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc as #11, grid size
+,480,480, pixel 0.95, shown at level 0.569, step 2, values float32
+> volume #11 level 2.423
+> volume #9 level 0.9574
+> volume #11 step 1
+> volume #9 step 1
+> volume #7 step 1
+> volume #7 level 0.2399
+> select add #7
+models selected
+> select add #9
+models selected
+> select add #11
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #7,-0.31536,0.44395,0.83873,0.5068,-0.77807,0.38503,-0.49635,422.96,-0.54329,-0.80911,0.224,478.2,#9,-0.31536,0.44395,0.83873,0.5068,-0.77807,0.38503,-0.49635,422.96,-0.54329,-0.80911,0.224,478.2,#11,-0.31536,0.44395,0.83873,0.5068,-0.77807,0.38503,-0.49635,422.96,-0.54329,-0.80911,0.224,478.2
+> view matrix models
+> #7,-0.73321,-0.54683,0.4042,411.11,0.31221,-0.79877,-0.51428,443.38,0.60409,-0.25088,0.7564,-22.885,#9,-0.73321,-0.54683,0.4042,411.11,0.31221,-0.79877,-0.51428,443.38,0.60409,-0.25088,0.7564,-22.885,#11,-0.73321,-0.54683,0.4042,411.11,0.31221,-0.79877,-0.51428,443.38,0.60409,-0.25088,0.7564,-22.885
+> view matrix models
+> #7,-0.27775,-0.26716,0.92276,128.06,0.32065,-0.93125,-0.1731,391.13,0.90556,0.2478,0.34432,-103.14,#9,-0.27775,-0.26716,0.92276,128.06,0.32065,-0.93125,-0.1731,391.13,0.90556,0.2478,0.34432,-103.14,#11,-0.27775,-0.26716,0.92276,128.06,0.32065,-0.93125,-0.1731,391.13,0.90556,0.2478,0.34432,-103.14
+> view matrix models
+> #7,0.8345,-0.016866,0.55076,-87.575,-0.27678,-0.87711,0.39251,380.66,0.47645,-0.47999,-0.73662,402.79,#9,0.8345,-0.016866,0.55076,-87.575,-0.27678,-0.87711,0.39251,380.66,0.47645,-0.47999,-0.73662,402.79,#11,0.8345,-0.016866,0.55076,-87.575,-0.27678,-0.87711,0.39251,380.66,0.47645,-0.47999,-0.73662,402.79
+> view matrix models
+> #7,0.93667,-0.11461,-0.33094,116.1,-0.073314,-0.98817,0.13471,419.63,-0.34246,-0.10191,-0.93399,548.21,#9,0.93667,-0.11461,-0.33094,116.1,-0.073314,-0.98817,0.13471,419.63,-0.34246,-0.10191,-0.93399,548.21,#11,0.93667,-0.11461,-0.33094,116.1,-0.073314,-0.98817,0.13471,419.63,-0.34246,-0.10191,-0.93399,548.21
+> view matrix models
+> #7,0.73012,-0.060917,-0.6806,231.63,-0.11744,-0.99238,-0.03716,470.33,-0.67315,0.10706,-0.73172,529.05,#9,0.73012,-0.060917,-0.6806,231.63,-0.11744,-0.99238,-0.03716,470.33,-0.67315,0.10706,-0.73172,529.05,#11,0.73012,-0.060917,-0.6806,231.63,-0.11744,-0.99238,-0.03716,470.33,-0.67315,0.10706,-0.73172,529.05
+> view matrix models
+> #7,-0.001777,-0.5744,-0.81857,538.78,-0.99932,-0.029179,0.022644,442.03,-0.036892,0.81806,-0.57396,195.39,#9,-0.001777,-0.5744,-0.81857,538.78,-0.99932,-0.029179,0.022644,442.03,-0.036892,0.81806,-0.57396,195.39,#11,-0.001777,-0.5744,-0.81857,538.78,-0.99932,-0.029179,0.022644,442.03,-0.036892,0.81806,-0.57396,195.39
+> view matrix models
+> #7,-0.19049,-0.64648,-0.73876,577.96,-0.97965,0.17364,0.10066,375.18,0.063205,0.74291,-0.66641,211.06,#9,-0.19049,-0.64648,-0.73876,577.96,-0.97965,0.17364,0.10066,375.18,0.063205,0.74291,-0.66641,211.06,#11,-0.19049,-0.64648,-0.73876,577.96,-0.97965,0.17364,0.10066,375.18,0.063205,0.74291,-0.66641,211.06
+> view matrix models
+> #7,0.12078,-0.88633,-0.44703,493.31,-0.85691,-0.32042,0.40377,385.39,-0.50111,0.33429,-0.79821,456.57,#9,0.12078,-0.88633,-0.44703,493.31,-0.85691,-0.32042,0.40377,385.39,-0.50111,0.33429,-0.79821,456.57,#11,0.12078,-0.88633,-0.44703,493.31,-0.85691,-0.32042,0.40377,385.39,-0.50111,0.33429,-0.79821,456.57
+> view matrix models
+> #7,0.37394,-0.74381,-0.554,430.71,-0.52804,-0.66181,0.53214,357.01,-0.76246,0.093543,-0.64024,530.6,#9,0.37394,-0.74381,-0.554,430.71,-0.52804,-0.66181,0.53214,357.01,-0.76246,0.093543,-0.64024,530.6,#11,0.37394,-0.74381,-0.554,430.71,-0.52804,-0.66181,0.53214,357.01,-0.76246,0.093543,-0.64024,530.6
+> view matrix models
+> #7,0.094335,-0.81529,-0.57132,512.56,-0.75251,-0.43412,0.49525,365.75,-0.65179,0.38321,-0.65446,445.97,#9,0.094335,-0.81529,-0.57132,512.56,-0.75251,-0.43412,0.49525,365.75,-0.65179,0.38321,-0.65446,445.97,#11,0.094335,-0.81529,-0.57132,512.56,-0.75251,-0.43412,0.49525,365.75,-0.65179,0.38321,-0.65446,445.97
+> ui mousemode right "translate selected models"
+> view matrix models
+> #7,0.094335,-0.81529,-0.57132,537.82,-0.75251,-0.43412,0.49525,374.18,-0.65179,0.38321,-0.65446,478.27,#9,0.094335,-0.81529,-0.57132,537.82,-0.75251,-0.43412,0.49525,374.18,-0.65179,0.38321,-0.65446,478.27,#11,0.094335,-0.81529,-0.57132,537.82,-0.75251,-0.43412,0.49525,374.18,-0.65179,0.38321,-0.65446,478.27
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #7,0.11661,-0.85928,-0.49804,525.44,-0.7549,-0.40255,0.51777,362.57,-0.64539,0.31559,-0.69561,501.2,#9,0.11661,-0.85928,-0.49804,525.44,-0.7549,-0.40255,0.51777,362.57,-0.64539,0.31559,-0.69561,501.2,#11,0.11661,-0.85928,-0.49804,525.44,-0.7549,-0.40255,0.51777,362.57,-0.64539,0.31559,-0.69561,501.2
+> view matrix models
+> #7,0.042668,-0.87433,-0.48344,541.79,-0.70941,-0.36724,0.60156,325.24,-0.70351,0.31729,-0.63593,499.88,#9,0.042668,-0.87433,-0.48344,541.79,-0.70941,-0.36724,0.60156,325.24,-0.70351,0.31729,-0.63593,499.88,#11,0.042668,-0.87433,-0.48344,541.79,-0.70941,-0.36724,0.60156,325.24,-0.70351,0.31729,-0.63593,499.88
+> ui mousemode right "translate selected models"
+> view matrix models
+> #7,0.042668,-0.87433,-0.48344,547.1,-0.70941,-0.36724,0.60156,161.23,-0.70351,0.31729,-0.63593,420.52,#9,0.042668,-0.87433,-0.48344,547.1,-0.70941,-0.36724,0.60156,161.23,-0.70351,0.31729,-0.63593,420.52,#11,0.042668,-0.87433,-0.48344,547.1,-0.70941,-0.36724,0.60156,161.23,-0.70351,0.31729,-0.63593,420.52
+> view matrix models
+> #7,0.042668,-0.87433,-0.48344,536.67,-0.70941,-0.36724,0.60156,152.08,-0.70351,0.31729,-0.63593,408.34,#9,0.042668,-0.87433,-0.48344,536.67,-0.70941,-0.36724,0.60156,152.08,-0.70351,0.31729,-0.63593,408.34,#11,0.042668,-0.87433,-0.48344,536.67,-0.70941,-0.36724,0.60156,152.08,-0.70351,0.31729,-0.63593,408.34
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #7,0.3552,-0.77911,-0.51654,454.02,-0.53271,-0.62278,0.57303,175.27,-0.76815,0.071622,-0.63625,476.51,#9,0.3552,-0.77911,-0.51654,454.02,-0.53271,-0.62278,0.57303,175.27,-0.76815,0.071622,-0.63625,476.51,#11,0.3552,-0.77911,-0.51654,454.02,-0.53271,-0.62278,0.57303,175.27,-0.76815,0.071622,-0.63625,476.51
+> view matrix models
+> #7,0.055668,-0.8551,-0.51546,537.02,-0.55774,-0.45484,0.6943,115.93,-0.82815,0.24884,-0.50224,419.95,#9,0.055668,-0.8551,-0.51546,537.02,-0.55774,-0.45484,0.6943,115.93,-0.82815,0.24884,-0.50224,419.95,#11,0.055668,-0.8551,-0.51546,537.02,-0.55774,-0.45484,0.6943,115.93,-0.82815,0.24884,-0.50224,419.95
+> view matrix models
+> #7,0.050991,-0.93462,-0.35197,517.42,-0.719,-0.27895,0.63657,126.78,-0.69313,0.2206,-0.68622,438.87,#9,0.050991,-0.93462,-0.35197,517.42,-0.719,-0.27895,0.63657,126.78,-0.69313,0.2206,-0.68622,438.87,#11,0.050991,-0.93462,-0.35197,517.42,-0.719,-0.27895,0.63657,126.78,-0.69313,0.2206,-0.68622,438.87
+> view matrix models
+> #7,-0.032857,-0.97559,-0.21713,513.67,-0.62463,-0.14955,0.76647,47.285,-0.78023,0.16081,-0.60447,452.3,#9,-0.032857,-0.97559,-0.21713,513.67,-0.62463,-0.14955,0.76647,47.285,-0.78023,0.16081,-0.60447,452.3,#11,-0.032857,-0.97559,-0.21713,513.67,-0.62463,-0.14955,0.76647,47.285,-0.78023,0.16081,-0.60447,452.3
+> view matrix models
+> #7,0.47176,-0.82185,-0.3194,391.59,-0.27024,-0.47958,0.83485,24.697,-0.8393,-0.30753,-0.44834,531.52,#9,0.47176,-0.82185,-0.3194,391.59,-0.27024,-0.47958,0.83485,24.697,-0.8393,-0.30753,-0.44834,531.52,#11,0.47176,-0.82185,-0.3194,391.59,-0.27024,-0.47958,0.83485,24.697,-0.8393,-0.30753,-0.44834,531.52
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> fitmap #7 inMap #23
+Fit map Jacob_cryosparc_P5_J117_006_volume_map.mrc in map
+cryosparc_P17_J842_005_volume_map.mrc using 611645 points
+correlation = 0.8586, correlation about mean = 0.4556, overlap = 8.71e+04
+steps = 244, shift = 17, angle = 22.5 degrees
+Position of Jacob_cryosparc_P5_J117_006_volume_map.mrc (#7) relative to
+cryosparc_P17_J842_005_volume_map.mrc (#23) coordinates:
+Matrix rotation and translation
+.55644781 -0.77930109 0.28819374 245.87868586
+-0.75685869 -0.33229301 0.56280215 362.24414012
+-0.34282757 -0.53129197 -0.77472452 653.58997201
+Axis -0.86611289 0.49953261 0.01776598
+Axis point 0.00000000 386.34237031 252.82329186
+Rotation angle (degrees) 140.83086649
+Shift along axis -20.39427278
+> hide #!7 models
+> show #!7 models
+> fitmap #9 inMap #23
+Fit map Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc in map
+cryosparc_P17_J842_005_volume_map.mrc using 166113 points
+correlation = 0.8354, correlation about mean = 0.2023, overlap = 1.093e+05
+steps = 240, shift = 17.3, angle = 22.5 degrees
+Position of Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc (#9) relative to
+cryosparc_P17_J842_005_volume_map.mrc (#23) coordinates:
+Matrix rotation and translation
+.55535502 -0.78023657 0.28777020 246.41094031
+-0.75768547 -0.33209636 0.56180488 362.67622759
+-0.34277328 -0.53004046 -0.77560530 653.54700022
+Axis -0.86582981 0.50001893 0.01788295
+Axis point 0.00000000 386.54023823 252.88749245
+Rotation angle (degrees) 140.91153143
+Shift along axis -20.31760982
+> fitmap #11 inMap #23
+Fit map Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc in map
+cryosparc_P17_J842_005_volume_map.mrc using 547647 points
+correlation = 0.755, correlation about mean = 0.2272, overlap = 1.157e+06
+steps = 244, shift = 16, angle = 22.6 degrees
+Position of Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc (#11) relative
+to cryosparc_P17_J842_005_volume_map.mrc (#23) coordinates:
+Matrix rotation and translation
+.55439930 -0.78039733 0.28917368 246.34842101
+-0.75807382 -0.33013049 0.56243927 362.20292573
+-0.34346106 -0.53103093 -0.77462290 653.67877730
+Axis -0.86543769 0.50070495 0.01766816
+Axis point 0.00000000 386.83809960 252.79416826
+Rotation angle (degrees) 140.82108735
+Shift along axis -20.29310612
+> ui mousemode right zoom
+> select subtract #7
+models selected
+> select subtract #9
+models selected
+> select subtract #11
+Nothing selected
+> hide #!7 models
+> show #!7 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> hide #!11 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> volume #9 level 0.7158
+> volume #9 level 0.7
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> volume #3 level 0.4
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!9 models
+> show #!9 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!20 models
+> hide #!9 models
+> show #!9 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> show #26 models
+> hide #26 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> show #26 models
+> hide #!20 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!50 models
+> hide #!9 models
+> hide #!50 models
+> show #!50 models
+> color #50 #b2b2b29c models
+> volume #50 level 3
+> volume #50 level 3.5
+> volume #50 level 3.6
+> volume #50 level 3.8
+> volume #50 level 4.5
+> show #!42 models
+> hide #!50 models
+> hide #!42 models
+> show #!3 models
+> select add #3
+models selected
+> color #3.1 gray
+> ui tool show "Color Actions"
+> color sel light blue
+> color sel light sky blue
+> color sel aquamarine
+> color sel light sky blue
+> select subtract #3
+Nothing selected
+> color #3 #87cefaa8 models
+> color #3 #87cefa98 models
+> color #3 #87cefaa7 models
+> color #3 #87cefa99 models
+> color #3 #87cefaa4 models
+> color #3 #87cefaa3 models
+> volume #3 level 0.35
+> fitmap #26 inMap #3
+Fit molecule fold_mrc1_323_337_tof1_model_0.cif (#26) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#3) using 10075 atoms
+average map value = 0.2438, steps = 52
+shifted from previous position = 0.293
+rotated from previous position = 0.36 degrees
+atoms outside contour = 7077, contour level = 0.35
+Position of fold_mrc1_323_337_tof1_model_0.cif (#26) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#3) coordinates:
+Matrix rotation and translation
+.84462737 0.15456521 -0.51255653 282.60576624
+.06681694 0.91949322 0.38738573 335.32756599
+.53116861 -0.36144406 0.76630157 241.89923621
+Axis -0.58158875 -0.81062320 -0.06815088
+Axis point -335.92841792 0.00000000 139.55904352
+Rotation angle (degrees) 40.07422511
+Shift along axis -452.67028623
+> volume #3 level 0.34
+> lighting soft
+> lighting full
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting full
+> lighting simple
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_J842_sharp_Mrc1_323-337_overview.png
+> supersample 6 width 1800 transparentBackground true
+> ui tool show "Side View"
+> rock y 20 136
+> volume #3 level 0.32
+> volume #3 level 0.33
+> rock y 20 136
+> movie record supersample 3 size 1800, 2000
+> rock y 20 136
+> wait
+> movie encode quality highest framerate 30 output
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MTC_J842_sharp_Mrc1_323-337_zoomed.mp4
+Movie saved to
+/Users/cvetkom/.../Replication_meeting_Cambridge_2024/CMGC4MTC_J842_sharp_Mrc1_323-337_zoomed.mp4
+> hide #!3 models
+> show #!50 models
+> volume #50 level 5
+> volume #50 level 4.6
+> movie encode quality highest framerate 30 output
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MTC_J842_EMReady_Mrc1_323-337_zoomed.mp4
+No frames have been recorded
+> movie record supersample 3 size 1800, 2000
+> rock y 20 136
+> wait
+> movie encode quality highest framerate 30 output
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MTC_J842_EMReady_Mrc1_323-337_zoomed.mp4
+Movie saved to
+/Users/cvetkom/.../Replication_meeting_Cambridge_2024/CMGC4MTC_J842_EMReady_Mrc1_323-337_zoomed.mp4
+> fitmap #26 inMap #50
+Fit molecule fold_mrc1_323_337_tof1_model_0.cif (#26) to map
+J842_005_volume_map_EMReady.mrc (#50) using 10075 atoms
+average map value = 2.525, steps = 52
+shifted from previous position = 0.107
+rotated from previous position = 0.359 degrees
+atoms outside contour = 7517, contour level = 4.6
+Position of fold_mrc1_323_337_tof1_model_0.cif (#26) relative to
+J842_005_volume_map_EMReady.mrc (#50) coordinates:
+Matrix rotation and translation
+.84685173 0.15716115 -0.50807727 282.58642125
+.06188411 0.91973007 0.38764280 335.21799844
+.52821633 -0.35971789 0.76914923 241.85487927
+Axis -0.58331859 -0.80883211 -0.07436418
+Axis point -334.58664400 0.00000000 135.85619956
+Rotation angle (degrees) 39.83740038
+Shift along axis -453.95833613
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_J842_EMReady_Mrc1_323-337_overview.png
+> supersample 6 width 1800 transparentBackground true
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
+> select add #26
+atoms, 10266 bonds, 1253 residues, 1 model selected
+> cartoon hide sel
+> show sel target ab
+> style sel ball
+Changed 10075 atom styles
+> color sel byhetero
+> select clear
+> cartoon #26,50
+> hide #26,50 target a
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> hide #26 models
+> show #26 models
+> hide #!50 models
+> show #!11 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!9 models
+> show #!7 models
+> hide #!11 models
+> hide #!7 models
+> show #!2 models
+> hide #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> select add #7
+models selected
+> ui tool show "Color Actions"
+> color sel turquoise
+> color sel light sea green
+> color #7 #b2ffff9d models
+> color #7 #b2ffffd9 models
+> color #7 #b2ffffb7 models
+> color #7 #b2ffffa7 models
+> color #7 #b2ffffa6 models
+> select clear
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/Jacob_J117_Mrc1_323-337_overview.png
+> supersample 6 width 1800 transparentBackground true
+> volume #7 level 0.22
+> volume #7 level 0.2
+> volume #7 level 0.18
+> volume #7 level 0.16
+> volume #7 level 0.18
+> volume #7 level 0.2
+> volume #7 level 0.18
+> rock y 20 136
+> movie record supersample 3 size 1800, 2000
+> rock y 20 136
+> wait
+> movie encode quality highest framerate 30 output
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/Jacob_J117_Mrc1_323-337_zoomed.mp4
+Movie saved to
+/Users/cvetkom/.../Replication_meeting_Cambridge_2024/Jacob_J117_Mrc1_323-337_zoomed.mp4
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
+===== Log before crash end =====
+Log:
+UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
+Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
+.27, shown at level 2.79, step 1, values float32
+Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
+at level 0.155, step 1, values float32
+Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
+#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
+float32
+Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
+shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
+pixel 0.95, shown at level 0.27, step 1, values float32
+Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
+pixel 0.95, shown at level 0.274, step 1, values float32
+Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
+.95, shown at level 4.6, step 1, values float32
+Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
+,588,588, pixel 0.95, shown at level 0.45, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
+pixel 0.95, shown at level 0.16, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
+pixel 0.95, shown at level 0.18, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map_EMready.mrc as #2, grid size
+,588,588, pixel 0.95, shown at level 1.65, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #3, grid size
+,588,588, pixel 0.95, shown at level 0.33, step 1, values float32
+Opened Jacob_cryosparc_P5_J117_006_volume_map.mrc as #7, grid size
+,480,480, pixel 0.95, shown at level 0.18, step 1, values float32
+Opened Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc as #9, grid size
+,480,480, pixel 0.95, shown at level 0.7, step 1, values float32
+Opened Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc as #11, grid size
+,480,480, pixel 0.95, shown at level 2.42, step 1, values float32
+Log from Mon Oct 7 10:20:32 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs
+Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
+.27, shown at level 2.79, step 1, values float32
+Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
+at level 0.155, step 1, values float32
+Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
+#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
+float32
+Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
+shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
+pixel 0.95, shown at level 0.27, step 1, values float32
+Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
+pixel 0.95, shown at level 0.274, step 1, values float32
+Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
+.95, shown at level 2.1, step 1, values float32
+Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
+,588,588, pixel 0.95, shown at level 0.45, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
+pixel 0.95, shown at level 0.16, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
+pixel 0.95, shown at level 0.18, step 1, values float32
+Log from Fri Oct 4 13:17:26 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
+Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
+.27, shown at level 2.79, step 1, values float32
+Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
+at level 0.155, step 1, values float32
+Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
+#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
+float32
+Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
+shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
+pixel 0.95, shown at level 0.27, step 1, values float32
+Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
+pixel 0.95, shown at level 0.274, step 1, values float32
+Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
+.95, shown at level 2.1, step 1, values float32
+Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
+level 0.32, step 1, values float32
+Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
+.255, step 1, values float32
+Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
+.78, step 1, values float32
+Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
+.78, step 1, values float32
+Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
+,588,588, pixel 0.95, shown at level 0.45, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
+pixel 0.95, shown at level 0.16, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
+pixel 0.95, shown at level 0.18, step 1, values float32
+Log from Wed Sep 25 19:02:23 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
+Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
+.27, shown at level 2.79, step 1, values float32
+Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
+at level 0.155, step 1, values float32
+Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
+#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
+float32
+Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
+shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
+pixel 0.95, shown at level 0.27, step 1, values float32
+Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
+pixel 0.95, shown at level 0.274, step 1, values float32
+Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
+.95, shown at level 2.1, step 1, values float32
+Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
+level 0.32, step 1, values float32
+Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
+.255, step 1, values float32
+Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
+.78, step 1, values float32
+Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
+.78, step 1, values float32
+Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
+,588,588, pixel 0.95, shown at level 0.45, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
+pixel 0.95, shown at level 0.16, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
+pixel 0.95, shown at level 0.18, step 1, values float32
+Log from Tue Sep 24 13:00:23 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
+Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
+.27, shown at level 2.79, step 1, values float32
+Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
+at level 0.155, step 1, values float32
+Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
+#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
+float32
+Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
+shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
+pixel 0.95, shown at level 0.27, step 1, values float32
+Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
+pixel 0.95, shown at level 0.274, step 1, values float32
+Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
+.95, shown at level 2.1, step 1, values float32
+Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
+level 0.32, step 1, values float32
+Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
+.255, step 1, values float32
+Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
+.78, step 1, values float32
+Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
+.78, step 1, values float32
+Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
+,588,588, pixel 0.95, shown at level 0.45, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
+pixel 0.95, shown at level 0.16, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
+pixel 0.95, shown at level 0.18, step 1, values float32
+Log from Mon Sep 16 15:36:42 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
+.27, shown at level 2.79, step 1, values float32
+Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
+at level 0.155, step 1, values float32
+Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
+#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
+float32
+Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
+shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
+pixel 0.95, shown at level 0.27, step 1, values float32
+Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
+pixel 0.95, shown at level 0.274, step 1, values float32
+Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
+.95, shown at level 2.1, step 1, values float32
+Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
+level 0.32, step 1, values float32
+Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
+.255, step 1, values float32
+Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
+.78, step 1, values float32
+Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
+.78, step 1, values float32
+Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Log from Wed Sep 11 12:56:29 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
+.27, shown at level 2.79, step 1, values float32
+Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
+at level 0.155, step 1, values float32
+Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
+#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
+float32
+Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
+shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
+pixel 0.95, shown at level 0.27, step 1, values float32
+Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
+pixel 0.95, shown at level 0.274, step 1, values float32
+Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
+.95, shown at level 2.1, step 1, values float32
+Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
+level 0.32, step 1, values float32
+Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
+.255, step 1, values float32
+Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
+.78, step 1, values float32
+Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
+.78, step 1, values float32
+Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Log from Mon Sep 9 04:24:31 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
+.27, shown at level 2.79, step 1, values float32
+Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
+at level 0.155, step 1, values float32
+Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
+#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
+float32
+Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
+shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
+pixel 0.95, shown at level 0.27, step 1, values float32
+Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
+pixel 0.95, shown at level 0.274, step 1, values float32
+Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
+.95, shown at level 2.1, step 1, values float32
+Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
+level 0.32, step 1, values float32
+Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
+.255, step 1, values float32
+Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
+.78, step 1, values float32
+Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
+.78, step 1, values float32
+Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
+level 2.78, step 1, values float32
+Opened volume sum 7 copy as #7, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Log from Fri Sep 6 19:48:00 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_2.cxs
+Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
+.27, shown at level 2.79, step 1, values float32
+Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
+at level 0.155, step 1, values float32
+Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
+#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
+float32
+Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
+shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
+pixel 0.95, shown at level 0.27, step 1, values float32
+Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
+pixel 0.95, shown at level 0.274, step 1, values float32
+Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
+.95, shown at level 2.1, step 1, values float32
+Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
+level 0.32, step 1, values float32
+Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
+.255, step 1, values float32
+Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Log from Fri Sep 6 19:04:03 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
+,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
+,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
+Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
+size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc as #3, grid size
+,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc as #4, grid size
+,440,440, pixel 0.95, shown at level 0.00374, step 2, values float32
+Opened cryosparc_P17_J1207_map_sharp.mrc as #5, grid size 440,440,440, pixel
+.95, shown at level 2.63e-06, step 2, values float32
+Opened cryosparc_P17_J1210_map_sharp.mrc as #6, grid size 440,440,440, pixel
+.95, shown at level 0.000291, step 2, values float32
+Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #7, grid size
+,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
+Opened cryosparc_P17_J1163_006_volume_map.mrc as #8, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #9, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J959_008_volume_map_zflip.mrc as #10, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened Ref3D_job802_run_class001.mrc as #11, grid size 588,588,588, pixel
+.95, shown at level 0.00416, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip as #12, grid size
+,440,440, pixel 0.95, shown at level 2.11, step 1, values float32
+Opened cryosparc_P17_J1207_map_sharp.mrc z flip as #13, grid size 440,440,440,
+pixel 0.95, shown at level 0.02, step 1, values float32
+Opened cryosparc_P17_J1210_map_sharp.mrc z flip as #14, grid size 440,440,440,
+pixel 0.95, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #15, grid size
+,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
+Opened cryosparc_P17_J535_003_volume_map_zflip.mrc as #16, grid size
+,588,588, pixel 0.95, shown at level 0.232, step 1, values float32
+Opened cryosparc_P17_J655_005_volume_map_sharp.mrc as #17, grid size
+,588,588, pixel 0.95, shown at level 0.427, step 1, values float32
+Opened cryosparc_P17_J645_010_volume_map_sharp.mrc as #18, grid size
+,588,588, pixel 0.95, shown at level 0.442, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #19, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #20, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #21, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc copy as #42, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy as #44, grid
+size 440,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #45, grid size
+,588,588, pixel 0.95, shown at level 0.957, step 1, values float32
+Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
+pixel 0.95, shown at level 0.27, step 1, values float32
+Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
+pixel 0.95, shown at level 0.227, step 1, values float32
+Log from Fri Sep 6 16:21:36 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
+,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
+,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
+Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
+size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc as #3, grid size
+,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc as #4, grid size
+,440,440, pixel 0.95, shown at level 0.00374, step 2, values float32
+Opened cryosparc_P17_J1207_map_sharp.mrc as #5, grid size 440,440,440, pixel
+.95, shown at level 2.63e-06, step 2, values float32
+Opened cryosparc_P17_J1210_map_sharp.mrc as #6, grid size 440,440,440, pixel
+.95, shown at level 0.000291, step 2, values float32
+Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #7, grid size
+,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
+Opened cryosparc_P17_J1163_006_volume_map.mrc as #8, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #9, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J959_008_volume_map_zflip.mrc as #10, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened Ref3D_job802_run_class001.mrc as #11, grid size 588,588,588, pixel
+.95, shown at level 0.00416, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip as #12, grid size
+,440,440, pixel 0.95, shown at level 2.11, step 1, values float32
+Opened cryosparc_P17_J1207_map_sharp.mrc z flip as #13, grid size 440,440,440,
+pixel 0.95, shown at level 0.02, step 1, values float32
+Opened cryosparc_P17_J1210_map_sharp.mrc z flip as #14, grid size 440,440,440,
+pixel 0.95, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #15, grid size
+,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
+Opened cryosparc_P17_J535_003_volume_map_zflip.mrc as #16, grid size
+,588,588, pixel 0.95, shown at level 0.232, step 1, values float32
+Opened cryosparc_P17_J655_005_volume_map_sharp.mrc as #17, grid size
+,588,588, pixel 0.95, shown at level 0.427, step 1, values float32
+Opened cryosparc_P17_J645_010_volume_map_sharp.mrc as #18, grid size
+,588,588, pixel 0.95, shown at level 0.442, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #19, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #20, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #21, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc copy as #42, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy as #44, grid
+size 440,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #45, grid size
+,588,588, pixel 0.95, shown at level 0.957, step 1, values float32
+Log from Wed Sep 4 08:32:44 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
+,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
+,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
+Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
+size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc as #3, grid size
+,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc as #4, grid size
+,440,440, pixel 0.95, shown at level 0.00374, step 2, values float32
+Opened cryosparc_P17_J1207_map_sharp.mrc as #5, grid size 440,440,440, pixel
+.95, shown at level 2.63e-06, step 2, values float32
+Opened cryosparc_P17_J1210_map_sharp.mrc as #6, grid size 440,440,440, pixel
+.95, shown at level 0.000291, step 2, values float32
+Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #7, grid size
+,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
+Opened cryosparc_P17_J1163_006_volume_map.mrc as #8, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #9, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J959_008_volume_map_zflip.mrc as #10, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened Ref3D_job802_run_class001.mrc as #11, grid size 588,588,588, pixel
+.95, shown at level 0.00416, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip as #12, grid size
+,440,440, pixel 0.95, shown at level 2.11, step 1, values float32
+Opened cryosparc_P17_J1207_map_sharp.mrc z flip as #13, grid size 440,440,440,
+pixel 0.95, shown at level 0.02, step 1, values float32
+Opened cryosparc_P17_J1210_map_sharp.mrc z flip as #14, grid size 440,440,440,
+pixel 0.95, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #15, grid size
+,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
+Opened cryosparc_P17_J535_003_volume_map_zflip.mrc as #16, grid size
+,588,588, pixel 0.95, shown at level 0.232, step 1, values float32
+Opened cryosparc_P17_J655_005_volume_map_sharp.mrc as #17, grid size
+,588,588, pixel 0.95, shown at level 0.427, step 1, values float32
+Opened cryosparc_P17_J645_010_volume_map_sharp.mrc as #18, grid size
+,588,588, pixel 0.95, shown at level 0.442, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #19, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #20, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #21, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc copy as #42, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Log from Wed Sep 4 05:32:36 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
+,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
+,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
+Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
+size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc as #3, grid size
+,440,440, pixel 0.95, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc as #4, grid size
+,440,440, pixel 0.95, shown at level 0.00374, step 2, values float32
+Opened cryosparc_P17_J1207_map_sharp.mrc as #5, grid size 440,440,440, pixel
+.95, shown at level 2.63e-06, step 2, values float32
+Opened cryosparc_P17_J1210_map_sharp.mrc as #6, grid size 440,440,440, pixel
+.95, shown at level 0.000291, step 2, values float32
+Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #7, grid size
+,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
+Opened cryosparc_P17_J1163_006_volume_map.mrc as #8, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #9, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J959_008_volume_map_zflip.mrc as #10, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened Ref3D_job802_run_class001.mrc as #11, grid size 588,588,588, pixel
+.95, shown at level 0.00416, step 1, values float32
+Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip as #12, grid size
+,440,440, pixel 0.95, shown at level 2.11, step 1, values float32
+Opened cryosparc_P17_J1207_map_sharp.mrc z flip as #13, grid size 440,440,440,
+pixel 0.95, shown at level 0.02, step 1, values float32
+Opened cryosparc_P17_J1210_map_sharp.mrc z flip as #14, grid size 440,440,440,
+pixel 0.95, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #15, grid size
+,440,440, pixel 0.95, shown at level 0.22, step 1, values float32
+Log from Tue Sep 3 13:30:10 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
+restore_snapshot for "Volume" returned None
+restore_snapshot for "VolumeSurface" returned None
+restore_snapshot for "Volume" returned None
+restore_snapshot for "VolumeSurface" returned None
+restore_snapshot for "Volume" returned None
+restore_snapshot for "VolumeSurface" returned None
+restore_snapshot for "Volume" returned None
+restore_snapshot for "VolumeSurface" returned None
+restore_snapshot for "Volume" returned None
+restore_snapshot for "VolumeSurface" returned None
+restore_snapshot for "Volume" returned None
+restore_snapshot for "VolumeSurface" returned None
+restore_snapshot for "Volume" returned None
+restore_snapshot for "VolumeSurface" returned None
+restore_snapshot for "Volume" returned None
+restore_snapshot for "VolumeSurface" returned None
+restore_snapshot for "Volume" returned None
+restore_snapshot for "VolumeSurface" returned None
+Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
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+Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
+pixel 1.9, shown at level 0.4, step 1, values float32
+Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
+pixel 1.9, shown at level 0.384, step 1, values float32
+Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
+.91, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
+pixel 1.9, shown at level 0.351, step 1, values float32
+Opened cryosparc_P17_J709_007_volume_map_sharp.mrc as #158, grid size
+,294,294, pixel 1.9, shown at level 0.338, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
+,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
+,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
+Opened cryosparc_P17_J786_005_volume_map_sharp.mrc as #181, grid size
+,588,588, pixel 0.95, shown at level 0.4, step 1, values float32
+Opened cryosparc_P17_J787_005_volume_map_sharp.mrc as #182, grid size
+,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
+Opened cryosparc_P17_J792_volume_map_sharp.mrc as #183, grid size 520,520,520,
+pixel 0.95, shown at level 0.392, step 1, values float32
+Opened cryosparc_P17_J757_volume_map.mrc as #186, grid size 520,520,520, pixel
+.95, shown at level 0.226, step 1, values float32
+Opened cryosparc_P17_J792_volume_map.mrc as #187, grid size 520,520,520, pixel
+.95, shown at level 0.247, step 1, values float32
+Opened cryosparc_P17_J797_009_volume_map_sharp.mrc as #184, grid size
+,520,520, pixel 0.95, shown at level 0.716, step 1, values float32
+Opened cryosparc_P17_J797_009_volume_map.mrc as #185, grid size 520,520,520,
+pixel 0.95, shown at level 0.31, step 1, values float32
+Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
+.95, shown at level 0.998, step 1, values float32
+Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
+pixel 0.95, shown at level 0.31, step 1, values float32
+Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
+,520,520, pixel 0.95, shown at level 0.6, step 1, values float32
+Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
+pixel 0.95, shown at level 0.301, step 1, values float32
+Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
+,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
+Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
+.95, shown at level 0.1, step 1, values float32
+Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
+pixel 0.95, shown at level 0.348, step 1, values float32
+Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
+,336,336, pixel 1.47, shown at level 0.283, step 1, values float32
+Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
+,336,336, pixel 1.47, shown at level 0.289, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
+pixel 0.95, shown at level 0.196, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
+,588,588, pixel 0.95, shown at level 0.46, step 1, values float32
+Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
+.95, shown at level 0.15, step 1, values float32
+Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
+,588,588, pixel 0.95, shown at level 0.35, step 1, values float32
+Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
+.95, shown at level 0.0845, step 1, values float32
+Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
+,192,192, pixel 2.91, shown at level 0.5, step 1, values float32
+Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
+,588,588, pixel 0.95, shown at level 0.239, step 1, values float32
+Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
+,588,588, pixel 0.95, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
+,520,520, pixel 0.95, shown at level 0.65, step 1, values float32
+Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
+pixel 1.9, shown at level 0.333, step 1, values float32
+Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
+,588,588, pixel 0.95, shown at level 0.158, step 1, values float32
+Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
+.95, shown at level 0.08, step 1, values float32
+Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
+.95, shown at level 0.15, step 1, values float32
+Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
+pixel 0.95, shown at level 0.154, step 1, values float32
+Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
+,128,128, pixel 4.36, shown at level 0.9, step 1, values float32
+Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 1, values float32
+Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
+pixel 0.95, shown at level 0.151, step 1, values float32
+Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
+,192,192, pixel 2.91, shown at level 0.348, step 1, values float32
+Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
+,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
+Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
+.9, shown at level 0.33, step 1, values float32
+Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
+.9, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
+,128,128, pixel 4.36, shown at level 1.25, step 1, values float32
+Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
+,128,128, pixel 4.36, shown at level 0.8, step 1, values float32
+Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
+.95, shown at level 0.0045, step 1, values float32
+Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
+.95, shown at level 0.0045, step 1, values float32
+Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
+level 1, step 1, values float32
+Opened Ref3D_job506_run_class001_bareNCP.mrc as #224, grid size 588,588,588,
+pixel 0.95, shown at level 0.0045, step 1, values float32
+Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
+pixel 1.9, shown at level 0.35, step 1, values float32
+Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
+pixel 1.9, shown at level 0.35, step 2, values float32
+Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
+pixel 1.9, shown at level 0.356, step 1, values float32
+Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc as #225, grid size
+,128,128, pixel 3.27, shown at level 1.6, step 1, values float32
+Opened cryosparc_P17_J981_class_00_00062_volume_sharp.mrc as #228, grid size
+,128,128, pixel 3.27, shown at level 1.82, step 1, values float32
+Opened cryosparc_P17_J967_class_00_final_volume.mrc as #229, grid size
+,192,192, pixel 2.18, shown at level 0.8, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #226, grid size
+,588,588, pixel 0.95, shown at level 0.33, step 1, values float32
+Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #230, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #231, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
+size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map.mrc as #239, grid size 588,588,588,
+pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map.mrc as #244, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J685_007_volume_map.mrc as #245, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J690_006_volume_map.mrc as #246, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J697_006_volume_map.mrc as #247, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J362_007_volume_map.mrc as #248, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J1103_006_volume_map.mrc as #249, grid size 294,294,294,
+pixel 1.9, shown at level 0.358, step 2, values float32
+Opened cryosparc_P17_J1105_008_volume_map.mrc as #250, grid size 294,294,294,
+pixel 1.9, shown at level 0.362, step 2, values float32
+Opened cryosparc_P17_J1106_006_volume_map.mrc as #251, grid size 294,294,294,
+pixel 1.9, shown at level 0.333, step 1, values float32
+Opened cryosparc_P17_J1107_006_volume_map.mrc as #252, grid size 294,294,294,
+pixel 1.9, shown at level 0.34, step 1, values float32
+Log from Tue Jul 30 11:34:25 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
+Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
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+Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
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+Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
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+Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
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+Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
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+Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
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+Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
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+Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
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+Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
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+Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
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+Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
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+Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
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+Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
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+Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
+.9, shown at level 0.0185, step 1, values float32
+Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
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+Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
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+Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
+,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
+Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
+.9, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
+,128,128, pixel 4.36, shown at level 1.25, step 1, values float32
+Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
+,128,128, pixel 4.36, shown at level 0.8, step 1, values float32
+Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
+.95, shown at level 0.0045, step 1, values float32
+Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
+.95, shown at level 0.0045, step 1, values float32
+Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
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+Opened Ref3D_job506_run_class001_bareNCP.mrc as #224, grid size 588,588,588,
+pixel 0.95, shown at level 0.0045, step 1, values float32
+Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
+pixel 1.9, shown at level 0.426, step 2, values float32
+Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
+pixel 1.9, shown at level 0.347, step 1, values float32
+Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
+pixel 1.9, shown at level 0.356, step 1, values float32
+Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc as #225, grid size
+,128,128, pixel 3.27, shown at level 1.6, step 1, values float32
+Opened cryosparc_P17_J981_class_00_00062_volume_sharp.mrc as #228, grid size
+,128,128, pixel 3.27, shown at level 1.82, step 1, values float32
+Opened cryosparc_P17_J967_class_00_final_volume.mrc as #229, grid size
+,192,192, pixel 2.18, shown at level 0.8, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #226, grid size
+,588,588, pixel 0.95, shown at level 0.33, step 1, values float32
+Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #230, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #231, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
+size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map.mrc as #239, grid size 588,588,588,
+pixel 0.95, shown at level 0.153, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 1, values float32
+Log from Wed Jul 24 16:21:27 2024UCSF ChimeraX version: 1.8 (2024-06-10)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
+Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
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+Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
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+Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
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+Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
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+Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
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+Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
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+Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
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+Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
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+Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
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+Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
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+Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
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+Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
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+Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
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+Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
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+Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
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+Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
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+Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
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+Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
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+Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
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+Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
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+Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
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+Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
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+Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
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+Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
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+Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
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+Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
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+Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
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+Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
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+Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
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+Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
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+Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
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+Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
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+Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
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+Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
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+Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
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+Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
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+Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
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+Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
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+Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
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+Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
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+Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
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+Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
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+Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
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+Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
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+Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
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+Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
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+Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
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+Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
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+Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
+,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
+Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
+pixel 1.9, shown at level 0.45, step 1, values float32
+Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
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+Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
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+Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
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+Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
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+Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
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+Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
+pixel 1.9, shown at level 0.45, step 1, values float32
+Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
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+Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
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+Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
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+Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
+pixel 1.9, shown at level 0.32, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
+pixel 1.9, shown at level 0.35, step 1, values float32
+Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
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+Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
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+Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
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+Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
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+Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
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+Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
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+Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
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+Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
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+Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
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+Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
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+Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
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+Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
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+Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
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+Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
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+Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
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+Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
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+Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
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+Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
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+Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
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+Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
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+Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
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+Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
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+Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
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+Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
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+Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
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+Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
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+Opened Cl3D_j590_run_it025_class001.mrc as #122, grid size 294,294,294, pixel
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+Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
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+Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
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+Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
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+Opened cryosparc_P17_J685_007_volume_map.mrc as #141, grid size 294,294,294,
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+Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
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+Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
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+Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
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+Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
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+Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
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+Opened cryosparc_P17_J690_006_volume_map.mrc as #147, grid size 294,294,294,
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+Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
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+Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
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+Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
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+Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
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+Opened cryosparc_P17_J691_008_volume_map.mrc z flip as #153, grid size
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+Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
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+Opened cryosparc_P17_J697_006_volume_map.mrc as #157, grid size 294,294,294,
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+Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
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+Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
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+Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
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+Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
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+Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
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+Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
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+Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
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+Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
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+Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
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+Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
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+Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
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+Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
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+Opened cryosparc_P17_J712_007_volume_map.mrc as #174, grid size 294,294,294,
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+Opened cryosparc_P17_J709_007_volume_map_sharp.mrc as #158, grid size
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+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
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+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
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+Opened cryosparc_P17_J786_005_volume_map_sharp.mrc as #181, grid size
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+Opened cryosparc_P17_J787_005_volume_map_sharp.mrc as #182, grid size
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+Opened cryosparc_P17_J792_volume_map_sharp.mrc as #183, grid size 520,520,520,
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+Opened cryosparc_P17_J757_volume_map.mrc as #186, grid size 520,520,520, pixel
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+Opened cryosparc_P17_J792_volume_map.mrc as #187, grid size 520,520,520, pixel
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+Opened cryosparc_P17_J797_009_volume_map_sharp.mrc as #184, grid size
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+Opened cryosparc_P17_J797_009_volume_map.mrc as #185, grid size 520,520,520,
+pixel 0.95, shown at level 0.31, step 1, values float32
+Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
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+Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
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+Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
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+Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
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+Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
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+Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
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+Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
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+Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
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+Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
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+Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
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+Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
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+Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
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+Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
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+Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
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+Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
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+Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
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+Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
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+Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
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+Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
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+Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
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+Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
+pixel 1.9, shown at level 0.333, step 1, values float32
+Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
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+Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
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+Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
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+Opened cryosparc_P17_J857_mask.mrc as #160, grid size 588,588,588, pixel 0.95,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
+pixel 0.95, shown at level 0.154, step 1, values float32
+Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
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+Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
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+Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
+pixel 0.95, shown at level 0.151, step 1, values float32
+Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
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+Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
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+Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
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+Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
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+Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
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+Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
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+Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
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+Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
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+Opened Ref3D_job506_run_class001_bareNCP.mrc as #224, grid size 588,588,588,
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+Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
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+Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
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+Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
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+Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc as #225, grid size
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+Opened cryosparc_P17_J981_class_00_00062_volume_sharp.mrc as #228, grid size
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+Opened cryosparc_P17_J967_class_00_final_volume.mrc as #229, grid size
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+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #226, grid size
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+Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #230, grid size
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+Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #231, grid size
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+Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
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+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
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+Opened cryosparc_P17_J864_007_volume_map.mrc as #239, grid size 588,588,588,
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+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #235, grid size
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+Log from Thu Jul 18 19:11:33 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
+© 2016-2023 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
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+Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
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+Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
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+Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
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+Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
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+Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
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+Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
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+Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
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+Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
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+Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
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+Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
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+Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
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+Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
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+Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
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+Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
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+Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
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+Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
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+Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
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+Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
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+Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
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+Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
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+Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
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+Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
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+Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
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+Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
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+Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
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+Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
+pixel 0.95, shown at level 0.348, step 1, values float32
+Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
+,336,336, pixel 1.47, shown at level 0.283, step 1, values float32
+Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
+,336,336, pixel 1.47, shown at level 0.289, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
+pixel 0.95, shown at level 0.196, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
+,588,588, pixel 0.95, shown at level 0.46, step 1, values float32
+Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
+.95, shown at level 0.15, step 1, values float32
+Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
+,588,588, pixel 0.95, shown at level 0.35, step 1, values float32
+Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
+.95, shown at level 0.0845, step 1, values float32
+Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
+,192,192, pixel 2.91, shown at level 0.5, step 1, values float32
+Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
+,588,588, pixel 0.95, shown at level 0.239, step 1, values float32
+Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
+,588,588, pixel 0.95, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
+,520,520, pixel 0.95, shown at level 0.55, step 1, values float32
+Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
+pixel 1.9, shown at level 0.333, step 1, values float32
+Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
+,588,588, pixel 0.95, shown at level 0.158, step 1, values float32
+Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
+.95, shown at level 0.08, step 1, values float32
+Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
+.95, shown at level 0.15, step 1, values float32
+Opened cryosparc_P17_J857_mask.mrc as #160, grid size 588,588,588, pixel 0.95,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
+pixel 0.95, shown at level 0.154, step 1, values float32
+Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
+,128,128, pixel 4.36, shown at level 0.9, step 1, values float32
+Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 1, values float32
+Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
+pixel 0.95, shown at level 0.151, step 1, values float32
+Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
+,192,192, pixel 2.91, shown at level 0.348, step 1, values float32
+Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
+,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
+Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
+.9, shown at level 0.33, step 1, values float32
+Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
+.9, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
+,128,128, pixel 4.36, shown at level 1.25, step 1, values float32
+Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
+,128,128, pixel 4.36, shown at level 0.8, step 1, values float32
+Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
+.95, shown at level 0.0045, step 1, values float32
+Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
+.95, shown at level 0.0045, step 1, values float32
+Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
+level 1, step 1, values float32
+Opened Ref3D_job506_run_class001_bareNCP.mrc as #224, grid size 588,588,588,
+pixel 0.95, shown at level 0.0045, step 1, values float32
+Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
+pixel 1.9, shown at level 0.426, step 2, values float32
+Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
+pixel 1.9, shown at level 0.347, step 1, values float32
+Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
+pixel 1.9, shown at level 0.356, step 1, values float32
+Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc as #225, grid size
+,128,128, pixel 3.27, shown at level 1.6, step 1, values float32
+Opened cryosparc_P17_J981_class_00_00062_volume_sharp.mrc as #228, grid size
+,128,128, pixel 3.27, shown at level 1.82, step 1, values float32
+Opened cryosparc_P17_J967_class_00_final_volume.mrc as #229, grid size
+,192,192, pixel 2.18, shown at level 0.8, step 1, values float32
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #226, grid size
+,588,588, pixel 0.95, shown at level 0.33, step 1, values float32
+Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #230, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #231, grid size
+,588,588, pixel 0.95, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc as #233, grid
+size 128,128,128, pixel 3.27, shown at level 1.4, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
+,588,588, pixel 0.95, shown at level 0.173, step 1, values float32
+Opened cryosparc_P17_J864_007_volume_map.mrc as #239, grid size 588,588,588,
+pixel 0.95, shown at level 0.153, step 1, values float32
+Log from Thu Jul 18 17:16:17 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
+© 2016-2023 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
+Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
+,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
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+Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
+.9, shown at level 0.0185, step 1, values float32
+Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
+.9, shown at level 0.0198, step 1, values float32
+Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
+.9, shown at level 0.0163, step 1, values float32
+Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
+.9, shown at level 0.0136, step 1, values float32
+Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
+,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
+Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
+,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
+Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
+pixel 1.9, shown at level 0.45, step 1, values float32
+Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
+pixel 1.9, shown at level 0.45, step 1, values float32
+Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
+,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
+Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
+,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
+Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
+pixel 1.9, shown at level 0.32, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
+pixel 1.9, shown at level 0.35, step 1, values float32
+Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
+,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
+Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
+pixel 1.9, shown at level 0.32, step 1, values float32
+Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
+pixel 1.9, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
+.9, shown at level 0.0146, step 1, values float32
+Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j590_run_it025_class001.mrc as #122, grid size 294,294,294, pixel
+.9, shown at level 0.015, step 1, values float32
+Opened Cl3D_j590_run_it025_class002.mrc as #123, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j590_run_it025_class003.mrc as #124, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j590_run_it025_class004.mrc as #125, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j590_run_it025_class005.mrc as #126, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j590_run_it025_class006.mrc as #127, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
+.9, shown at level 0.014, step 1, values float32
+Opened Cl3D_j591_run_it025_class001.mrc as #129, grid size 294,294,294, pixel
+.9, shown at level 0.014, step 1, values float32
+Opened Cl3D_j591_run_it025_class002.mrc as #130, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j591_run_it025_class003.mrc as #131, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j591_run_it025_class004.mrc as #132, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j591_run_it025_class005.mrc as #133, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j591_run_it025_class006.mrc as #134, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j591_run_it025_class007.mrc as #135, grid size 294,294,294, pixel
+.9, shown at level 0.014, step 1, values float32
+Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
+.9, shown at level 0.314, step 1, values float32
+Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J681_volume_map.mrc as #139, grid size 294,294,294, pixel
+.9, shown at level 0.294, step 1, values float32
+Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J685_007_volume_map.mrc as #141, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
+,192,192, pixel 2.91, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
+pixel 1.9, shown at level 0.365, step 1, values float32
+Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
+pixel 1.9, shown at level 0.365, step 1, values float32
+Opened cryosparc_P17_J690_006_volume_map.mrc as #147, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
+pixel 1.9, shown at level 0.365, step 1, values float32
+Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
+pixel 1.9, shown at level 0.366, step 1, values float32
+Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
+pixel 1.9, shown at level 0.2, step 1, values float32
+Opened cryosparc_P17_J688_007_volume_map.mrc z flip as #151, grid size
+,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
+,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
+Opened cryosparc_P17_J691_008_volume_map.mrc z flip as #153, grid size
+,294,294, pixel 1.9, shown at level 0.365, step 1, values float32
+Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
+,294,294, pixel 1.9, shown at level 0.366, step 1, values float32
+Opened cryosparc_P17_J697_006_volume_map.mrc as #157, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
+,294,294, pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
+,294,294, pixel 1.9, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
+pixel 1.9, shown at level 0.4, step 1, values float32
+Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
+pixel 1.9, shown at level 0.384, step 1, values float32
+Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
+.91, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
+pixel 1.9, shown at level 0.351, step 1, values float32
+Opened cryosparc_P17_J712_007_volume_map.mrc as #174, grid size 294,294,294,
+pixel 1.9, shown at level 0.329, step 1, values float32
+Opened cryosparc_P17_J709_007_volume_map_sharp.mrc as #158, grid size
+,294,294, pixel 1.9, shown at level 0.338, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
+,588,588, pixel 0.95, shown at level 0.995, step 1, values float32
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
+,588,588, pixel 0.95, shown at level 0.16, step 1, values float32
+Opened cryosparc_P17_J786_005_volume_map_sharp.mrc as #181, grid size
+,588,588, pixel 0.95, shown at level 0.4, step 1, values float32
+Opened cryosparc_P17_J787_005_volume_map_sharp.mrc as #182, grid size
+,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
+Opened cryosparc_P17_J792_volume_map_sharp.mrc as #183, grid size 520,520,520,
+pixel 0.95, shown at level 0.392, step 1, values float32
+Opened cryosparc_P17_J757_volume_map.mrc as #186, grid size 520,520,520, pixel
+.95, shown at level 0.226, step 1, values float32
+Opened cryosparc_P17_J792_volume_map.mrc as #187, grid size 520,520,520, pixel
+.95, shown at level 0.247, step 1, values float32
+Opened cryosparc_P17_J797_009_volume_map_sharp.mrc as #184, grid size
+,520,520, pixel 0.95, shown at level 0.716, step 1, values float32
+Opened cryosparc_P17_J797_009_volume_map.mrc as #185, grid size 520,520,520,
+pixel 0.95, shown at level 0.31, step 1, values float32
+Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
+.95, shown at level 0.998, step 1, values float32
+Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
+pixel 0.95, shown at level 0.31, step 1, values float32
+Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
+,520,520, pixel 0.95, shown at level 0.6, step 1, values float32
+Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
+pixel 0.95, shown at level 0.301, step 1, values float32
+Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
+,588,588, pixel 0.95, shown at level 0.39, step 1, values float32
+Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
+.95, shown at level 0.1, step 1, values float32
+Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
+pixel 0.95, shown at level 0.348, step 1, values float32
+Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
+,336,336, pixel 1.47, shown at level 0.283, step 1, values float32
+Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
+,336,336, pixel 1.47, shown at level 0.289, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
+pixel 0.95, shown at level 0.196, step 1, values float32
+Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
+,588,588, pixel 0.95, shown at level 0.46, step 1, values float32
+Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
+.95, shown at level 0.15, step 1, values float32
+Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
+,588,588, pixel 0.95, shown at level 0.35, step 1, values float32
+Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
+.95, shown at level 0.0845, step 1, values float32
+Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
+,192,192, pixel 2.91, shown at level 0.5, step 1, values float32
+Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
+,588,588, pixel 0.95, shown at level 0.239, step 1, values float32
+Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
+,588,588, pixel 0.95, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
+,520,520, pixel 0.95, shown at level 0.55, step 1, values float32
+Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
+pixel 1.9, shown at level 0.333, step 1, values float32
+Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
+,588,588, pixel 0.95, shown at level 0.158, step 1, values float32
+Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
+.95, shown at level 0.08, step 1, values float32
+Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
+.95, shown at level 0.15, step 1, values float32
+Opened cryosparc_P17_J857_mask.mrc as #160, grid size 588,588,588, pixel 0.95,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
+pixel 0.95, shown at level 0.154, step 1, values float32
+Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
+,128,128, pixel 4.36, shown at level 0.9, step 1, values float32
+Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 1, values float32
+Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
+pixel 0.95, shown at level 0.151, step 1, values float32
+Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
+,192,192, pixel 2.91, shown at level 0.348, step 1, values float32
+Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
+,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
+Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
+.9, shown at level 0.33, step 1, values float32
+Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
+.9, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
+,128,128, pixel 4.36, shown at level 1.25, step 1, values float32
+Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
+,128,128, pixel 4.36, shown at level 0.8, step 1, values float32
+Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
+.95, shown at level 0.0045, step 1, values float32
+Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
+.95, shown at level 0.0045, step 1, values float32
+Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
+level 1, step 1, values float32
+Opened Ref3D_job506_run_class001_bareNCP.mrc as #224, grid size 588,588,588,
+pixel 0.95, shown at level 0.0045, step 1, values float32
+Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
+pixel 1.9, shown at level 0.426, step 2, values float32
+Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
+pixel 1.9, shown at level 0.347, step 1, values float32
+Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
+pixel 1.9, shown at level 0.356, step 1, values float32
+Log from Thu Jul 11 13:31:37 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
+© 2016-2023 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes_ref.cxs
+restore_snapshot for "Volume" returned None
+restore_snapshot for "VolumeSurface" returned None
+Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
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+.91, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 1, values float32
+Opened cryosparc_P17_J710_008_volume_map.mrc as #173, grid size 294,294,294,
+pixel 1.9, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J712_007_volume_map.mrc as #174, grid size 294,294,294,
+pixel 1.9, shown at level 0.2, step 1, values float32
+Opened cryosparc_P17_J711_009_volume_map.mrc as #175, grid size 294,294,294,
+pixel 1.9, shown at level 0.2, step 1, values float32
+Opened cryosparc_P17_J716_mask.mrc as #176, grid size 294,294,294, pixel 1.9,
+shown at level 1, step 1, values float32
+Log from Fri Jun 21 11:35:11 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
+© 2016-2023 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
+Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
+,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
+.9, shown at level 0.0185, step 1, values float32
+Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
+.9, shown at level 0.0198, step 1, values float32
+Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
+.9, shown at level 0.0163, step 1, values float32
+Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
+.9, shown at level 0.0136, step 1, values float32
+Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
+,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
+Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
+,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
+Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
+pixel 1.9, shown at level 0.45, step 1, values float32
+Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
+pixel 1.9, shown at level 0.45, step 1, values float32
+Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
+,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
+Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
+,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
+Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
+pixel 1.9, shown at level 0.32, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
+pixel 1.9, shown at level 0.35, step 1, values float32
+Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
+,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
+Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
+pixel 1.9, shown at level 0.32, step 1, values float32
+Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
+pixel 1.9, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
+.9, shown at level 0.0146, step 1, values float32
+Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+Log from Tue Jun 11 16:35:40 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
+© 2016-2023 Regents of the University of California. All rights reserved.
+> open
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
+Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
+shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
+,294,294, pixel 1.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
+.9, shown at level 0.0185, step 1, values float32
+Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
+.9, shown at level 0.0198, step 1, values float32
+Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
+.9, shown at level 0.0163, step 1, values float32
+Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
+.9, shown at level 0.0136, step 1, values float32
+Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
+,128,128, pixel 4.36, shown at level 1.63, step 1, values float32
+Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
+,128,128, pixel 4.36, shown at level 1.36, step 1, values float32
+Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
+pixel 1.9, shown at level 0.45, step 1, values float32
+Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
+pixel 1.9, shown at level 0.45, step 1, values float32
+Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
+,192,192, pixel 2.91, shown at level 0.3, step 1, values float32
+Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
+,192,192, pixel 2.91, shown at level 0.416, step 1, values float32
+Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
+,192,192, pixel 2.91, shown at level 0.373, step 1, values float32
+Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
+pixel 1.9, shown at level 0.32, step 1, values float32
+Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
+pixel 1.9, shown at level 0.35, step 1, values float32
+Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
+,192,192, pixel 2.91, shown at level 0.414, step 1, values float32
+Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
+pixel 1.9, shown at level 0.32, step 1, values float32
+Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
+pixel 1.9, shown at level 0.25, step 1, values float32
+Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
+,128,128, pixel 4.36, shown at level 1, step 1, values float32
+Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
+.9, shown at level 0.0146, step 1, values float32
+Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
+.9, shown at level 0.012, step 1, values float32
+Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 1, values float32
+Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
+.9, shown at level 0.0156, step 2, values float32
+Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
+.9, shown at level 0.0158, step 2, values float32
+Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
+.9, shown at level 0.0195, step 2, values float32
+Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
+.9, shown at level 0.0161, step 2, values float32
+Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
+.9, shown at level 0.0197, step 2, values float32
+Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
+.9, shown at level 0.0161, step 2, values float32
+Log from Mon Jun 3 09:50:12 2024 Startup Messages
+---
+note | available bundle cache has not been initialized yet
+UCSF ChimeraX version: 1.7.1 (2024-01-23)
+© 2016-2023 Regents of the University of California. All rights reserved.
+How to cite UCSF ChimeraX
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class001.mrc
+Opened Cl3D_job357_run_it025_class001.mrc as #1, grid size 294,294,294, pixel
+.9, shown at level 0.0106, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class002.mrc
+Opened Cl3D_job357_run_it025_class002.mrc as #2, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class003.mrc
+Opened Cl3D_job357_run_it025_class003.mrc as #3, grid size 294,294,294, pixel
+.9, shown at level 0.0124, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class004.mrc
+Opened Cl3D_job357_run_it025_class004.mrc as #4, grid size 294,294,294, pixel
+.9, shown at level 0.0133, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class005.mrc
+Opened Cl3D_job357_run_it025_class005.mrc as #5, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job357/Cl3D_job357_run_it025_class006.mrc
+Opened Cl3D_job357_run_it025_class006.mrc as #6, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+> volume all step 1
+> hide #!1 models
+> hide #!2 models
+> hide #!3 models
+> hide #!4 models
+> hide #!5 models
+> hide #!6 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class001.mrc
+Opened Cl3D_job358_run_it025_class001.mrc as #7, grid size 294,294,294, pixel
+.9, shown at level 0.0153, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class002.mrc
+Opened Cl3D_job358_run_it025_class002.mrc as #8, grid size 294,294,294, pixel
+.9, shown at level 0.0105, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class003.mrc
+Opened Cl3D_job358_run_it025_class003.mrc as #9, grid size 294,294,294, pixel
+.9, shown at level 0.0136, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class004.mrc
+Opened Cl3D_job358_run_it025_class004.mrc as #10, grid size 294,294,294, pixel
+.9, shown at level 0.0132, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class005.mrc
+Opened Cl3D_job358_run_it025_class005.mrc as #11, grid size 294,294,294, pixel
+.9, shown at level 0.0142, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job358/Cl3D_job358_run_it025_class006.mrc
+Opened Cl3D_job358_run_it025_class006.mrc as #12, grid size 294,294,294, pixel
+.9, shown at level 0.0149, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class001.mrc
+Opened Cl3D_job411_run_it025_class001.mrc as #13, grid size 294,294,294, pixel
+.9, shown at level 0.0144, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class002.mrc
+Opened Cl3D_job411_run_it025_class002.mrc as #14, grid size 294,294,294, pixel
+.9, shown at level 0.014, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class003.mrc
+Opened Cl3D_job411_run_it025_class003.mrc as #15, grid size 294,294,294, pixel
+.9, shown at level 0.0161, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class004.mrc
+Opened Cl3D_job411_run_it025_class004.mrc as #16, grid size 294,294,294, pixel
+.9, shown at level 0.0153, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class005.mrc
+Opened Cl3D_job411_run_it025_class005.mrc as #17, grid size 294,294,294, pixel
+.9, shown at level 0.0143, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job411/Cl3D_job411_run_it025_class006.mrc
+Opened Cl3D_job411_run_it025_class006.mrc as #18, grid size 294,294,294, pixel
+.9, shown at level 0.014, step 2, values float32
+> hide #!7 models
+> hide #!8 models
+> hide #!9 models
+> hide #!10 models
+> hide #!11 models
+> hide #!12 models
+> hide #!13 models
+> hide #!14 models
+> hide #!15 models
+> hide #!16 models
+> hide #!17 models
+> hide #!18 models
+> volume all step 1
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job417_run_class001.mrc
+Opened Ref3D_job417_run_class001.mrc as #19, grid size 294,294,294, pixel 1.9,
+shown at level 0.0163, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/postprocess_masked_job423.mrc
+Opened postprocess_masked_job423.mrc as #20, grid size 294,294,294, pixel 1.9,
+shown at level 0.0162, step 2, values float32
+> hide #!19 models
+> volume #19 step 1
+> volume #20 step 1
+> hide #!20 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J368_007_volume_map_sharp.mrc
+Opened cryosparc_P17_J368_007_volume_map_sharp.mrc as #21, grid size
+,294,294, pixel 1.9, shown at level 0.362, step 2, values float32
+> volume #21 step 1
+> volume #21 level 0.4566
+> volume #21 level 0.421
+> volume #21 level 0.4151
+> show #!19 models
+> hide #!19 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
+> show #!13 models
+> hide #!13 models
+> show #!14 models
+> hide #!14 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!15 models
+> show #!3 models
+> hide #!3 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!4 models
+> hide #!4 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!13 models
+> hide #!13 models
+> show #!14 models
+> hide #!14 models
+> show #!15 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> hide #!15 models
+> show #!7 models
+> hide #!7 models
+> show #!8 models
+> show #!10 models
+> hide #!10 models
+> hide #!8 models
+> show #!7 models
+> show #!9 models
+> volume #7 level 0.01497
+> volume #9 level 0.01231
+> show #!10 models
+> hide #!10 models
+> show #!11 models
+> show #!12 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class001.mrc
+Opened Cl3D_job414_run_it025_class001.mrc as #22, grid size 294,294,294, pixel
+.9, shown at level 0.0146, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class002.mrc
+Opened Cl3D_job414_run_it025_class002.mrc as #23, grid size 294,294,294, pixel
+.9, shown at level 0.0139, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class003.mrc
+Opened Cl3D_job414_run_it025_class003.mrc as #24, grid size 294,294,294, pixel
+.9, shown at level 0.0161, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class004.mrc
+Opened Cl3D_job414_run_it025_class004.mrc as #25, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class005.mrc
+Opened Cl3D_job414_run_it025_class005.mrc as #26, grid size 294,294,294, pixel
+.9, shown at level 0.014, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job414/Cl3D_job414_run_it025_class006.mrc
+Opened Cl3D_job414_run_it025_class006.mrc as #27, grid size 294,294,294, pixel
+.9, shown at level 0.0181, step 2, values float32
+> hide #!7 models
+> hide #!9 models
+> hide #!11 models
+> hide #!12 models
+> volume all step 1
+> hide #!23 models
+> hide #!24 models
+> hide #!25 models
+> hide #!26 models
+> hide #!27 models
+> volume #22 level 0.01345
+> volume #22 level 0.0119
+> volume #23 level 0.01121
+> volume #24 level 0.01399
+> volume #24 level 0.01119
+> volume #24 level 0.01287
+> volume #25 level 0.01349
+> hide #!25 models
+> show #!26 models
+> volume #26 level 0.01133
+> hide #!26 models
+> show #!27 models
+> volume #27 level 0.01296
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!2 models
+> hide #!3 models
+> show #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!4 models
+> hide #!2 models
+> volume #4 level 0.01157
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> hide #!4 models
+> hide #!2 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> show #!3 models
+> show #!4 models
+> show #!5 models
+> show #!6 models
+> hide #!2 models
+> hide #!3 models
+> hide #!4 models
+> hide #!5 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!5 models
+> hide #!5 models
+> show #!4 models
+> hide #!4 models
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> hide #!2 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job559/Cl3D_j559_run_it025_class001.mrc
+Opened Cl3D_j559_run_it025_class001.mrc as #28, grid size 294,294,294, pixel
+.9, shown at level 0.0155, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job559/Cl3D_j559_run_it025_class002.mrc
+Opened Cl3D_j559_run_it025_class002.mrc as #29, grid size 294,294,294, pixel
+.9, shown at level 0.0155, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job559/Cl3D_j559_run_it025_class003.mrc
+Opened Cl3D_j559_run_it025_class003.mrc as #30, grid size 294,294,294, pixel
+.9, shown at level 0.0194, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job559/Cl3D_j559_run_it025_class004.mrc
+Opened Cl3D_j559_run_it025_class004.mrc as #31, grid size 294,294,294, pixel
+.9, shown at level 0.0153, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job560/Cl3D_j560_run_it025_class001.mrc
+Opened Cl3D_j560_run_it025_class001.mrc as #32, grid size 294,294,294, pixel
+.9, shown at level 0.0156, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job560/Cl3D_j560_run_it025_class002.mrc
+Opened Cl3D_j560_run_it025_class002.mrc as #33, grid size 294,294,294, pixel
+.9, shown at level 0.0153, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job560/Cl3D_j560_run_it025_class003.mrc
+Opened Cl3D_j560_run_it025_class003.mrc as #34, grid size 294,294,294, pixel
+.9, shown at level 0.0161, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job560/Cl3D_j560_run_it025_class004.mrc
+Opened Cl3D_j560_run_it025_class004.mrc as #35, grid size 294,294,294, pixel
+.9, shown at level 0.0189, step 2, values float32
+> volume all step 1
+> hide #!29 models
+> hide #!30 models
+> hide #!31 models
+> hide #!32 models
+> hide #!33 models
+> hide #!34 models
+> hide #!35 models
+> volume #28 level 0.01275
+> volume #28 level 0.01205
+> volume #28 level 0.01231
+> volume #29 level 0.01315
+> volume #29 level 0.013
+> volume #30 level 0.01741
+> volume #31 level 0.01451
+> volume #31 level 0.01487
+> volume #32 level 0.01315
+> volume #33 level 0.01302
+> volume #34 level 0.01352
+> volume #35 level 0.01616
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job561/Cl3D_j561_run_it025_class001.mrc
+Opened Cl3D_j561_run_it025_class001.mrc as #36, grid size 294,294,294, pixel
+.9, shown at level 0.0153, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job561/Cl3D_j561_run_it025_class002.mrc
+Opened Cl3D_j561_run_it025_class002.mrc as #37, grid size 294,294,294, pixel
+.9, shown at level 0.0162, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job561/Cl3D_j561_run_it025_class003.mrc
+Opened Cl3D_j561_run_it025_class003.mrc as #38, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job569/Cl3D_j569_run_it025_class001.mrc
+Opened Cl3D_j569_run_it025_class001.mrc as #39, grid size 294,294,294, pixel
+.9, shown at level 0.0155, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job569/Cl3D_j569_run_it025_class002.mrc
+Opened Cl3D_j569_run_it025_class002.mrc as #40, grid size 294,294,294, pixel
+.9, shown at level 0.0162, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job569/Cl3D_j569_run_it025_class003.mrc
+Opened Cl3D_j569_run_it025_class003.mrc as #41, grid size 294,294,294, pixel
+.9, shown at level 0.0152, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job569/Cl3D_j569_run_it025_class004.mrc
+Opened Cl3D_j569_run_it025_class004.mrc as #42, grid size 294,294,294, pixel
+.9, shown at level 0.0168, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job569/Cl3D_j569_run_it025_class005.mrc
+Opened Cl3D_j569_run_it025_class005.mrc as #43, grid size 294,294,294, pixel
+.9, shown at level 0.0159, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class001.mrc
+Opened Cl3D_j570_run_it025_class001.mrc as #44, grid size 294,294,294, pixel
+.9, shown at level 0.0155, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class002.mrc
+Opened Cl3D_j570_run_it025_class002.mrc as #45, grid size 294,294,294, pixel
+.9, shown at level 0.0187, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class003.mrc
+Opened Cl3D_j570_run_it025_class003.mrc as #46, grid size 294,294,294, pixel
+.9, shown at level 0.0159, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class004.mrc
+Opened Cl3D_j570_run_it025_class004.mrc as #47, grid size 294,294,294, pixel
+.9, shown at level 0.016, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class005.mrc
+Opened Cl3D_j570_run_it025_class005.mrc as #48, grid size 294,294,294, pixel
+.9, shown at level 0.0153, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job570/Cl3D_j570_run_it025_class006.mrc
+Opened Cl3D_j570_run_it025_class006.mrc as #49, grid size 294,294,294, pixel
+.9, shown at level 0.0158, step 2, values float32
+> volume all step 1
+> hide #!49 models
+> hide #!48 models
+> hide #!47 models
+> hide #!46 models
+> hide #!45 models
+> hide #!44 models
+> hide #!43 models
+> hide #!42 models
+> hide #!41 models
+> hide #!40 models
+> hide #!39 models
+> hide #!38 models
+> hide #!37 models
+> hide #!36 models
+> show #!36 models
+> hide #!36 models
+> show #!36 models
+> show #!37 models
+> show #!38 models
+> volume #36 level 0.013
+> volume #37 level 0.013
+> volume #38 level 0.013
+> volume #39 level 0.013
+> volume #40 level 0.013
+> hide #!40 models
+> show #!41 models
+> volume #41 level 0.013
+> show #!40 models
+> hide #!40 models
+> show #!39 models
+> hide #!39 models
+> show #!40 models
+> hide #!40 models
+> hide #!41 models
+> show #!41 models
+> hide #!41 models
+> show #!42 models
+> volume #42 level 0.013
+> hide #!42 models
+> show #!43 models
+> volume #43 level 0.013
+> volume #43 level 0.012
+> volume #44 level 0.013
+> volume #45 level 0.013
+> volume #46 level 0.013
+> volume #47 level 0.013
+> volume #48 level 0.013
+> volume #49 level 0.013
+> show #!44 models
+> hide #!49 models
+> show #!45 models
+> hide #!45 models
+> show #!46 models
+> hide #!46 models
+> show #!47 models
+> hide #!47 models
+> show #!48 models
+> hide #!48 models
+> show #!49 models
+> hide #!49 models
+> show #!48 models
+> hide #!48 models
+> hide #!44 models
+> show #!43 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!43 models
+> hide #!42 models
+> show #!40 models
+> hide #!40 models
+> show #!39 models
+> show #!38 models
+> hide #!38 models
+> hide #!39 models
+> show #!49 models
+> hide #!49 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job542/Cl3D_job542_run_it025_class001.mrc
+Opened Cl3D_job542_run_it025_class001.mrc as #50, grid size 294,294,294, pixel
+.9, shown at level 0.0156, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job542/Cl3D_job542_run_it025_class002.mrc
+Opened Cl3D_job542_run_it025_class002.mrc as #51, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job542/Cl3D_job542_run_it025_class003.mrc
+Opened Cl3D_job542_run_it025_class003.mrc as #52, grid size 294,294,294, pixel
+.9, shown at level 0.0189, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job545/Cl3D_job545_run_it025_class001.mrc
+Opened Cl3D_job545_run_it025_class001.mrc as #53, grid size 294,294,294, pixel
+.9, shown at level 0.0193, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job545/Cl3D_job545_run_it025_class002.mrc
+Opened Cl3D_job545_run_it025_class002.mrc as #54, grid size 294,294,294, pixel
+.9, shown at level 0.0155, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job545/Cl3D_job545_run_it025_class003.mrc
+Opened Cl3D_job545_run_it025_class003.mrc as #55, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+> volume all step 1
+> hide #!51 models
+> hide #!52 models
+> hide #!53 models
+> hide #!54 models
+> hide #!55 models
+> volume #50 level 0.013
+> show #!51 models
+> volume #51 level 0.013
+> volume all level 0.013
+> hide #!51 models
+> hide #!50 models
+> show #!52 models
+> hide #!52 models
+> show #!53 models
+> hide #!53 models
+> show #!50 models
+> show #!51 models
+> show #!52 models
+> hide #!52 models
+> show #!52 models
+> hide #!51 models
+> hide #!50 models
+> hide #!52 models
+> show #!51 models
+> show #!50 models
+> hide #!51 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> volume #50 level 0.012
+> show #!13 models
+> hide #!13 models
+> show #!14 models
+> hide #!14 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> ui tool show "Fit in Map"
+> fitmap #50 inMap #15
+Fit map Cl3D_job542_run_it025_class001.mrc in map
+Cl3D_job411_run_it025_class003.mrc using 342972 points
+correlation = 0.9888, correlation about mean = 0.813, overlap = 133.4
+steps = 68, shift = 1.95, angle = 0.993 degrees
+Position of Cl3D_job542_run_it025_class001.mrc (#50) relative to
+Cl3D_job411_run_it025_class003.mrc (#15) coordinates:
+Matrix rotation and translation
+.99987080 0.01439337 0.00715694 -5.19984751
+-0.01434662 0.99987569 -0.00654060 6.68005810
+-0.00725019 0.00643707 0.99995300 -1.28059948
+Axis 0.37432567 0.41555671 -0.82897100
+Axis point 407.25464445 414.10389399 0.00000000
+Rotation angle (degrees) 0.99325686
+Shift along axis 1.89108642
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> hide #!50 models
+> show #!53 models
+> hide #!53 models
+> show #!54 models
+> hide #!54 models
+> show #!55 models
+> hide #!55 models
+> show #!54 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> volume #54 level 0.012
+> hide #!54 models
+> show #!54 models
+> hide #!54 models
+> show #!54 models
+> fitmap #50 inMap #54
+Fit map Cl3D_job542_run_it025_class001.mrc in map
+Cl3D_job545_run_it025_class002.mrc using 342972 points
+correlation = 0.9989, correlation about mean = 0.9796, overlap = 133
+steps = 56, shift = 2.3, angle = 1.62 degrees
+Position of Cl3D_job542_run_it025_class001.mrc (#50) relative to
+Cl3D_job545_run_it025_class002.mrc (#54) coordinates:
+Matrix rotation and translation
+.99982077 -0.01310087 0.01366700 -0.20479433
+.01319269 0.99989086 -0.00664955 -1.77455886
+-0.01357839 0.00682866 0.99988449 1.74879695
+Axis 0.33535327 0.67789597 0.65421345
+Axis point 134.82260247 0.00000000 13.62266755
+Rotation angle (degrees) 1.15146770
+Shift along axis -0.12755828
+> hide #!54 models
+> show #!54 models
+> hide #!50 models
+> show #!50 models
+> hide #!54 models
+> show #!54 models
+> hide #!54 models
+> show #!54 models
+> hide #!54 models
+> show #!54 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!54 models
+> show #!54 models
+> hide #!54 models
+> show #!54 models
+> hide #!50 models
+> show #!50 models
+> hide #!54 models
+> hide #!50 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job563/Cl3D_j563_run_it025_class001.mrc
+Opened Cl3D_j563_run_it025_class001.mrc as #56, grid size 294,294,294, pixel
+.9, shown at level 0.0153, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job563/Cl3D_j563_run_it025_class002.mrc
+Opened Cl3D_j563_run_it025_class002.mrc as #57, grid size 294,294,294, pixel
+.9, shown at level 0.0159, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job563/Cl3D_j563_run_it025_class003.mrc
+Opened Cl3D_j563_run_it025_class003.mrc as #58, grid size 294,294,294, pixel
+.9, shown at level 0.0184, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job566/Cl3D_job566_run_it025_class001.mrc
+Opened Cl3D_job566_run_it025_class001.mrc as #59, grid size 294,294,294, pixel
+.9, shown at level 0.0155, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job566/Cl3D_job566_run_it025_class002.mrc
+Opened Cl3D_job566_run_it025_class002.mrc as #60, grid size 294,294,294, pixel
+.9, shown at level 0.0166, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job566/Cl3D_job566_run_it025_class003.mrc
+Opened Cl3D_job566_run_it025_class003.mrc as #61, grid size 294,294,294, pixel
+.9, shown at level 0.0195, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job566/Cl3D_job566_run_it025_class004.mrc
+Opened Cl3D_job566_run_it025_class004.mrc as #62, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+> volume all step 1
+> volume all level 0.013
+> hide #!57 models
+> hide #!58 models
+> hide #!59 models
+> hide #!60 models
+> hide #!61 models
+> hide #!62 models
+> show #!57 models
+> hide #!56 models
+> show #!58 models
+> hide #!57 models
+> volume #58 level 0.01852
+> hide #!58 models
+> show #!57 models
+> hide #!57 models
+> show #!56 models
+> volume #56 level 0.012
+> hide #!56 models
+> show #!59 models
+> volume #59 level 0.012
+> show #!56 models
+> hide #!56 models
+> show #!56 models
+> hide #!56 models
+> show #!56 models
+> hide #!56 models
+> show #!60 models
+> hide #!60 models
+> show #!60 models
+> hide #!59 models
+> hide #!60 models
+> show #!61 models
+> hide #!61 models
+> show #!62 models
+> show #!59 models
+> hide #!59 models
+> volume #62 level 0.012
+> hide #!62 models
+> show #!62 models
+> hide #!62 models
+> show #!61 models
+> hide #!61 models
+> show #!60 models
+> hide #!60 models
+> show #!59 models
+> show #!56 models
+> hide #!56 models
+> show #!56 models
+> hide #!56 models
+> show #!56 models
+> hide #!56 models
+> show #!56 models
+> hide #!59 models
+> show #!59 models
+> hide #!59 models
+> show #!59 models
+> hide #!56 models
+> hide #!59 models
+> show #!59 models
+> hide #!59 models
+> show #!60 models
+> hide #!60 models
+> show #!61 models
+> hide #!61 models
+> show #!62 models
+> hide #!62 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job567/Cl3D_j567_run_it025_class001.mrc
+Opened Cl3D_j567_run_it025_class001.mrc as #63, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job567/Cl3D_j567_run_it025_class002.mrc
+Opened Cl3D_j567_run_it025_class002.mrc as #64, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job567/Cl3D_j567_run_it025_class003.mrc
+Opened Cl3D_j567_run_it025_class003.mrc as #65, grid size 294,294,294, pixel
+.9, shown at level 0.0198, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job567/Cl3D_j567_run_it025_class004.mrc
+Opened Cl3D_j567_run_it025_class004.mrc as #66, grid size 294,294,294, pixel
+.9, shown at level 0.0163, step 2, values float32
+> volume all step 1
+> hide #!66 models
+> hide #!65 models
+> hide #!64 models
+> volume #63 level 0.013
+> volume #64 level 0.013
+> volume #63 level 0.012
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job568/Cl3D_j568_run_it025_class001.mrc
+Opened Cl3D_j568_run_it025_class001.mrc as #67, grid size 294,294,294, pixel
+.9, shown at level 0.0187, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job568/Cl3D_j568_run_it025_class002.mrc
+Opened Cl3D_j568_run_it025_class002.mrc as #68, grid size 294,294,294, pixel
+.9, shown at level 0.0155, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job568/Cl3D_j568_run_it025_class003.mrc
+Opened Cl3D_j568_run_it025_class003.mrc as #69, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> volume all step 1
+> hide #!68 models
+> hide #!69 models
+> show #!68 models
+> hide #!67 models
+> show #!69 models
+> hide #!68 models
+> volume #69 level 0.013
+> volume #68 level 0.013
+> volume #67 level 0.013
+> show #!67 models
+> hide #!67 models
+> show #!68 models
+> hide #!68 models
+> show #!69 models
+> hide #!69 models
+> show #!29 models
+> hide #!29 models
+> show #!30 models
+> hide #!30 models
+> show #!31 models
+> show #!29 models
+> hide #!29 models
+> hide #!31 models
+> show #!28 models
+> show #!29 models
+> hide #!29 models
+> hide #!28 models
+> show #!50 models
+> hide #!50 models
+> show #!51 models
+> hide #!51 models
+> show #!52 models
+> hide #!52 models
+> show #!50 models
+> show #!51 models
+> hide #!50 models
+> hide #!51 models
+> show #!53 models
+> hide #!53 models
+> show #!54 models
+> show #!55 models
+> hide #!55 models
+> hide #!54 models
+> show #!50 models
+> show #!51 models
+> hide #!51 models
+> show #!51 models
+> hide #!51 models
+> show #!51 models
+> hide #!51 models
+> show #!52 models
+> hide #!52 models
+> show #!53 models
+> hide #!53 models
+> show #!54 models
+> hide #!54 models
+> show #!54 models
+> hide #!54 models
+> hide #!50 models
+> show #!56 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class001.mrc
+Opened Cl3D_j576_run_it025_class001.mrc as #70, grid size 294,294,294, pixel
+.9, shown at level 0.0156, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class002.mrc
+Opened Cl3D_j576_run_it025_class002.mrc as #71, grid size 294,294,294, pixel
+.9, shown at level 0.0131, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class003.mrc
+Opened Cl3D_j576_run_it025_class003.mrc as #72, grid size 294,294,294, pixel
+.9, shown at level 0.014, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class004.mrc
+Opened Cl3D_j576_run_it025_class004.mrc as #73, grid size 294,294,294, pixel
+.9, shown at level 0.0132, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class005.mrc
+Opened Cl3D_j576_run_it025_class005.mrc as #74, grid size 294,294,294, pixel
+.9, shown at level 0.0165, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job576/Cl3D_j576_run_it025_class006.mrc
+Opened Cl3D_j576_run_it025_class006.mrc as #75, grid size 294,294,294, pixel
+.9, shown at level 0.0159, step 2, values float32
+> hide #!56 models
+> volume all step 1
+> hide #!71 models
+> hide #!72 models
+> hide #!73 models
+> hide #!74 models
+> hide #!75 models
+> volume #70 level 0.013
+> volume #71 level 0.013
+> volume #71 level 0.01
+> volume #71 level 0.012
+> volume #72 level 0.013
+> volume #72 level 0.01
+> volume #72 level 0.012
+> volume #73 level 0.012
+> volume #74 level 0.013
+> volume #75 level 0.013
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class001.mrc
+Opened Cl3D_j577_run_it025_class001.mrc as #76, grid size 294,294,294, pixel
+.9, shown at level 0.0166, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class002.mrc
+Opened Cl3D_j577_run_it025_class002.mrc as #77, grid size 294,294,294, pixel
+.9, shown at level 0.0135, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class003.mrc
+Opened Cl3D_j577_run_it025_class003.mrc as #78, grid size 294,294,294, pixel
+.9, shown at level 0.0153, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class004.mrc
+Opened Cl3D_j577_run_it025_class004.mrc as #79, grid size 294,294,294, pixel
+.9, shown at level 0.015, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class005.mrc
+Opened Cl3D_j577_run_it025_class005.mrc as #80, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job577/Cl3D_j577_run_it025_class006.mrc
+Opened Cl3D_j577_run_it025_class006.mrc as #81, grid size 294,294,294, pixel
+.9, shown at level 0.0136, step 2, values float32
+> volume all step 1
+> hide #!77 models
+> hide #!78 models
+> hide #!79 models
+> hide #!80 models
+> hide #!81 models
+> volume #76 level 0.013
+> volume #77 level 0.013
+> volume #78 level 0.013
+> volume #79 level 0.013
+> volume #80 level 0.007565
+> volume #80 level 0.02
+> volume #80 level 0.012
+> volume #81 level 0.012
+> volume #81 level 0.01
+> volume #81 level 0.008841
+> volume #81 level 0.012
+> volume #81 level 0.01
+> show #!80 models
+> hide #!80 models
+> show #!80 models
+> hide #!80 models
+> show #!79 models
+> hide #!79 models
+> show #!78 models
+> hide #!81 models
+> hide #!78 models
+> show #!77 models
+> hide #!77 models
+> show #!76 models
+> hide #!76 models
+> show #!81 models
+> hide #!81 models
+> show #!80 models
+> hide #!80 models
+> show #!79 models
+> hide #!79 models
+> show #!78 models
+> hide #!78 models
+> show #!77 models
+> hide #!77 models
+> show #!77 models
+> hide #!77 models
+> show #!76 models
+> hide #!76 models
+> show #!76 models
+> hide #!76 models
+> show #!77 models
+> hide #!77 models
+> show #!78 models
+> hide #!78 models
+> show #!78 models
+> hide #!78 models
+> show #!79 models
+> hide #!79 models
+> show #!80 models
+> hide #!80 models
+> show #!81 models
+> hide #!81 models
+> show #!75 models
+> hide #!75 models
+> show #!74 models
+> volume #74 level 0.01584
+> volume #74 level 0.01357
+> hide #!74 models
+> show #!73 models
+> hide #!73 models
+> show #!72 models
+> hide #!72 models
+> show #!71 models
+> hide #!71 models
+> show #!70 models
+> hide #!70 models
+> show #!70 models
+> hide #!70 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J577_class_02_00082_volume.mrc
+Opened cryosparc_P17_J577_class_02_00082_volume.mrc as #82, grid size
+,128,128, pixel 4.36, shown at level 0.888, step 1, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J583_class_02_00082_volume.mrc
+Opened cryosparc_P17_J583_class_02_00082_volume.mrc as #83, grid size
+,128,128, pixel 4.36, shown at level 0.827, step 1, values float32
+> hide #!83 models
+> volume #82 level 1.108
+> volume #82 level 1.632
+> volume #83 level 1.361
+> open /Users/cvetkom/Downloads/cryosparc_P17_J610_002_volume_map.mrc
+Opened cryosparc_P17_J610_002_volume_map.mrc as #84, grid size 294,294,294,
+pixel 1.9, shown at level 0.289, step 2, values float32
+> volume #84 step 1
+> volume #84 level 0.3974
+> volume #84 level 0.3145
+> volume #84 level 0.3879
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class001.mrc
+Opened Cl3D_j574_run_it025_class001.mrc as #85, grid size 294,294,294, pixel
+.9, shown at level 0.0156, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class002.mrc
+Opened Cl3D_j574_run_it025_class002.mrc as #86, grid size 294,294,294, pixel
+.9, shown at level 0.0134, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class003.mrc
+Opened Cl3D_j574_run_it025_class003.mrc as #87, grid size 294,294,294, pixel
+.9, shown at level 0.0132, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class004.mrc
+Opened Cl3D_j574_run_it025_class004.mrc as #88, grid size 294,294,294, pixel
+.9, shown at level 0.0143, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class005.mrc
+Opened Cl3D_j574_run_it025_class005.mrc as #89, grid size 294,294,294, pixel
+.9, shown at level 0.0158, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job574/Cl3D_j574_run_it025_class006.mrc
+Opened Cl3D_j574_run_it025_class006.mrc as #90, grid size 294,294,294, pixel
+.9, shown at level 0.0179, step 2, values float32
+> hide #!84 models
+> volume all step 1
+> hide #!86 models
+> hide #!87 models
+> hide #!88 models
+> hide #!89 models
+> hide #!90 models
+> volume #85 level 0.013
+> volume #86 level 0.013
+> volume #86 level 0.012
+> volume #87 level 0.012
+> show #!85 models
+> hide #!85 models
+> show #!85 models
+> hide #!85 models
+> volume #88 level 0.013
+> volume #88 level 0.012
+> show #!86 models
+> hide #!86 models
+> show #!85 models
+> hide #!85 models
+> hide #!88 models
+> show #!89 models
+> show #!88 models
+> hide #!88 models
+> volume #89 level 0.013
+> volume #90 level 0.013
+> hide #!90 models
+> show #!90 models
+> hide #!90 models
+> show #!89 models
+> show #!88 models
+> show #!87 models
+> hide #!87 models
+> show #!87 models
+> hide #!87 models
+> hide #!89 models
+> hide #!88 models
+> show #!87 models
+> hide #!87 models
+> show #!86 models
+> hide #!86 models
+> show #!85 models
+> hide #!85 models
+> show #!84 models
+> hide #!84 models
+> show #!85 models
+> show #!86 models
+> hide #!86 models
+> show #!86 models
+> hide #!86 models
+> show #!86 models
+> hide #!86 models
+> show #!87 models
+> hide #!87 models
+> show #!88 models
+> hide #!88 models
+> show #!88 models
+> show #!89 models
+> hide #!89 models
+> show #!90 models
+> hide #!90 models
+> hide #!88 models
+> show #!88 models
+> hide #!88 models
+> hide #!85 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class001.mrc
+Opened Cl3D_j575_run_it025_class001.mrc as #91, grid size 294,294,294, pixel
+.9, shown at level 0.0167, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class002.mrc
+Opened Cl3D_j575_run_it025_class002.mrc as #92, grid size 294,294,294, pixel
+.9, shown at level 0.014, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class003.mrc
+Opened Cl3D_j575_run_it025_class003.mrc as #93, grid size 294,294,294, pixel
+.9, shown at level 0.014, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class004.mrc
+Opened Cl3D_j575_run_it025_class004.mrc as #94, grid size 294,294,294, pixel
+.9, shown at level 0.0158, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class005.mrc
+Opened Cl3D_j575_run_it025_class005.mrc as #95, grid size 294,294,294, pixel
+.9, shown at level 0.0132, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job575/Cl3D_j575_run_it025_class006.mrc
+Opened Cl3D_j575_run_it025_class006.mrc as #96, grid size 294,294,294, pixel
+.9, shown at level 0.0132, step 2, values float32
+> hide #!92 models
+> hide #!93 models
+> hide #!94 models
+> hide #!95 models
+> hide #!96 models
+> volume all step 1
+> volume #91 level 0.013
+> volume #92 level 0.012
+> volume #93 level 0.012
+> volume #94 level 0.013
+> volume #95 level 0.013
+> close #91-96
+> show #!85 models
+> show #!86 models
+> hide #!85 models
+> show #!85 models
+> hide #!85 models
+> show #!85 models
+> hide #!85 models
+> hide #!86 models
+> show #!87 models
+> hide #!87 models
+> show #!87 models
+> hide #!87 models
+> show #!88 models
+> show #!86 models
+> hide #!86 models
+> show #!85 models
+> hide #!85 models
+> hide #!88 models
+> show #!89 models
+> hide #!89 models
+> show #!90 models
+> hide #!90 models
+> show #!89 models
+> show #!88 models
+> hide #!88 models
+> show #!87 models
+> hide #!87 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
+> show #!14 models
+> hide #!14 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> hide #!89 models
+> show #!90 models
+> hide #!90 models
+> show #!89 models
+> hide #!89 models
+> show #!88 models
+> hide #!88 models
+> show #!88 models
+> show #!87 models
+> hide #!87 models
+> show #!87 models
+> hide #!87 models
+> show #!87 models
+> hide #!87 models
+> show #!86 models
+> hide #!86 models
+> hide #!88 models
+> show #!70 models
+> show #!71 models
+> hide #!71 models
+> show #!72 models
+> hide #!70 models
+> hide #!72 models
+> show #!73 models
+> hide #!73 models
+> show #!74 models
+> hide #!74 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> show #!86 models
+> hide #!86 models
+> show #!85 models
+> hide #!85 models
+> show #!87 models
+> hide #!87 models
+> show #!88 models
+> hide #!88 models
+> show #!89 models
+> hide #!89 models
+> show #!89 models
+> hide #!89 models
+> show #!89 models
+> hide #!89 models
+> show #!89 models
+> hide #!89 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!74 models
+> hide #!74 models
+> show #!73 models
+> hide #!73 models
+> show #!72 models
+> hide #!72 models
+> show #!71 models
+> hide #!71 models
+> show #!70 models
+> hide #!70 models
+> show #!70 models
+> hide #!70 models
+> show #!69 models
+> hide #!69 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> hide #!32 models
+> hide #!34 models
+> show #!34 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!35 models
+> hide #!32 models
+> hide #!35 models
+> show #!36 models
+> hide #!36 models
+> show #!36 models
+> hide #!36 models
+> show #!37 models
+> hide #!37 models
+> show #!38 models
+> show #!39 models
+> hide #!39 models
+> show #!40 models
+> hide #!40 models
+> show #!39 models
+> show #!40 models
+> hide #!40 models
+> hide #!39 models
+> show #!41 models
+> hide #!41 models
+> hide #!38 models
+> show #!82 models
+> show #!83 models
+> hide #!83 models
+> hide #!82 models
+> show #!84 models
+> hide #!84 models
+> show #!82 models
+> hide #!82 models
+> show #!83 models
+> hide #!83 models
+> show #!84 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J611_002_volume_map.mrc
+Opened cryosparc_P17_J611_002_volume_map.mrc as #91, grid size 294,294,294,
+pixel 1.9, shown at level 0.273, step 2, values float32
+> hide #!84 models
+> show #!84 models
+> hide #!84 models
+> volume #91 step 1
+> show #!84 models
+> volume #84 level 0.4
+> volume #84 level 0.36
+> hide #!91 models
+> volume #91 level 0.36
+> hide #!84 models
+> show #!84 models
+> hide #!84 models
+> volume #91 level 0.4
+> volume #91 level 0.45
+> show #!84 models
+> volume #84 level 0.45
+> hide #!84 models
+> show #!84 models
+> hide #!84 models
+> show #!84 models
+> hide #!84 models
+> show #!84 models
+> hide #!91 models
+> show #!91 models
+> hide #!91 models
+> show #!91 models
+> hide #!91 models
+> show #!91 models
+> hide #!84 models
+> show #!84 models
+> hide #!84 models
+> show #!84 models
+> hide #!84 models
+> show #!84 models
+> hide #!84 models
+> hide #!91 models
+> show #!91 models
+> hide #!91 models
+> show #!91 models
+> hide #!91 models
+> show #!90 models
+> hide #!90 models
+> show #!85 models
+> show #!86 models
+> hide #!86 models
+> hide #!85 models
+> show #!85 models
+> show #!86 models
+> hide #!85 models
+> show #!85 models
+> hide #!85 models
+> show #!85 models
+> hide #!85 models
+> show #!85 models
+> hide #!85 models
+> show #!87 models
+> hide #!87 models
+> show #!88 models
+> hide #!88 models
+> show #!89 models
+> hide #!89 models
+> show #!90 models
+> hide #!90 models
+> hide #!86 models
+> show #!28 models
+> hide #!28 models
+> show #!29 models
+> show #!28 models
+> hide #!28 models
+> show #!28 models
+> hide #!28 models
+> hide #!29 models
+> show #!29 models
+> show #!28 models
+> hide #!28 models
+> hide #!29 models
+> show #!30 models
+> hide #!30 models
+> show #!31 models
+> show #!28 models
+> hide #!28 models
+> hide #!31 models
+> show #!32 models
+> show #!33 models
+> hide #!33 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> hide #!32 models
+> show #!28 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!28 models
+> hide #!34 models
+> show #!28 models
+> show #!29 models
+> hide #!29 models
+> show #!29 models
+> hide #!28 models
+> hide #!29 models
+> show #!30 models
+> hide #!30 models
+> show #!31 models
+> hide #!31 models
+> show #!32 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> hide #!34 models
+> show #!33 models
+> hide #!32 models
+> show #!31 models
+> hide #!31 models
+> show #!32 models
+> hide #!32 models
+> show #!34 models
+> hide #!33 models
+> hide #!34 models
+> show #!35 models
+> show #!32 models
+> hide #!35 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> hide #!32 models
+> hide #!34 models
+> show #!36 models
+> show #!37 models
+> hide #!36 models
+> show #!38 models
+> hide #!38 models
+> show #!38 models
+> hide #!37 models
+> show #!37 models
+> show #!36 models
+> hide #!36 models
+> show #!36 models
+> hide #!36 models
+> hide #!38 models
+> hide #!37 models
+> show #!39 models
+> show #!40 models
+> hide #!39 models
+> hide #!40 models
+> show #!41 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!41 models
+> show #!43 models
+> hide #!42 models
+> hide #!43 models
+> show #!44 models
+> show #!45 models
+> hide #!45 models
+> show #!46 models
+> hide #!44 models
+> hide #!46 models
+> show #!47 models
+> hide #!47 models
+> show #!48 models
+> hide #!48 models
+> show #!49 models
+> hide #!49 models
+> show #!50 models
+> show #!51 models
+> hide #!51 models
+> show #!52 models
+> hide #!52 models
+> hide #!50 models
+> show #!53 models
+> hide #!53 models
+> show #!54 models
+> hide #!54 models
+> show #!55 models
+> hide #!55 models
+> show #!56 models
+> hide #!56 models
+> show #!57 models
+> hide #!57 models
+> show #!58 models
+> hide #!58 models
+> show #!59 models
+> show #!60 models
+> hide #!60 models
+> show #!61 models
+> hide #!61 models
+> show #!62 models
+> hide #!62 models
+> hide #!59 models
+> show #!63 models
+> show #!64 models
+> show #!65 models
+> hide #!65 models
+> show #!66 models
+> hide #!64 models
+> hide #!63 models
+> hide #!66 models
+> show #!63 models
+> show #!64 models
+> hide #!63 models
+> hide #!64 models
+> show #!67 models
+> hide #!67 models
+> show #!68 models
+> show #!69 models
+> hide #!68 models
+> show #!68 models
+> hide #!69 models
+> show #!69 models
+> hide #!68 models
+> hide #!69 models
+> show #!70 models
+> show #!71 models
+> hide #!71 models
+> show #!72 models
+> hide #!72 models
+> show #!73 models
+> hide #!73 models
+> hide #!70 models
+> show #!75 models
+> show #!74 models
+> show #!73 models
+> hide #!73 models
+> hide #!74 models
+> hide #!75 models
+> show #!72 models
+> hide #!72 models
+> show #!71 models
+> hide #!71 models
+> show #!70 models
+> show #!71 models
+> hide #!71 models
+> hide #!70 models
+> show #!71 models
+> hide #!71 models
+> show #!72 models
+> hide #!72 models
+> show #!73 models
+> hide #!73 models
+> show #!74 models
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+> hide #!74 models
+> show #!74 models
+> show #!73 models
+> hide #!73 models
+> hide #!74 models
+> hide #!75 models
+> show #!76 models
+> show #!77 models
+> hide #!77 models
+> show #!78 models
+> hide #!78 models
+> show #!79 models
+> hide #!79 models
+> show #!80 models
+> hide #!80 models
+> show #!81 models
+> hide #!81 models
+> hide #!76 models
+> show #!85 models
+> show #!86 models
+> hide #!86 models
+> show #!87 models
+> hide #!87 models
+> show #!88 models
+> hide #!88 models
+> hide #!85 models
+> show #!86 models
+> hide #!86 models
+> show #!87 models
+> hide #!87 models
+> show #!88 models
+> hide #!88 models
+> show #!88 models
+> hide #!88 models
+> show #!89 models
+> hide #!89 models
+> show #!90 models
+> hide #!90 models
+> show #!89 models
+> show #!88 models
+> hide #!88 models
+> show #!87 models
+> hide #!87 models
+> show #!86 models
+> hide #!86 models
+> show #!85 models
+> hide #!85 models
+> show #!84 models
+> hide #!84 models
+> hide #!89 models
+> show #!33 models
+> show #!32 models
+> hide #!32 models
+> hide #!33 models
+> show #!33 models
+> hide #!33 models
+> show #!32 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> show #!35 models
+> hide #!35 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!33 models
+> hide #!33 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> show #!33 models
+> hide #!33 models
+> show #!35 models
+> hide #!35 models
+> show #!33 models
+> hide #!33 models
+> show #!35 models
+> hide #!35 models
+> show #!35 models
+> hide #!35 models
+> hide #!34 models
+> show #!34 models
+> hide #!32 models
+> hide #!34 models
+> show #!36 models
+> hide #!36 models
+> show #!37 models
+> hide #!37 models
+> show #!38 models
+> hide #!38 models
+> show #!39 models
+> hide #!39 models
+> show #!40 models
+> hide #!40 models
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+> show #!40 models
+> hide #!40 models
+> show #!40 models
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+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!40 models
+> hide #!39 models
+> show #!41 models
+> hide #!41 models
+> show #!41 models
+> hide #!41 models
+> show #!42 models
+> hide #!42 models
+> show #!70 models
+> show #!71 models
+> hide #!71 models
+> show #!72 models
+> hide #!70 models
+> hide #!72 models
+> show #!73 models
+> hide #!73 models
+> show #!74 models
+> show #!75 models
+> hide #!74 models
+> hide #!75 models
+> show #!76 models
+> show #!75 models
+> hide #!75 models
+> show #!77 models
+> hide #!77 models
+> show #!78 models
+> hide #!78 models
+> show #!79 models
+> hide #!79 models
+> hide #!76 models
+> show #!85 models
+> hide #!85 models
+> show #!86 models
+> hide #!86 models
+> show #!87 models
+> hide #!87 models
+> show #!88 models
+> hide #!88 models
+> show #!89 models
+> hide #!89 models
+> show #!89 models
+> show #!90 models
+> hide #!90 models
+> show #!32 models
+> show #!34 models
+> hide #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> show #!32 models
+> hide #!34 models
+> show #!34 models
+> hide #!32 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> show #!13 models
+> hide #!13 models
+> show #!14 models
+> hide #!14 models
+> show #!15 models
+> hide #!15 models
+> show #!16 models
+> hide #!16 models
+> show #!17 models
+> hide #!17 models
+> show #!15 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> hide #!15 models
+> show #!50 models
+> show #!51 models
+> show #!52 models
+> hide #!51 models
+> show #!51 models
+> hide #!51 models
+> hide #!50 models
+> hide #!52 models
+> show #!51 models
+> hide #!51 models
+> show #!50 models
+> hide #!50 models
+> show #!53 models
+> hide #!53 models
+> show #!54 models
+> hide #!54 models
+> show #!55 models
+> hide #!55 models
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+> hide #!55 models
+> show #!50 models
+> hide #!50 models
+> show #!51 models
+> show #!56 models
+> hide #!56 models
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+> hide #!57 models
+> show #!57 models
+> hide #!51 models
+> show #!51 models
+> hide #!57 models
+> show #!55 models
+> hide #!55 models
+> show #!55 models
+> hide #!51 models
+> show #!51 models
+> hide #!51 models
+> show #!51 models
+> hide #!55 models
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+> hide #!55 models
+> show #!55 models
+> hide #!55 models
+> hide #!51 models
+> show #!50 models
+> show #!52 models
+> hide #!52 models
+> show #!54 models
+> hide #!54 models
+> show #!54 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!54 models
+> show #!54 models
+> hide #!54 models
+> show #!54 models
+> hide #!54 models
+> show #!54 models
+> hide #!54 models
+> show #!54 models
+> hide #!54 models
+> show #!54 models
+> hide #!54 models
+> hide #!50 models
+> show #!50 models
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+> show #!50 models
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+> hide #!50 models
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+> show #!52 models
+> hide #!52 models
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+> hide #!53 models
+> show #!54 models
+> show #!50 models
+> show #!14 models
+> hide #!14 models
+> show #!13 models
+> hide #!13 models
+> show #!15 models
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+> show #!15 models
+> hide #!15 models
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+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!16 models
+> hide #!16 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
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+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!56 models
+> hide #!56 models
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+> hide #!57 models
+> show #!58 models
+> hide #!58 models
+> show #!57 models
+> hide #!57 models
+> show #!56 models
+> hide #!56 models
+> show #!56 models
+> volume #56 level 0.013
+> volume #56 level 0.012
+> show #!57 models
+> hide #!57 models
+> show #!57 models
+> hide #!56 models
+> hide #!57 models
+> show #!58 models
+> hide #!58 models
+> show #!56 models
+> hide #!56 models
+> show #!59 models
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+> show #!56 models
+> show #!50 models
+> hide #!56 models
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+> hide #!56 models
+> show #!56 models
+> hide #!50 models
+> show #!57 models
+> hide #!57 models
+> show #!58 models
+> hide #!58 models
+> show #!58 models
+> hide #!58 models
+> show #!58 models
+> hide #!58 models
+> show #!14 models
+> hide #!14 models
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+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> hide #!56 models
+> show #!56 models
+> hide #!56 models
+> show #!59 models
+> show #!60 models
+> hide #!59 models
+> hide #!60 models
+> show #!61 models
+> hide #!61 models
+> show #!61 models
+> hide #!61 models
+> show #!62 models
+> hide #!62 models
+> show #!59 models
+> show #!56 models
+> hide #!56 models
+> show #!56 models
+> show #!57 models
+> hide #!57 models
+> hide #!56 models
+> show #!56 models
+> hide #!56 models
+> show #!56 models
+> hide #!56 models
+> show #!56 models
+> hide #!56 models
+> show #!56 models
+> hide #!59 models
+> show #!59 models
+> hide #!59 models
+> show #!59 models
+> hide #!59 models
+> show #!59 models
+> hide #!59 models
+> show #!59 models
+> hide #!56 models
+> show #!56 models
+> hide #!56 models
+> show #!56 models
+> hide #!59 models
+> show #!14 models
+> hide #!14 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!59 models
+> hide #!59 models
+> show #!59 models
+> hide #!59 models
+> show #!59 models
+> hide #!59 models
+> show #!59 models
+> hide #!56 models
+> show #!60 models
+> hide #!59 models
+> show #!59 models
+> hide #!60 models
+> show #!61 models
+> hide #!61 models
+> show #!62 models
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+> hide #!32 models
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+> show #!32 models
+> show #!15 models
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+> show #!34 models
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+> show #!32 models
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+> show #!34 models
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+> show #!32 models
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+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
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+> hide #!38 models
+> hide #!32 models
+> show #!39 models
+> hide #!39 models
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+> hide #!40 models
+> show #!40 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
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+> show #!40 models
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+> hide #!39 models
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+> hide #!41 models
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+> hide #!42 models
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+> hide #!43 models
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+> hide #!42 models
+> hide #!41 models
+> show #!39 models
+> show #!40 models
+> hide #!39 models
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+> hide #!40 models
+> show #!40 models
+> hide #!39 models
+> hide #!40 models
+> show #!44 models
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+> hide #!44 models
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+> show #!46 models
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+> hide #!45 models
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+> hide #!46 models
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+> show #!48 models
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+> hide #!48 models
+> hide #!49 models
+> show #!44 models
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+> hide #!45 models
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+> hide #!44 models
+> hide #!46 models
+> show #!47 models
+> hide #!47 models
+> show #!48 models
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+> hide #!48 models
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+> show #!39 models
+> hide #!39 models
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+> show #!35 models
+> hide #!35 models
+> show #!35 models
+> hide #!35 models
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+> hide #!37 models
+> hide #!45 models
+> show #!45 models
+> hide #!45 models
+> show #!70 models
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+> hide #!70 models
+> hide #!71 models
+> show #!72 models
+> hide #!72 models
+> show #!73 models
+> hide #!73 models
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+> hide #!74 models
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+> show #!70 models
+> hide #!70 models
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+> hide #!72 models
+> show #!73 models
+> hide #!73 models
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+> hide #!74 models
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+> show #!72 models
+> hide #!72 models
+> show #!71 models
+> show #!73 models
+> hide #!73 models
+> hide #!71 models
+> show #!71 models
+> hide #!71 models
+> show #!70 models
+> hide #!70 models
+> show #!70 models
+> hide #!70 models
+> show #!70 models
+> hide #!74 models
+> show #!74 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> hide #!74 models
+> hide #!70 models
+> show #!76 models
+> hide #!76 models
+> show #!75 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> hide #!75 models
+> show #!76 models
+> show #!77 models
+> hide #!76 models
+> show #!78 models
+> hide #!78 models
+> show #!79 models
+> hide #!79 models
+> show #!80 models
+> hide #!80 models
+> show #!81 models
+> hide #!81 models
+> close #76-81
+> show #!85 models
+> show #!86 models
+> hide #!86 models
+> hide #!85 models
+> show #!85 models
+> show #!86 models
+> hide #!85 models
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+> hide #!87 models
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+> hide #!86 models
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+> show #!88 models
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+> show #!85 models
+> hide #!85 models
+> show #!85 models
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+> show #!90 models
+> hide #!90 models
+> show #!90 models
+> hide #!90 models
+> hide #!85 models
+> show #!85 models
+> hide #!88 models
+> show #!88 models
+> hide #!88 models
+> show #!88 models
+> hide #!88 models
+> show #!88 models
+> hide #!88 models
+> hide #!89 models
+> hide #!85 models
+> show #!85 models
+> hide #!85 models
+> show #!86 models
+> hide #!86 models
+> show #!87 models
+> hide #!87 models
+> show #!88 models
+> hide #!88 models
+> show #!88 models
+> hide #!88 models
+> show #!89 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!90 models
+> hide #!89 models
+> hide #!90 models
+> show #!89 models
+> hide #!89 models
+> show #!88 models
+> hide #!88 models
+> show #!87 models
+> hide #!87 models
+> show #!86 models
+> hide #!86 models
+> show #!56 models
+> show #!57 models
+> hide #!57 models
+> show #!57 models
+> hide #!57 models
+> show #!58 models
+> hide #!58 models
+> show #!59 models
+> hide #!56 models
+> show #!60 models
+> hide #!60 models
+> show #!61 models
+> hide #!61 models
+> show #!62 models
+> hide #!62 models
+> show #!62 models
+> hide #!62 models
+> hide #!59 models
+> show #!59 models
+> hide #!59 models
+> show #!32 models
+> show #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!34 models
+> show #!34 models
+> hide #!32 models
+> hide #!34 models
+> show #!56 models
+> show #!59 models
+> hide #!59 models
+> hide #!56 models
+> show #!32 models
+> show #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> hide #!34 models
+> show #!33 models
+> hide #!33 models
+> show #!35 models
+> hide #!35 models
+> show #!35 models
+> show #!90 models
+> hide #!90 models
+> show #!90 models
+> hide #!90 models
+> show #!89 models
+> hide #!89 models
+> show #!90 models
+> hide #!90 models
+> show #!90 models
+> hide #!90 models
+> show #!90 models
+> hide #!90 models
+> hide #!35 models
+> show #!85 models
+> show #!86 models
+> hide #!86 models
+> show #!87 models
+> hide #!87 models
+> show #!88 models
+> hide #!88 models
+> hide #!85 models
+> show #!86 models
+> show #!87 models
+> hide #!87 models
+> show #!87 models
+> hide #!87 models
+> show #!87 models
+> hide #!86 models
+> show #!86 models
+> hide #!86 models
+> show #!86 models
+> hide #!86 models
+> hide #!87 models
+> show #!89 models
+> hide #!89 models
+> show #!90 models
+> hide #!90 models
+> show #!85 models
+> hide #!85 models
+> show #!86 models
+> show #!87 models
+> show #!88 models
+> hide #!88 models
+> show #!88 models
+> hide #!88 models
+> hide #!87 models
+> hide #!86 models
+> show #!86 models
+> hide #!86 models
+> show #!86 models
+> show #!87 models
+> hide #!86 models
+> show #!86 models
+> hide #!87 models
+> show #!87 models
+> hide #!87 models
+> show #!87 models
+> show #!89 models
+> hide #!89 models
+> show #!89 models
+> hide #!89 models
+> hide #!87 models
+> show #!87 models
+> hide #!87 models
+> hide #!86 models
+> show #!86 models
+> show #!87 models
+> hide #!87 models
+> show #!87 models
+> hide #!87 models
+> hide #!86 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> show #!40 models
+> hide #!39 models
+> hide #!40 models
+> show #!41 models
+> hide #!41 models
+> show #!42 models
+> hide #!42 models
+> show #!43 models
+> hide #!43 models
+> show #!42 models
+> hide #!42 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> show #!40 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> hide #!40 models
+> show #!39 models
+> show #!40 models
+> hide #!40 models
+> hide #!39 models
+> show #!41 models
+> show #!42 models
+> hide #!42 models
+> hide #!41 models
+> show #!43 models
+> show #!41 models
+> show #!42 models
+> hide #!42 models
+> hide #!41 models
+> show #!42 models
+> hide #!42 models
+> hide #!43 models
+> show #!41 models
+> show #!42 models
+> hide #!41 models
+> hide #!42 models
+> show #!43 models
+> show #!41 models
+> show #!42 models
+> hide #!41 models
+> hide #!42 models
+> hide #!43 models
+> show #!41 models
+> show #!42 models
+> hide #!41 models
+> hide #!42 models
+> show #!43 models
+> hide #!43 models
+> show #!41 models
+> show #!42 models
+> show #!43 models
+> hide #!43 models
+> hide #!42 models
+> hide #!41 models
+> show #!32 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> hide #!32 models
+> hide #!34 models
+> show #!35 models
+> hide #!35 models
+> show #!35 models
+> hide #!35 models
+> show #!36 models
+> hide #!36 models
+> show #!35 models
+> show #!34 models
+> hide #!35 models
+> show #!35 models
+> hide #!34 models
+> show #!39 models
+> hide #!39 models
+> show #!40 models
+> hide #!40 models
+> show #!34 models
+> hide #!34 models
+> hide #!35 models
+> show #!34 models
+> hide #!34 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> hide #!34 models
+> show #!35 models
+> hide #!35 models
+> show #!91 models
+> hide #!91 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J615_class_00_final_volume.mrc
+Opened cryosparc_P17_J615_class_00_final_volume.mrc as #76, grid size
+,192,192, pixel 2.91, shown at level 0.526, step 1, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J616_class_00_final_volume.mrc
+Opened cryosparc_P17_J616_class_00_final_volume.mrc as #77, grid size
+,192,192, pixel 2.91, shown at level 0.499, step 1, values float32
+> volume #76 level 0.4164
+> volume #77 level 0.4158
+> volume #76 level 0.4
+> volume #76 level 0.3
+> volume #76 level 0.35
+> volume #76 level 0.3
+> open /Users/cvetkom/Downloads/cryosparc_P17_J621_mask.mrc
+Opened cryosparc_P17_J621_mask.mrc as #78, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+> volume #78 level 1
+> volume #78 color #cccc9980
+> open /Users/cvetkom/Downloads/cryosparc_P17_J617_class_00_final_volume.mrc
+Opened cryosparc_P17_J617_class_00_final_volume.mrc as #79, grid size
+,192,192, pixel 2.91, shown at level 0.517, step 1, values float32
+> hide #!78 models
+> hide #!79 models
+> show #!79 models
+> hide #!79 models
+> show #!79 models
+> hide #!76 models
+> volume #79 level 0.3
+> volume #79 level 0.4
+> volume #79 level 0.35
+> volume #79 level 0.3
+> open /Users/cvetkom/Downloads/cryosparc_P17_J620_007_volume_map.mrc
+Opened cryosparc_P17_J620_007_volume_map.mrc as #80, grid size 294,294,294,
+pixel 1.9, shown at level 0.339, step 2, values float32
+> hide #!79 models
+> volume #80 step 1
+> volume #80 level 0.3095
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J368_007_volume_map.mrc
+Opened cryosparc_P17_J368_007_volume_map.mrc as #81, grid size 294,294,294,
+pixel 1.9, shown at level 0.37, step 2, values float32
+> hide #!81 models
+> show #!81 models
+> hide #!80 models
+> volume #81 step 1
+> show #!80 models
+> hide #!80 models
+> volume #81 level 0.35
+> hide #!81 models
+> show #!80 models
+> volume #80 level 0.35
+> volume #80 level 0.32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J619_class_00_final_volume.mrc
+Opened cryosparc_P17_J619_class_00_final_volume.mrc as #92, grid size
+,192,192, pixel 2.91, shown at level 0.517, step 1, values float32
+> hide #!80 models
+> show #!79 models
+> hide #!79 models
+> volume #92 level 0.35
+> volume #92 level 0.4
+> volume #92 level 0.4136
+> show #!79 models
+> hide #!92 models
+> volume #79 level 0.3729
+> show #!76 models
+> hide #!79 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J623_007_volume_map.mrc
+Opened cryosparc_P17_J623_007_volume_map.mrc as #93, grid size 294,294,294,
+pixel 1.9, shown at level 0.341, step 2, values float32
+> hide #!76 models
+> volume #93 step 1
+> volume #93 level 0.32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J626_class_01_00400_volume.mrc
+Opened cryosparc_P17_J626_class_01_00400_volume.mrc as #94, grid size
+,128,128, pixel 4.36, shown at level 1.11, step 1, values float32
+> hide #!93 models
+> volume #94 level 0.8311
+> close #94
+> open /Users/cvetkom/Downloads/cryosparc_P17_J625_007_volume_map.mrc
+Opened cryosparc_P17_J625_007_volume_map.mrc as #94, grid size 294,294,294,
+pixel 1.9, shown at level 0.341, step 2, values float32
+> volume #94 step 1
+> volume #94 level 0.3
+> volume #94 level 0.25
+> open /Users/cvetkom/Downloads/cryosparc_P17_J631_class_01_00042_volume.mrc
+Opened cryosparc_P17_J631_class_01_00042_volume.mrc as #95, grid size
+,128,128, pixel 4.36, shown at level 1.32, step 1, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J629_class_01_00042_volume.mrc
+Opened cryosparc_P17_J629_class_01_00042_volume.mrc as #96, grid size
+,128,128, pixel 4.36, shown at level 1.32, step 1, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J628_class_01_00042_volume.mrc
+Opened cryosparc_P17_J628_class_01_00042_volume.mrc as #97, grid size
+,128,128, pixel 4.36, shown at level 1.32, step 1, values float32
+> hide #!94 models
+> hide #!95 models
+> hide #!96 models
+> volume #97 level 1.082
+> volume #97 level 1
+> volume #96 level 1
+> volume #95 level 1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J620_007_volume_map.mrc
+Opened cryosparc_P17_J620_007_volume_map.mrc as #98, grid size 294,294,294,
+pixel 1.9, shown at level 0.339, step 2, values float32
+> close #98
+> show #!80 models
+> show #!93 models
+Drag select of 80 cryosparc_P17_J620_007_volume_map.mrc , 93
+cryosparc_P17_J623_007_volume_map.mrc
+> select clear
+> hide #!93 models
+> show #!93 models
+> hide #!80 models
+> show #!80 models
+> hide #!80 models
+> show #!80 models
+> hide #!80 models
+> show #!80 models
+> hide #!80 models
+> show #!80 models
+> lighting soft
+> hide #!80 models
+> show #!80 models
+> hide #!80 models
+> show #!80 models
+> hide #!80 models
+> show #!80 models
+> hide #!80 models
+> show #!82 models
+> hide #!82 models
+> show #!80 models
+> hide #!80 models
+> show #!80 models
+> hide #!80 models
+> show #!80 models
+> hide #!80 models
+> hide #!93 models
+> show #!81 models
+> show #!80 models
+> hide #!80 models
+> volume #81 level 0.32
+> volume #81 level 0.35
+> show #!80 models
+> select add #81
+models selected
+> ui mousemode right "rotate selected models"
+> select subtract #81
+Nothing selected
+> hide #!81 models
+> open /Volumes/lab-
+> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job581/run_it025_class006.mrc
+Opened run_it025_class006.mrc as #98, grid size 294,294,294, pixel 1.9, shown
+at level 0.0154, step 2, values float32
+> open /Volumes/lab-
+> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job581/run_it025_class003.mrc
+Opened run_it025_class003.mrc as #99, grid size 294,294,294, pixel 1.9, shown
+at level 0.0157, step 2, values float32
+> hide #!80 models
+> hide #!98 models
+> hide #!99 models
+> show #!99 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> hide #!99 models
+> open /Volumes/lab-
+> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job581/run_it025_class001.mrc
+Opened run_it025_class001.mrc as #100, grid size 294,294,294, pixel 1.9, shown
+at level 0.0158, step 2, values float32
+> open /Volumes/lab-
+> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Class3D/job581/run_it025_class002.mrc
+Opened run_it025_class002.mrc as #101, grid size 294,294,294, pixel 1.9, shown
+at level 0.0166, step 2, values float32
+> hide #!101 models
+> volume #98 step 1
+> volume #99 step 1
+> volume #100 step 1
+> volume #101 step 1
+> volume #100 level 0.01165
+> volume #101 level 0.01425
+> volume #101 level 0.01268
+> show #!98 models
+> show #!99 models
+> hide #!99 models
+> hide #!98 models
+> show #!100 models
+> hide #!100 models
+> show #!100 models
+> show #!32 models
+> volume #100 level 0.02
+> hide #!32 models
+> show #!32 models
+> volume #100 level 0.015
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> volume #100 level 0.014
+> volume #100 level 0.013
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> volume #101 level 0.014
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> hide #!101 models
+> show #!99 models
+> show #!98 models
+> show #!85 models
+> hide #!85 models
+> show #!85 models
+> hide #!85 models
+> show #!85 models
+> hide #!85 models
+> show #!88 models
+> hide #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!88 models
+> show #!88 models
+> hide #!88 models
+> show #!88 models
+> hide #!88 models
+> show #!88 models
+> hide #!88 models
+> show #!39 models
+> hide #!39 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> hide #!40 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!40 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> show #!40 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> hide #!40 models
+> show #!40 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!40 models
+> show #!40 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> show #!39 models
+> hide #!39 models
+> show #!39 models
+> hide #!39 models
+> hide #!40 models
+> close #98-101
+> show #!97 models
+> hide #!97 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class001.mrc
+Opened Cl3D_j581_run_it025_class001.mrc as #98, grid size 294,294,294, pixel
+.9, shown at level 0.0158, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class002.mrc
+Opened Cl3D_j581_run_it025_class002.mrc as #99, grid size 294,294,294, pixel
+.9, shown at level 0.0166, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class003.mrc
+Opened Cl3D_j581_run_it025_class003.mrc as #100, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class004.mrc
+Opened Cl3D_j581_run_it025_class004.mrc as #101, grid size 294,294,294, pixel
+.9, shown at level 0.0131, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class005.mrc
+Opened Cl3D_j581_run_it025_class005.mrc as #102, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class006.mrc
+Opened Cl3D_j581_run_it025_class006.mrc as #103, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job581/Cl3D_j581_run_it025_class007.mrc
+Opened Cl3D_j581_run_it025_class007.mrc as #104, grid size 294,294,294, pixel
+.9, shown at level 0.018, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class001.mrc
+Opened Cl3D_j585_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
+.9, shown at level 0.0155, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class002.mrc
+Opened Cl3D_j585_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
+.9, shown at level 0.0159, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class003.mrc
+Opened Cl3D_j585_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
+.9, shown at level 0.0197, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class004.mrc
+Opened Cl3D_j585_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class005.mrc
+Opened Cl3D_j585_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
+.9, shown at level 0.016, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job585/Cl3D_j585_run_it025_class006.mrc
+Opened Cl3D_j585_run_it025_class006.mrc as #110, grid size 294,294,294, pixel
+.9, shown at level 0.0002, step 2, values float32
+> volume all step 1
+> hide #!99 models
+> hide #!100 models
+> hide #!101 models
+> hide #!102 models
+> hide #!103 models
+> hide #!104 models
+> hide #!105 models
+> hide #!106 models
+> hide #!107 models
+> hide #!108 models
+> hide #!109 models
+> hide #!110 models
+> volume #98 level 0.013
+> volume #98 level 0.012
+> volume #99 level 0.012
+> volume #100 level 0.013
+> volume #101 level 0.012
+> volume #102 level 0.012
+> volume #103 level 0.013
+> ui mousemode right zoom
+> lighting simple
+> show #!98 models
+> hide #!98 models
+> show #!100 models
+> hide #!100 models
+> show #!100 models
+> hide #!100 models
+> hide #!103 models
+> show #!104 models
+> show #!103 models
+> hide #!104 models
+> show #!104 models
+> volume #104 level 0.013
+> show #!103 models
+> hide #!103 models
+> volume #105 level 0.013
+> volume #106 level 0.013
+> volume #106 level 0.012
+> volume #105 level 0.012
+> volume #107 level 0.013
+> volume #108 level 0.013
+> volume #109 level 0.013
+> volume #110 level -0.02134
+> close #110
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class001.mrc
+Opened Cl3D_j586_run_it025_class001.mrc as #110, grid size 294,294,294, pixel
+.9, shown at level 0.0159, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class002.mrc
+Opened Cl3D_j586_run_it025_class002.mrc as #111, grid size 294,294,294, pixel
+.9, shown at level 0.017, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class003.mrc
+Opened Cl3D_j586_run_it025_class003.mrc as #112, grid size 294,294,294, pixel
+.9, shown at level 0.0158, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class004.mrc
+Opened Cl3D_j586_run_it025_class004.mrc as #113, grid size 294,294,294, pixel
+.9, shown at level 0.0134, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class005.mrc
+Opened Cl3D_j586_run_it025_class005.mrc as #114, grid size 294,294,294, pixel
+.9, shown at level 0.0127, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class006.mrc
+Opened Cl3D_j586_run_it025_class006.mrc as #115, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job586/Cl3D_j586_run_it025_class007.mrc
+Opened Cl3D_j586_run_it025_class007.mrc as #116, grid size 294,294,294, pixel
+.9, shown at level 0.0179, step 2, values float32
+> close #105-109
+> hide #!111 models
+> hide #!112 models
+> hide #!113 models
+> hide #!114 models
+> hide #!115 models
+> hide #!116 models
+> volume #110 level 0.012
+> volume #111 level 0.012
+> volume #111 level 0.013
+> volume #110 step 1
+> volume #111 step 1
+> volume #112 step 1
+> volume #112 level 0.013
+> volume #113 step 1
+> volume #113 level 0.012
+> volume #114 step 1
+> volume #114 level 0.012
+> volume #115 step 1
+> volume #115 level 0.013
+> show #!112 models
+> hide #!112 models
+> show #!112 models
+> hide #!112 models
+> show #!112 models
+> hide #!112 models
+> show #!112 models
+> hide #!112 models
+> show #!112 models
+> hide #!112 models
+> volume #116 step 1
+> volume #116 level 0.013
+> show #!110 models
+> show #!111 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> volume #111 level 0.01556
+> volume #111 level 0.01455
+> show #!110 models
+> hide #!110 models
+> hide #!111 models
+> show #!111 models
+> show #!99 models
+> hide #!111 models
+> show #!98 models
+> hide #!99 models
+> show #!110 models
+> hide #!110 models
+> hide #!98 models
+> show #!110 models
+> hide #!110 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job583/Cl3D_j583_run_it025_class001.mrc
+Opened Cl3D_j583_run_it025_class001.mrc as #105, grid size 294,294,294, pixel
+.9, shown at level 0.0156, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job583/Cl3D_j583_run_it025_class002.mrc
+Opened Cl3D_j583_run_it025_class002.mrc as #106, grid size 294,294,294, pixel
+.9, shown at level 0.0158, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job583/Cl3D_j583_run_it025_class003.mrc
+Opened Cl3D_j583_run_it025_class003.mrc as #107, grid size 294,294,294, pixel
+.9, shown at level 0.0195, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job583/Cl3D_j583_run_it025_class004.mrc
+Opened Cl3D_j583_run_it025_class004.mrc as #108, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job583/Cl3D_j583_run_it025_class005.mrc
+Opened Cl3D_j583_run_it025_class005.mrc as #109, grid size 294,294,294, pixel
+.9, shown at level 0.0161, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job587/Cl3D_j587_run_it025_class001.mrc
+Opened Cl3D_j587_run_it025_class001.mrc as #117, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job587/Cl3D_j587_run_it025_class002.mrc
+Opened Cl3D_j587_run_it025_class002.mrc as #118, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job587/Cl3D_j587_run_it025_class003.mrc
+Opened Cl3D_j587_run_it025_class003.mrc as #119, grid size 294,294,294, pixel
+.9, shown at level 0.0197, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job587/Cl3D_j587_run_it025_class004.mrc
+Opened Cl3D_j587_run_it025_class004.mrc as #120, grid size 294,294,294, pixel
+.9, shown at level 0.0154, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job587/Cl3D_j587_run_it025_class005.mrc
+Opened Cl3D_j587_run_it025_class005.mrc as #121, grid size 294,294,294, pixel
+.9, shown at level 0.0161, step 2, values float32
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
+\u2014\u2014\u2014 End of log from Mon Jun 3 09:50:12 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> hide #!105 models
+> show #!105 models
+> show #!111 models
+> hide #!111 models
+> hide #!105 models
+> show #!105 models
+> hide #!105 models
+> show #!105 models
+> volume #105,106,107,108,109,117,118,119,120,121 level 0.013
+> hide #!106 models
+> show #!106 models
+> hide #!109 models
+> hide #!121 models
+> hide #!120 models
+> hide #!119 models
+> hide #!118 models
+> hide #!117 models
+> hide #!108 models
+> hide #!107 models
+> hide #!106 models
+> show #!106 models
+> hide #!106 models
+> hide #!105 models
+> show #!105 models
+> show #!106 models
+> hide #!106 models
+> hide #!105 models
+> show #!107 models
+> hide #!107 models
+> show #!108 models
+> hide #!108 models
+> show #!109 models
+> hide #!109 models
+> show #!108 models
+> show #!109 models
+> hide #!109 models
+> show #!109 models
+> hide #!109 models
+> hide #!108 models
+> show #!121 models
+> hide #!121 models
+> show #!1 models
+> show #!2 models
+> hide #!1 models
+> hide #!2 models
+> show #!2 models
+> show #!1 models
+> hide #!1 models
+> hide #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!4 models
+> hide #!4 models
+> show #!5 models
+> hide #!5 models
+> show #!6 models
+> hide #!6 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job325_0p95apix.mrc
+Opened Ref3D_job325_0p95apix.mrc as #122, grid size 588,588,588, pixel 0.95,
+shown at level 0.0107, step 4, values float32
+> close #122
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
+> show #!2 models
+> volume #2 level 0.003218
+> volume #2 level 0.006199
+> volume #2 level 0.013
+> hide #!2 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
+\u2014\u2014\u2014 End of log from Tue Jun 11 16:35:40 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> show #!119 models
+> hide #!119 models
+> show #!120 models
+> hide #!120 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class001.mrc
+Opened Cl3D_j590_run_it025_class001.mrc as #122, grid size 294,294,294, pixel
+.9, shown at level 0.0174, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class002.mrc
+Opened Cl3D_j590_run_it025_class002.mrc as #123, grid size 294,294,294, pixel
+.9, shown at level 0.0159, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class003.mrc
+Opened Cl3D_j590_run_it025_class003.mrc as #124, grid size 294,294,294, pixel
+.9, shown at level 0.0127, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class004.mrc
+Opened Cl3D_j590_run_it025_class004.mrc as #125, grid size 294,294,294, pixel
+.9, shown at level 0.0134, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class005.mrc
+Opened Cl3D_j590_run_it025_class005.mrc as #126, grid size 294,294,294, pixel
+.9, shown at level 0.0158, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class006.mrc
+Opened Cl3D_j590_run_it025_class006.mrc as #127, grid size 294,294,294, pixel
+.9, shown at level 0.0155, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job590/Cl3D_j590_run_it025_class007.mrc
+Opened Cl3D_j590_run_it025_class007.mrc as #128, grid size 294,294,294, pixel
+.9, shown at level 0.0175, step 2, values float32
+> volume all step 1
+> hide #!123 models
+> hide #!124 models
+> hide #!125 models
+> hide #!126 models
+> hide #!127 models
+> hide #!128 models
+> volume #122 level 0.01525
+> volume #122 level 0.013
+> volume #123 level 0.013
+> show #!74 models
+> volume #122 level 0.014
+> volume #122 level 0.015
+> hide #!74 models
+> volume #124 level 0.013
+> volume #125 level 0.013
+> volume #126 level 0.013
+> volume #127 level 0.013
+> volume #128 level 0.014
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/run_it025_class001.mrc
+Opened run_it025_class001.mrc as #129, grid size 294,294,294, pixel 1.9, shown
+at level 0.0173, step 2, values float32
+> close #129
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class001.mrc
+Opened Cl3D_j591_run_it025_class001.mrc as #129, grid size 294,294,294, pixel
+.9, shown at level 0.0173, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class002.mrc
+Opened Cl3D_j591_run_it025_class002.mrc as #130, grid size 294,294,294, pixel
+.9, shown at level 0.0159, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class003.mrc
+Opened Cl3D_j591_run_it025_class003.mrc as #131, grid size 294,294,294, pixel
+.9, shown at level 0.013, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class004.mrc
+Opened Cl3D_j591_run_it025_class004.mrc as #132, grid size 294,294,294, pixel
+.9, shown at level 0.0132, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class005.mrc
+Opened Cl3D_j591_run_it025_class005.mrc as #133, grid size 294,294,294, pixel
+.9, shown at level 0.0157, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class006.mrc
+Opened Cl3D_j591_run_it025_class006.mrc as #134, grid size 294,294,294, pixel
+.9, shown at level 0.0156, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job591/Cl3D_j591_run_it025_class007.mrc
+Opened Cl3D_j591_run_it025_class007.mrc as #135, grid size 294,294,294, pixel
+.9, shown at level 0.0169, step 2, values float32
+> volume all step 1
+> hide #!130 models
+> hide #!131 models
+> hide #!132 models
+> hide #!133 models
+> hide #!134 models
+> hide #!135 models
+> volume #129 level 0.015
+> volume #129 level 0.014
+> show #!130 models
+> hide #!129 models
+> volume #130 level 0.013
+> volume #132 level 0.013
+> volume #133 level 0.013
+> volume #134 level 0.014
+> volume #134 level 0.013
+> volume #135 level 0.014
+> show #!134 models
+> hide #!134 models
+> show #!134 models
+> hide #!134 models
+> show #!133 models
+> hide #!133 models
+> hide #!135 models
+> show #!134 models
+> show #!133 models
+> hide #!133 models
+> show #!133 models
+> hide #!133 models
+> hide #!134 models
+> show #!132 models
+> hide #!132 models
+> show #!131 models
+> hide #!131 models
+> show #!130 models
+> hide #!130 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!135 models
+> hide #!135 models
+> show #!134 models
+> hide #!134 models
+> show #!133 models
+> hide #!133 models
+> show #!134 models
+> show #!133 models
+> hide #!133 models
+> show #!133 models
+> hide #!133 models
+> hide #!134 models
+> show #!132 models
+> hide #!132 models
+> show #!131 models
+> hide #!131 models
+> show #!130 models
+> hide #!130 models
+> show #!129 models
+> hide #!129 models
+> show #!130 models
+> hide #!130 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes.cxs
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class001.mrc
+Opened Cl3D_j619_run_it025_class001.mrc as #136, grid size 320,320,320, pixel
+.9, shown at level 0.0108, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class002.mrc
+Opened Cl3D_j619_run_it025_class002.mrc as #137, grid size 320,320,320, pixel
+.9, shown at level 0.00682, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class003.mrc
+Opened Cl3D_j619_run_it025_class003.mrc as #138, grid size 320,320,320, pixel
+.9, shown at level 0.0091, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class004.mrc
+Opened Cl3D_j619_run_it025_class004.mrc as #139, grid size 320,320,320, pixel
+.9, shown at level 0.0104, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class005.mrc
+Opened Cl3D_j619_run_it025_class005.mrc as #140, grid size 320,320,320, pixel
+.9, shown at level 0.0128, step 2, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job619/Cl3D_j619_run_it025_class006.mrc
+Opened Cl3D_j619_run_it025_class006.mrc as #141, grid size 320,320,320, pixel
+.9, shown at level 0.013, step 2, values float32
+> volume all step 1
+> hide #!137 models
+> hide #!138 models
+> hide #!139 models
+> hide #!140 models
+> hide #!141 models
+> hide #!136 models
+> show #!136 models
+> hide #!136 models
+> show #!136 models
+> hide #!136 models
+> show #!137 models
+> hide #!137 models
+> show #!136 models
+> hide #!136 models
+> show #!136 models
+> hide #!136 models
+> show #!137 models
+> show #!138 models
+> hide #!138 models
+> show #!138 models
+> hide #!137 models
+> hide #!138 models
+> show #!139 models
+> hide #!139 models
+> show #!140 models
+> show #!141 models
+> hide #!140 models
+> hide #!141 models
+> close #136-141
+> show #!130 models
+> show #!123 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!123 models
+> show #!123 models
+> hide #!130 models
+> show #!130 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!123 models
+> hide #!130 models
+> show #!117 models
+> show #!118 models
+> hide #!118 models
+> show #!118 models
+> hide #!118 models
+> show #!118 models
+> hide #!117 models
+> show #!117 models
+> hide #!118 models
+> show #!118 models
+> hide #!117 models
+> hide #!118 models
+> show #!110 models
+> show #!111 models
+> hide #!110 models
+> show #!110 models
+> hide #!111 models
+> hide #!110 models
+> show #!105 models
+> show #!106 models
+> hide #!106 models
+> show #!106 models
+> hide #!106 models
+> show #!106 models
+> hide #!106 models
+> hide #!105 models
+> show #!105 models
+> show #!106 models
+> hide #!105 models
+> hide #!106 models
+> show #!110 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> show #!122 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!122 models
+> hide #!123 models
+> show #!123 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!129 models
+> hide #!129 models
+> show #!130 models
+> hide #!110 models
+> show #!99 models
+> hide #!99 models
+> show #!98 models
+> volume #98 level 0.013
+> hide #!130 models
+> show #!130 models
+> volume #99 level 0.013
+> hide #!130 models
+> show #!110 models
+> hide #!98 models
+> show #!99 models
+> hide #!99 models
+> show #!98 models
+> volume #110 level 0.013
+> hide #!98 models
+> show #!98 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!110 models
+> show #!110 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!98 models
+> show #!111 models
+> hide #!110 models
+> show #!110 models
+> hide #!111 models
+> hide #!110 models
+> show #!32 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!34 models
+> hide #!32 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!129 models
+> hide #!129 models
+> show #!130 models
+> show #!129 models
+> hide #!129 models
+> show #!123 models
+> hide #!130 models
+> show #!130 models
+> hide #!123 models
+> show #!123 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!123 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J680_volume_map.mrc
+Opened cryosparc_P17_J680_volume_map.mrc as #136, grid size 294,294,294, pixel
+.9, shown at level 0.413, step 2, values float32
+> hide #!130 models
+> volume #136 step 1
+> volume #136 level 0.314
+> open /Users/cvetkom/Downloads/cryosparc_P17_J676_class_00_final_volume.mrc
+Opened cryosparc_P17_J676_class_00_final_volume.mrc as #137, grid size
+,192,192, pixel 2.91, shown at level 0.536, step 1, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J678_class_00_final_volume.mrc
+Opened cryosparc_P17_J678_class_00_final_volume.mrc as #138, grid size
+,192,192, pixel 2.91, shown at level 0.529, step 1, values float32
+> hide #!136 models
+> hide #!138 models
+> volume #137 level 0.5
+> volume #137 level 0.4
+> volume #137 level 0.3
+> volume #138 level 0.3
+> hide #!138 models
+> show #!137 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J681_volume_map.mrc
+Opened cryosparc_P17_J681_volume_map.mrc as #139, grid size 294,294,294, pixel
+.9, shown at level 0.411, step 2, values float32
+> hide #!137 models
+> volume #139 step 1
+> volume #139 level 0.2939
+> open /Users/cvetkom/Downloads/cryosparc_P17_J684_010_volume_map.mrc
+Opened cryosparc_P17_J684_010_volume_map.mrc as #140, grid size 294,294,294,
+pixel 1.9, shown at level 0.365, step 2, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J685_007_volume_map.mrc
+Opened cryosparc_P17_J685_007_volume_map.mrc as #141, grid size 294,294,294,
+pixel 1.9, shown at level 0.361, step 2, values float32
+> hide #!139 models
+> hide #!141 models
+> volume #140 step 1
+> volume #141 step 1
+> volume #141 level 0.35
+> volume #140 level 0.36
+> volume #141 level 0.36
+> open /Users/cvetkom/Downloads/cryosparc_P17_J677_class_00_final_volume.mrc
+Opened cryosparc_P17_J677_class_00_final_volume.mrc as #142, grid size
+,192,192, pixel 2.91, shown at level 0.561, step 1, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J679_class_00_final_volume.mrc
+Opened cryosparc_P17_J679_class_00_final_volume.mrc as #143, grid size
+,192,192, pixel 2.91, shown at level 0.55, step 1, values float32
+> hide #!141 models
+> hide #!143 models
+> volume #142 level 0.3
+> hide #!142 models
+> show #!143 models
+> volume #143 level 0.3
+> volume #143 level 0.25
+> volume #142 level 0.25
+> open /Users/cvetkom/Downloads/cryosparc_P17_J686_mask.mrc
+Opened cryosparc_P17_J686_mask.mrc as #144, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+> volume #144 level 1
+> transparency #142.1#144.1 50
+> transparency #142.1#144.1 0
+> volume #144 color #cccc9980
+> volume #142 level 0.3
+> open /Users/cvetkom/Downloads/cryosparc_P17_J688_007_volume_map.mrc
+Opened cryosparc_P17_J688_007_volume_map.mrc as #145, grid size 294,294,294,
+pixel 1.9, shown at level 0.365, step 2, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J689_008_volume_map.mrc
+Opened cryosparc_P17_J689_008_volume_map.mrc as #146, grid size 294,294,294,
+pixel 1.9, shown at level 0.365, step 2, values float32
+> hide #!142 models
+> hide #!144 models
+> hide #!146 models
+> volume #145 step 1
+> show #!146 models
+> hide #!145 models
+> volume #146 step 1
+> show #!145 models
+> hide #!145 models
+> show #!145 models
+> hide #!146 models
+> show #!146 models
+> hide #!145 models
+> show #!145 models
+> hide #!146 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J690_006_volume_map.mrc
+Opened cryosparc_P17_J690_006_volume_map.mrc as #147, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 2, values float32
+> hide #!145 models
+> volume #147 step 1
+> lighting soft
+> show #!145 models
+> hide #!147 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J691_008_volume_map.mrc
+Opened cryosparc_P17_J691_008_volume_map.mrc as #148, grid size 294,294,294,
+pixel 1.9, shown at level 0.365, step 2, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J692_009_volume_map.mrc
+Opened cryosparc_P17_J692_009_volume_map.mrc as #149, grid size 294,294,294,
+pixel 1.9, shown at level 0.366, step 2, values float32
+> hide #!145 models
+> hide #!149 models
+> volume #148 step 1
+> volume #149 step 1
+> lighting soft
+> lighting simple
+> lighting soft
+> show #!145 models
+> hide #!149 models
+> show #!146 models
+> hide #!145 models
+> hide #!146 models
+> show #!145 models
+> show #!148 models
+> hide #!148 models
+> show #!148 models
+> show #!149 models
+> hide #!149 models
+> hide #!148 models
+> show #!147 models
+> hide #!147 models
+> hide #!145 models
+> show #!147 models
+> hide #!147 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J693_006_volume_map.mrc
+Opened cryosparc_P17_J693_006_volume_map.mrc as #150, grid size 294,294,294,
+pixel 1.9, shown at level 0.37, step 2, values float32
+> volume #150 step 1
+> show #!149 models
+> hide #!149 models
+> show #!149 models
+> hide #!149 models
+> show #!145 models
+> hide #!150 models
+> hide #!145 models
+> show #!146 models
+> hide #!146 models
+> volume flip #145,146,148,149
+Opened cryosparc_P17_J688_007_volume_map.mrc z flip as #151, grid size
+,294,294, pixel 1.9, shown at step 1, values float32
+Opened cryosparc_P17_J689_008_volume_map.mrc z flip as #152, grid size
+,294,294, pixel 1.9, shown at step 1, values float32
+Opened cryosparc_P17_J691_008_volume_map.mrc z flip as #153, grid size
+,294,294, pixel 1.9, shown at step 1, values float32
+Opened cryosparc_P17_J692_009_volume_map.mrc z flip as #154, grid size
+,294,294, pixel 1.9, shown at step 1, values float32
+> hide #!154 models
+> hide #!153 models
+> hide #!152 models
+> show #!150 models
+> show #!152 models
+> show #!153 models
+> show #!154 models
+> select add #150
+models selected
+> select add #151
+models selected
+> select add #152
+models selected
+> select add #153
+models selected
+> select add #154
+models selected
+> lighting simple
+> select subtract #150
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #151,-0.054748,0.92128,0.38502,-64.171,0.99522,0.081557,-0.053637,-1.6415,-0.080816,0.38024,-0.92135,386.87,#152,-0.054748,0.92128,0.38502,-64.171,0.99522,0.081557,-0.053637,-1.6415,-0.080816,0.38024,-0.92135,386.87,#153,-0.054748,0.92128,0.38502,-64.171,0.99522,0.081557,-0.053637,-1.6415,-0.080816,0.38024,-0.92135,386.87,#154,-0.054748,0.92128,0.38502,-64.171,0.99522,0.081557,-0.053637,-1.6415,-0.080816,0.38024,-0.92135,386.87
+> view matrix models
+> #151,-0.99227,0.014424,0.12328,522.63,0.06591,0.90285,0.42487,-95.335,-0.10517,0.42971,-0.89682,373.38,#152,-0.99227,0.014424,0.12328,522.63,0.06591,0.90285,0.42487,-95.335,-0.10517,0.42971,-0.89682,373.38,#153,-0.99227,0.014424,0.12328,522.63,0.06591,0.90285,0.42487,-95.335,-0.10517,0.42971,-0.89682,373.38,#154,-0.99227,0.014424,0.12328,522.63,0.06591,0.90285,0.42487,-95.335,-0.10517,0.42971,-0.89682,373.38
+> view matrix models
+> #151,-0.97431,0.0085096,0.22505,494.23,0.077208,0.95135,0.29828,-81.204,-0.21157,0.30799,-0.92757,445.58,#152,-0.97431,0.0085096,0.22505,494.23,0.077208,0.95135,0.29828,-81.204,-0.21157,0.30799,-0.92757,445.58,#153,-0.97431,0.0085096,0.22505,494.23,0.077208,0.95135,0.29828,-81.204,-0.21157,0.30799,-0.92757,445.58,#154,-0.97431,0.0085096,0.22505,494.23,0.077208,0.95135,0.29828,-81.204,-0.21157,0.30799,-0.92757,445.58
+> view matrix models
+> #151,-0.99088,0.024916,0.13239,517,0.052496,0.97647,0.20914,-59.535,-0.12406,0.21419,-0.96888,458.2,#152,-0.99088,0.024916,0.13239,517,0.052496,0.97647,0.20914,-59.535,-0.12406,0.21419,-0.96888,458.2,#153,-0.99088,0.024916,0.13239,517,0.052496,0.97647,0.20914,-59.535,-0.12406,0.21419,-0.96888,458.2,#154,-0.99088,0.024916,0.13239,517,0.052496,0.97647,0.20914,-59.535,-0.12406,0.21419,-0.96888,458.2
+> ui mousemode right "translate selected models"
+> view matrix models
+> #151,-0.99088,0.024916,0.13239,510.53,0.052496,0.97647,0.20914,-71.716,-0.12406,0.21419,-0.96888,519.84,#152,-0.99088,0.024916,0.13239,510.53,0.052496,0.97647,0.20914,-71.716,-0.12406,0.21419,-0.96888,519.84,#153,-0.99088,0.024916,0.13239,510.53,0.052496,0.97647,0.20914,-71.716,-0.12406,0.21419,-0.96888,519.84,#154,-0.99088,0.024916,0.13239,510.53,0.052496,0.97647,0.20914,-71.716,-0.12406,0.21419,-0.96888,519.84
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #151,-0.9994,0.032362,0.012172,540.39,0.033337,0.99529,0.091041,-42.658,-0.0091686,0.091392,-0.99577,529.57,#152,-0.9994,0.032362,0.012172,540.39,0.033337,0.99529,0.091041,-42.658,-0.0091686,0.091392,-0.99577,529.57,#153,-0.9994,0.032362,0.012172,540.39,0.033337,0.99529,0.091041,-42.658,-0.0091686,0.091392,-0.99577,529.57,#154,-0.9994,0.032362,0.012172,540.39,0.033337,0.99529,0.091041,-42.658,-0.0091686,0.091392,-0.99577,529.57
+> ui mousemode right "translate selected models"
+> view matrix models
+> #151,-0.9994,0.032362,0.012172,544.8,0.033337,0.99529,0.091041,-38.35,-0.0091686,0.091392,-0.99577,530.75,#152,-0.9994,0.032362,0.012172,544.8,0.033337,0.99529,0.091041,-38.35,-0.0091686,0.091392,-0.99577,530.75,#153,-0.9994,0.032362,0.012172,544.8,0.033337,0.99529,0.091041,-38.35,-0.0091686,0.091392,-0.99577,530.75,#154,-0.9994,0.032362,0.012172,544.8,0.033337,0.99529,0.091041,-38.35,-0.0091686,0.091392,-0.99577,530.75
+> select subtract #151
+models selected
+> select subtract #152
+models selected
+> select add #152
+models selected
+> select add #151
+models selected
+> select subtract #151
+models selected
+> select subtract #152
+models selected
+> select subtract #153
+models selected
+> select subtract #154
+Nothing selected
+> ui tool show "Fit in Map"
+> fitmap #151 inMap #150
+Fit map cryosparc_P17_J688_007_volume_map.mrc z flip in map
+cryosparc_P17_J693_006_volume_map.mrc using 254273 points
+correlation = 0.995, correlation about mean = 0.9397, overlap = 9.223e+04
+steps = 100, shift = 5.99, angle = 2.29 degrees
+Position of cryosparc_P17_J688_007_volume_map.mrc z flip (#151) relative to
+cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
+Matrix rotation and translation
+-0.99999140 -0.00359338 0.00207026 559.46992299
+-0.00342330 0.99702499 0.07700290 -19.07074818
+-0.00234080 0.07699515 -0.99702872 534.50211369
+Axis -0.00175550 0.99925597 0.03852822
+Axis point 280.01335285 0.00000000 267.30976851
+Rotation angle (degrees) 179.87353804
+Shift along axis 0.55470700
+> fitmap #152 inMap #150
+Fit map cryosparc_P17_J689_008_volume_map.mrc z flip in map
+cryosparc_P17_J693_006_volume_map.mrc using 253853 points
+correlation = 0.995, correlation about mean = 0.939, overlap = 9.217e+04
+steps = 80, shift = 5.92, angle = 2.24 degrees
+Position of cryosparc_P17_J689_008_volume_map.mrc z flip (#152) relative to
+cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
+Matrix rotation and translation
+-0.99999493 -0.00290598 0.00130357 559.46976174
+-0.00279515 0.99693412 0.07819562 -19.59657377
+-0.00152681 0.07819157 -0.99693718 533.82278737
+Axis -0.00142641 0.99923323 0.03912681
+Axis point 279.91004169 0.00000000 267.09682063
+Rotation angle (degrees) 179.91885345
+Shift along axis 0.50720275
+> fitmap #153 inMap #150
+Fit map cryosparc_P17_J691_008_volume_map.mrc z flip in map
+cryosparc_P17_J693_006_volume_map.mrc using 254067 points
+correlation = 0.9949, correlation about mean = 0.9379, overlap = 9.218e+04
+steps = 100, shift = 5.99, angle = 2.29 degrees
+Position of cryosparc_P17_J691_008_volume_map.mrc z flip (#153) relative to
+cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
+Matrix rotation and translation
+-0.99999153 -0.00354328 0.00209321 559.43919323
+-0.00337135 0.99701735 0.07710412 -19.11074723
+-0.00236017 0.07709641 -0.99702085 534.50415261
+Axis -0.00172997 0.99925406 0.03857895
+Axis point 280.00103027 0.00000000 267.30909738
+Rotation angle (degrees) 179.87232473
+Shift along axis 0.55630498
+> fitmap #154 inMap #150
+Fit map cryosparc_P17_J692_009_volume_map.mrc z flip in map
+cryosparc_P17_J693_006_volume_map.mrc using 253930 points
+correlation = 0.9949, correlation about mean = 0.9381, overlap = 9.218e+04
+steps = 76, shift = 5.97, angle = 2.31 degrees
+Position of cryosparc_P17_J692_009_volume_map.mrc z flip (#154) relative to
+cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
+Matrix rotation and translation
+-0.99999289 -0.00347463 0.00146599 559.52836319
+-0.00335259 0.99707669 0.07633372 -18.91952628
+-0.00172694 0.07632826 -0.99708125 534.48491699
+Axis -0.00170809 0.99926890 0.03819344
+Axis point 279.96163715 0.00000000 267.38037953
+Rotation angle (degrees) 179.90846237
+Shift along axis 0.55239822
+> hide #!152 models
+> hide #!153 models
+> hide #!154 models
+> volume #151 level 0.37
+> ui mousemode right zoom
+> lighting soft
+> hide #!153 models
+> show #!153 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!153 models
+> show #!153 models
+> hide #!153 models
+> show #!153 models
+> hide #!153 models
+> show #!154 models
+> hide #!154 models
+> show #!153 models
+> show #!154 models
+> hide #!153 models
+> show #!153 models
+> hide #!154 models
+> show #!154 models
+> hide #!154 models
+> show #!154 models
+> hide #!153 models
+> show #!153 models
+> hide #!153 models
+> hide #!154 models
+> show #!154 models
+> hide #!154 models
+> show #!154 models
+> hide #!154 models
+> show #!154 models
+> hide #!150 models
+> hide #!154 models
+> show #!32 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!74 models
+> hide #!74 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> show #!74 models
+> hide #!74 models
+> hide #!32 models
+> show #!32 models
+> hide #!75 models
+> show #!75 models
+> show #!74 models
+> hide #!75 models
+> show #!75 models
+> hide #!74 models
+> hide #!32 models
+> show #!32 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!32 models
+> show #!130 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J699_class_00_00042_volume.mrc
+Opened cryosparc_P17_J699_class_00_00042_volume.mrc as #155, grid size
+,128,128, pixel 4.36, shown at level 1.37, step 1, values float32
+> hide #!75 models
+> hide #!130 models
+> volume #155 level 1.1
+> volume #155 level 0.5
+> volume #155 level 0.6
+> volume #155 level 0.55
+> open /Users/cvetkom/Downloads/cryosparc_P17_J700_mask.mrc
+Opened cryosparc_P17_J700_mask.mrc as #156, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+> volume #156 level 1
+> volume #156 color #ffffb27e
+> volume #156 color #ffffb27d
+> open /Users/cvetkom/Downloads/cryosparc_P17_J697_006_volume_map.mrc
+Opened cryosparc_P17_J697_006_volume_map.mrc as #157, grid size 294,294,294,
+pixel 1.9, shown at level 0.358, step 2, values float32
+> hide #!155 models
+> hide #!156 models
+> volume #157 step 1
+> volume #157 level 0.3
+> volume #157 level 0.32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J700_mask(1).mrc
+Opened cryosparc_P17_J700_mask(1).mrc as #158, grid size 128,128,128, pixel
+.36, shown at level 1, step 1, values float32
+> hide #!157 models
+> show #!155 models
+> show #!156 models
+> hide #!156 models
+> volume #158 color #b2b2ff7e
+> volume #158 color #b2b2ff7d
+> volume #158 level 1
+> volume #155 level 0.8
+> open /Users/cvetkom/Downloads/cryosparc_P17_J701_006_volume_map.mrc
+Opened cryosparc_P17_J701_006_volume_map.mrc as #159, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 2, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J703_007_volume_map.mrc
+Opened cryosparc_P17_J703_007_volume_map.mrc as #160, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 2, values float32
+> hide #!155 models
+> hide #!158 models
+> volume #159 step 1
+> volume #160 step 1
+> show #!159 models
+> show #!160 models
+> hide #!159 models
+> show #!159 models
+> hide #!159 models
+> show #!159 models
+> hide #!160 models
+> show #!157 models
+> hide #!159 models
+> show #!149 models
+> hide #!149 models
+> show #!149 models
+> hide #!149 models
+> show #!159 models
+> show #!160 models
+> select add #159
+models selected
+> select add #160
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #159,0.97634,0.21152,-0.044828,-40.291,0.16623,-0.86687,-0.47,584,-0.13828,0.45143,-0.88153,384.73,#160,0.97634,0.21152,-0.044828,-40.291,0.16623,-0.86687,-0.47,584,-0.13828,0.45143,-0.88153,384.73
+> view matrix models
+> #159,0.89639,-0.43386,0.09079,125.71,-0.43377,-0.90076,-0.021732,649.03,0.091209,-0.019902,-0.99563,478.69,#160,0.89639,-0.43386,0.09079,125.71,-0.43377,-0.90076,-0.021732,649.03,0.091209,-0.019902,-0.99563,478.69
+> select subtract #159
+models selected
+> select subtract #160
+Nothing selected
+> hide #!159 models
+> hide #!160 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!154 models
+> hide #!154 models
+> show #!159 models
+> hide #!159 models
+> hide #!157 models
+> show #!159 models
+> show #!160 models
+> hide #!159 models
+> hide #!160 models
+> show #!157 models
+> volume #157 level 0.36
+> show #!159 models
+> hide #!159 models
+> show #!159 models
+> hide #!157 models
+> volume flip #157
+Opened cryosparc_P17_J697_006_volume_map.mrc z flip as #161, grid size
+,294,294, pixel 1.9, shown at step 1, values float32
+> hide #!159 models
+> show #!159 models
+> hide #!161 models
+> show #!161 models
+> select add #161
+models selected
+> view matrix models
+> #161,0.76891,-0.22832,0.5972,-18.442,0.24486,-0.75768,-0.60494,582.05,0.59061,0.61138,-0.52668,39.302
+> view matrix models
+> #161,0.67534,0.22196,0.70331,-146.74,0.10898,-0.9732,0.20249,480.95,0.72941,-0.060102,-0.68143,229.96
+> view matrix models
+> #161,-0.93098,0.36002,0.06057,425.2,0.36288,0.89435,0.26166,-136.94,0.040032,0.26557,-0.96326,401.04
+> view matrix models
+> #161,-0.89701,0.43896,0.051772,395.36,0.44113,0.89642,0.042718,-105.12,-0.027658,0.061157,-0.99774,486.85
+> select subtract #161
+Nothing selected
+> fitmap #161 inMap #159
+Fit map cryosparc_P17_J697_006_volume_map.mrc z flip in map
+cryosparc_P17_J701_006_volume_map.mrc using 252025 points
+correlation = 0.9982, correlation about mean = 0.9798, overlap = 9.355e+04
+steps = 112, shift = 10, angle = 4.47 degrees
+Position of cryosparc_P17_J697_006_volume_map.mrc z flip (#161) relative to
+cryosparc_P17_J701_006_volume_map.mrc (#159) coordinates:
+Matrix rotation and translation
+-0.99987255 -0.01520153 -0.00487783 564.75986128
+.01517723 -0.99987242 0.00497921 552.56953504
+-0.00495290 0.00490455 0.99997571 0.88182116
+Axis -0.00245783 0.00247107 0.99999393
+Axis point 280.28257868 278.42842383 0.00000000
+Rotation angle (degrees) 179.12967387
+Shift along axis 0.85917190
+> hide #!161 models
+> show #!161 models
+> hide #!159 models
+> show #!159 models
+> hide #!161 models
+> show #!161 models
+> hide #!159 models
+> show #!159 models
+> hide #!161 models
+> hide #!159 models
+> show #!155 models
+> hide #!155 models
+> show #!151 models
+> volume #151 level 0.36
+> ui mousemode right zoom
+> show #!153 models
+> show #!154 models
+> hide #!153 models
+> hide #!154 models
+> hide #!151 models
+> show #!151 models
+> show #!81 models
+> hide #!81 models
+> show #!81 models
+> hide #!151 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> volume #150 level 0.36
+> hide #!81 models
+> show #!81 models
+> hide #!81 models
+> show #!81 models
+> hide #!81 models
+> show #!81 models
+> hide #!81 models
+> hide #!150 models
+> show #!150 models
+> show #!157 models
+> hide #!157 models
+> show #!159 models
+> hide #!159 models
+> show #!159 models
+> hide #!159 models
+> show #!159 models
+> show #!160 models
+> select add #159
+models selected
+> select add #160
+models selected
+> ui mousemode right "translate selected models"
+> view matrix models
+> #159,0.89639,-0.43386,0.09079,116.59,-0.43377,-0.90076,-0.021732,665.59,0.091209,-0.019902,-0.99563,541.66,#160,0.89639,-0.43386,0.09079,116.59,-0.43377,-0.90076,-0.021732,665.59,0.091209,-0.019902,-0.99563,541.66
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #159,0.99562,-0.092981,0.009532,15.384,-0.093433,-0.98726,0.12878,556.58,-0.0025637,-0.12911,-0.99163,596.92,#160,0.99562,-0.092981,0.009532,15.384,-0.093433,-0.98726,0.12878,556.58,-0.0025637,-0.12911,-0.99163,596.92
+> select subtract #160
+models selected
+> select subtract #159
+Nothing selected
+> fitmap #159 inMap #150
+Fit map cryosparc_P17_J701_006_volume_map.mrc in map
+cryosparc_P17_J693_006_volume_map.mrc using 253555 points
+correlation = 0.995, correlation about mean = 0.9467, overlap = 9.384e+04
+steps = 92, shift = 15.9, angle = 4.91 degrees
+Position of cryosparc_P17_J701_006_volume_map.mrc (#159) relative to
+cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
+Matrix rotation and translation
+.99990377 -0.01280700 0.00533263 1.75411257
+-0.01349030 -0.98727395 0.15845557 514.15896836
+.00323543 -0.15851226 -0.98735171 596.92132464
+Axis -0.99997579 0.00661630 -0.00215569
+Axis point 0.00000000 280.88748875 277.95683594
+Rotation angle (degrees) 170.88086929
+Shift along axis 0.36097960
+> fitmap #160 inMap #150
+Fit map cryosparc_P17_J703_007_volume_map.mrc in map
+cryosparc_P17_J693_006_volume_map.mrc using 254051 points
+correlation = 0.9949, correlation about mean = 0.946, overlap = 9.382e+04
+steps = 140, shift = 15.9, angle = 4.85 degrees
+Position of cryosparc_P17_J703_007_volume_map.mrc (#160) relative to
+cryosparc_P17_J693_006_volume_map.mrc (#150) coordinates:
+Matrix rotation and translation
+.99989095 -0.01388197 0.00503895 2.09422029
+-0.01450557 -0.98723491 0.15860902 514.34229109
+.00277282 -0.15866482 -0.98732861 597.00803822
+Axis -0.99997256 0.00714230 -0.00196544
+Axis point 0.00000000 281.00771740 277.97254777
+Rotation angle (degrees) 170.87196021
+Shift along axis 0.40604025
+> hide #!160 models
+> hide #!159 models
+> show #!159 models
+> hide #!150 models
+> show #!157 models
+> hide #!157 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> hide #!159 models
+> show #!159 models
+> hide #!159 models
+> show #!160 models
+> hide #!160 models
+> show #!161 models
+> hide #!161 models
+> show #!159 models
+> show #!161 models
+> hide #!161 models
+> show #!160 models
+> hide #!159 models
+> show #!159 models
+> hide #!160 models
+> show #!160 models
+> hide #!159 models
+> show #!159 models
+> hide #!160 models
+> show #!160 models
+> hide #!160 models
+> hide #!159 models
+> show #!159 models
+> show #!160 models
+> hide #!159 models
+> show #!159 models
+> hide #!159 models
+> show #!159 models
+> hide #!160 models
+> show #!160 models
+> hide #!159 models
+> show #!159 models
+> hide #!159 models
+> hide #!160 models
+> show #!159 models
+> hide #!159 models
+> show #!157 models
+> show #!159 models
+> hide #!159 models
+> hide #!157 models
+> show #!150 models
+> show #!159 models
+> hide #!159 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> show #!159 models
+> hide #!150 models
+> show #!150 models
+> hide #!159 models
+> hide #!150 models
+> show #!151 models
+> show #!150 models
+> hide #!151 models
+> show #!151 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> show #!150 models
+> hide #!150 models
+> hide #!151 models
+> show #!150 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J693_006_volume_mask_refine.mrc
+Opened cryosparc_P17_J693_006_volume_mask_refine.mrc as #162, grid size
+,294,294, pixel 1.9, shown at level 1, step 2, values float32
+> volume #162 step 1
+> volume #162 color #e5bf9980
+> volume #162 level 1
+> volume #162 color #e5bf9967
+> volume #162 color #e5bf9966
+> volume #150 level 0.3
+> volume #150 level 0.2
+> hide #!162 models
+> show #!162 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J704_mask.mrc
+Opened cryosparc_P17_J704_mask.mrc as #163, grid size 294,294,294, pixel 1.9,
+shown at level 1, step 2, values float32
+> hide #!162 models
+> volume #163 step 1
+> volume #163 color #99bfe565
+> volume #163 color #99bfe566
+> volume #163 level 1
+> show #!162 models
+> hide #!163 models
+> show #!163 models
+> hide #!163 models
+> show #!163 models
+> hide #!163 models
+> show #!163 models
+> hide #!163 models
+> show #!163 models
+> hide #!162 models
+> show #!162 models
+> hide #!162 models
+> show #!162 models
+> hide #!162 models
+> volume #163 level 0.5
+> volume #163 level 1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J707_009_volume_map.mrc
+Opened cryosparc_P17_J707_009_volume_map.mrc as #164, grid size 294,294,294,
+pixel 1.9, shown at level 0.358, step 2, values float32
+> hide #!163 models
+> hide #!150 models
+> volume #164 step 1
+> volume #164 level 0.384
+> volume #164 level 0.35
+> volume #164 level 0.3
+> volume #164 level 0.2
+> open /Users/cvetkom/Downloads/cryosparc_P17_J708_mask.mrc
+Opened cryosparc_P17_J708_mask.mrc as #165, grid size 294,294,294, pixel 1.9,
+shown at level 1, step 2, values float32
+> hide #!164 models
+> show #!164 models
+> hide #!165 models
+> show #!165 models
+> volume #165 step 1
+> volume #165 level 1
+> volume #165 color #b2b2b27c
+> volume #165 color #b2b2b26b
+> volume #165 color #b2b2b263
+> volume #165 color #b2b2b265
+> volume #165 color #b2b2b266
+> hide #!165 models
+> volume #164 level 0.5
+> volume #164 level 0.4
+> open /Users/cvetkom/Downloads/cryosparc_P17_J705_006_volume_map.mrc
+Opened cryosparc_P17_J705_006_volume_map.mrc as #166, grid size 294,294,294,
+pixel 1.9, shown at level 0.359, step 2, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J706_004_volume_map.mrc
+Opened cryosparc_P17_J706_004_volume_map.mrc as #167, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 2, values float32
+> hide #!164 models
+> volume #166 step 1
+> volume #167 step 1
+> show #!164 models
+> hide #!167 models
+> show #!165 models
+> hide #!165 models
+> hide #!164 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J695_class_00_final_volume.mrc
+Opened cryosparc_P17_J695_class_00_final_volume.mrc as #168, grid size
+,192,192, pixel 2.91, shown at level 0.544, step 1, values float32
+> volume #168 level 0.3
+> volume #168 level 0.25
+> volume #168 level 0.3
+> open /Users/cvetkom/Downloads/cryosparc_P17_J714_mask.mrc
+Opened cryosparc_P17_J714_mask.mrc as #169, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+> volume #169 color #ffb2ff7d
+> volume #169 color #ffb2ff67
+> volume #169 color #ffb2ff66
+> volume #169 level 1
+> hide #!168 models
+> show #!168 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J715_mask.mrc
+Opened cryosparc_P17_J715_mask.mrc as #170, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+> volume #170 color #ffb2b266
+> volume #170 level 1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J715_mask(1).mrc
+Opened cryosparc_P17_J715_mask(1).mrc as #171, grid size 192,192,192, pixel
+.91, shown at level 1, step 1, values float32
+> volume #171 color #b2ffb266
+> volume #171 level 1
+> show #!169 models
+> hide #!171 models
+> show #!171 models
+> hide #!169 models
+> show #!169 models
+> hide #!169 models
+> show #!169 models
+> hide #!169 models
+> show #!169 models
+> hide #!169 models
+> show #!169 models
+> hide #!169 models
+> show #!169 models
+> hide #!169 models
+> show #!170 models
+> hide #!171 models
+> show #!171 models
+> hide #!171 models
+> show #!171 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J709_007_volume_map.mrc
+Opened cryosparc_P17_J709_007_volume_map.mrc as #172, grid size 294,294,294,
+pixel 1.9, shown at level 0.354, step 2, values float32
+> hide #!168 models
+> hide #!170 models
+> hide #!171 models
+> volume #172 step 1
+> show #!168 models
+> hide #!168 models
+> show #!168 models
+> hide #!168 models
+> show #!164 models
+> hide #!164 models
+> show #!164 models
+> hide #!172 models
+> show #!172 models
+> hide #!164 models
+> volume #172 level 0.4
+> volume #172 level 0.38
+> volume #172 level 0.36
+> open /Users/cvetkom/Downloads/cryosparc_P17_J710_008_volume_map.mrc
+Opened cryosparc_P17_J710_008_volume_map.mrc as #173, grid size 294,294,294,
+pixel 1.9, shown at level 0.354, step 2, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J712_007_volume_map.mrc
+Opened cryosparc_P17_J712_007_volume_map.mrc as #174, grid size 294,294,294,
+pixel 1.9, shown at level 0.349, step 2, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J711_009_volume_map.mrc
+Opened cryosparc_P17_J711_009_volume_map.mrc as #175, grid size 294,294,294,
+pixel 1.9, shown at level 0.353, step 2, values float32
+> hide #!172 models
+> hide #!174 models
+> hide #!173 models
+> show #!173 models
+> hide #!175 models
+> volume #173 step 1
+> volume #174 step 1
+> volume #175 step 1
+> volume #173 level 0.3
+> volume #173 level 0.2
+> show #!164 models
+> hide #!164 models
+> show #!175 models
+> volume #175 level 0.2
+> hide #!175 models
+> show #!175 models
+> hide #!173 models
+> show #!173 models
+> hide #!175 models
+> show #!175 models
+> hide #!175 models
+> volume #173 level 0.25
+> volume #173 level 0.2
+> volume #173 level 0.25
+> open /Users/cvetkom/Downloads/cryosparc_P17_J716_mask.mrc
+Opened cryosparc_P17_J716_mask.mrc as #176, grid size 294,294,294, pixel 1.9,
+shown at level 1, step 2, values float32
+> volume #176 step 1
+> volume #176 color #ffffb266
+> volume #176 level 1
+> close #176
+> open /Users/cvetkom/Downloads/cryosparc_P17_J716_mask.mrc
+Opened cryosparc_P17_J716_mask.mrc as #176, grid size 294,294,294, pixel 1.9,
+shown at level 1, step 2, values float32
+> volume #176 step 1
+> volume #176 color #b2ffff66
+> volume #176 level 1
+> show #!174 models
+> hide #!173 models
+> hide #!176 models
+> volume #174 level 0.2
+> volume #174 level 0.25
+> volume #174 level 0.2
+> show #!173 models
+> hide #!174 models
+> show #!174 models
+> hide #!173 models
+> hide #!174 models
+> show #!151 models
+> show #!152 models
+> show #!153 models
+> show #!154 models
+> hide #!154 models
+> hide #!153 models
+> hide #!152 models
+> show #!152 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!152 models
+> show #!152 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!152 models
+> show #!152 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!152 models
+> show #!153 models
+> hide #!151 models
+> show #!154 models
+> hide #!153 models
+> show #!153 models
+> hide #!153 models
+> show #!153 models
+> hide #!154 models
+> show #!154 models
+> hide #!154 models
+> show #!154 models
+> hide #!153 models
+> show #!153 models
+> hide #!154 models
+> show #!154 models
+> hide #!153 models
+> show #!153 models
+> hide #!153 models
+> show #!153 models
+> hide #!154 models
+> show #!152 models
+> hide #!152 models
+> hide #!153 models
+> show #!152 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!152 models
+> show #!152 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!151 models
+> show #!151 models
+> hide #!152 models
+> show #!153 models
+> hide #!153 models
+> show #!147 models
+> hide #!151 models
+> hide #!147 models
+> show #!147 models
+> show #!145 models
+> hide #!145 models
+> hide #!147 models
+> show #!145 models
+> hide #!145 models
+> show #!175 models
+> show #!174 models
+> hide #!175 models
+> hide #!174 models
+> show #!167 models
+> hide #!167 models
+> show #!168 models
+> hide #!168 models
+> show #!167 models
+> hide #!167 models
+> show #!168 models
+> hide #!168 models
+> show #!166 models
+> hide #!166 models
+> show #!173 models
+> show #!174 models
+> hide #!174 models
+> hide #!173 models
+> show #!161 models
+> hide #!161 models
+> show #!160 models
+> hide #!160 models
+> show #!154 models
+> show #!153 models
+> hide #!154 models
+> show #!154 models
+> hide #!154 models
+> hide #!153 models
+> show #!152 models
+> show #!153 models
+> hide #!153 models
+> hide #!152 models
+> show #!151 models
+> hide #!151 models
+> show #!150 models
+> hide #!150 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes_ref.cxs
+> ui mousemode right zoom
+[Repeated 1 time(s)]
+> show #!176 models
+> hide #!176 models
+> show #!175 models
+> hide #!175 models
+> show #!175 models
+> hide #!175 models
+> show #!174 models
+> hide #!174 models
+> show #!173 models
+> hide #!173 models
+> show #!172 models
+> hide #!172 models
+> show #!171 models
+> hide #!171 models
+> open 6SKL fromDatabase pdb format mmcif
+skl title:
+Cryo-EM structure of the CMG Fork Protection Complex at a replication fork -
+Conformation 1 [more info...]
+Chain information for 6skl #177
+---
+Chain | Description | UniProt
+| DNA replication licensing factor MCM2 | MCM2_YEAST 1-868
+| DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
+| DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
+| Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
+| DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
+| DNA replication licensing factor MCM7 | MCM7_YEAST 1-845
+A | DNA replication complex GINS protein PSF1 | PSF1_YEAST 1-208
+B | DNA replication complex GINS protein PSF2 | PSF2_YEAST 1-213
+C | DNA replication complex GINS protein PSF3 | PSF3_YEAST 1-194
+D | DNA replication complex GINS protein SLD5 | SLD5_YEAST 1-294
+E | Cell division control protein 45 | CDC45_YEAST 1-650
+F G H | DNA polymerase alpha-binding protein | CTF4_YEAST 1-927
+I | DNA fork, leading-strand template |
+J | DNA fork, lagging-strand template |
+X | Topoisomerase 1-associated factor 1 | TOF1_YEAST 1-1238
+Y | Chromosome segregation in meiosis protein 3 | CSM3_YEAST 1-317
+Non-standard residues in 6skl #177
+---
+ANP \u2014 phosphoaminophosphonic acid-adenylate ester
+MG \u2014 magnesium ion
+ZN \u2014 zinc ion
+> lighting simple
+> select /2
+atoms, 10708 bonds, 8 pseudobonds, 672 residues, 3 models selected
+> select /6
+atoms, 10126 bonds, 9 pseudobonds, 638 residues, 3 models selected
+> select /4
+atoms, 10952 bonds, 11 pseudobonds, 680 residues, 3 models selected
+> select /5
+atoms, 9789 bonds, 11 pseudobonds, 614 residues, 3 models selected
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240529_CMGC4MCT_Fpl20MN_krios_II_merged_3D_classes_ref.cxs
+\u2014\u2014\u2014 End of log from Fri Jun 21 11:35:11 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> select add #177
+atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
+> select subtract #177
+Nothing selected
+> hide #!177 models
+> show #!174 models
+> hide #!174 models
+> show #!166 models
+> show #!167 models
+> hide #!166 models
+> show #!166 models
+> hide #!167 models
+> show #!167 models
+> hide #!166 models
+> show #!166 models
+> hide #!167 models
+> hide #!166 models
+> show #!166 models
+> show #!172 models
+> hide #!166 models
+> show #!166 models
+> hide #!166 models
+> show #!166 models
+> hide #!166 models
+> show #!166 models
+> hide #!166 models
+> show #!166 models
+> hide #!166 models
+> show #!166 models
+> hide #!166 models
+> show #!166 models
+> hide #!172 models
+> hide #!166 models
+> show #!172 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J721_006_volume_map.mrc
+Opened cryosparc_P17_J721_006_volume_map.mrc as #158, grid size 294,294,294,
+pixel 1.9, shown at level 0.346, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J719_007_volume_map.mrc
+Opened cryosparc_P17_J719_007_volume_map.mrc as #178, grid size 294,294,294,
+pixel 1.9, shown at level 0.35, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J717_007_volume_map.mrc
+Opened cryosparc_P17_J717_007_volume_map.mrc as #179, grid size 294,294,294,
+pixel 1.9, shown at level 0.35, step 2, values float32
+> hide #!172 models
+> show #!172 models
+> hide #!172 models
+> volume #179 step 1
+> volume #178 step 1
+> volume #178 level 0.4299
+> volume #158 step 1
+> close #158
+> close #179
+> close #178
+> open /Users/cvetkom/Downloads/cryosparc_P17_J709_007_volume_map_sharp.mrc
+Opened cryosparc_P17_J709_007_volume_map_sharp.mrc as #158, grid size
+,294,294, pixel 1.9, shown at level 0.35, step 2, values float32
+> volume #158 step 1
+> volume #158 level 0.4035
+> volume #158 level 0.3381
+> show #!172 models
+> show #!166 models
+> hide #!172 models
+> hide #!166 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J645_010_volume_map_sharp.mrc
+Opened cryosparc_P17_J645_010_volume_map_sharp.mrc as #178, grid size
+,588,588, pixel 0.95, shown at level 0.158, step 4, values float32
+> volume #178 step 1
+> volume #178 level 0.5544
+> volume #178 level 0.3502
+> close #178
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc
+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #178, grid size
+,588,588, pixel 0.95, shown at level 0.957, step 4, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J544_007_volume_map_zflip.mrc
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #179, grid size
+,588,588, pixel 0.95, shown at level 0.158, step 4, values float32
+> volume #178 step 1
+> volume #178 level 0.9947
+> volume #179 step 1
+> volume #179 level 0.1617
+> volume #179 level 0.152
+> show #!172 models
+> hide #!172 models
+> lighting soft
+> volume #179 level 0.1695
+> hide #!179 models
+> show #!172 models
+> volume #172 level 0.3737
+> show #!166 models
+> hide #!166 models
+> show #!166 models
+> hide #!166 models
+> show #!166 models
+> hide #!172 models
+> volume #166 level 0.3843
+> show #!172 models
+> hide #!172 models
+> show #!172 models
+> hide #!172 models
+> show #!172 models
+> hide #!166 models
+> hide #!172 models
+> show #!178 models
+> hide #!178 models
+> show #!172 models
+> volume #172 level 0.3509
+> show #!171 models
+> hide #!171 models
+> hide #!172 models
+> show #!179 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J709_007_volume_map.mrc
+Opened cryosparc_P17_J709_007_volume_map.mrc as #180, grid size 294,294,294,
+pixel 1.9, shown at level 0.354, step 2, values float32
+> hide #!179 models
+> hide #!180 models
+> close #180
+> open /Users/cvetkom/Downloads/cryosparc_P17_J787_004_volume_map_sharp.mrc
+Opened cryosparc_P17_J787_004_volume_map_sharp.mrc as #180, grid size
+,588,588, pixel 0.95, shown at level 0.196, step 4, values float32
+> volume #180 level 0.3198
+> volume #180 step 1
+> volume #180 level 0.4233
+> volume #180 level 0.4003
+> open /Users/cvetkom/Downloads/cryosparc_P17_J786_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J786_005_volume_map_sharp.mrc as #181, grid size
+,588,588, pixel 0.95, shown at level 0.204, step 4, values float32
+> volume #181 step 1
+> volume #181 level 0.3442
+> volume #181 level 0.4
+> open /Users/cvetkom/Downloads/cryosparc_P17_J787_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J787_005_volume_map_sharp.mrc as #182, grid size
+,588,588, pixel 0.95, shown at level 0.21, step 4, values float32
+> hide #!181 models
+> volume #182 step 1
+> volume #182 level 0.3526
+> volume #182 level 0.4
+> show #!181 models
+> hide #!181 models
+> show #!181 models
+> hide #!181 models
+> show #!181 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!181 models
+> open /Volumes/lab-
+> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/MaskCreate/job690/mask.mrc
+Opened mask.mrc as #183, grid size 588,588,588, pixel 0.95, shown at level 1,
+step 4, values float32
+> close #183
+> open /Users/cvetkom/Downloads/cryosparc_P17_J792_volume_map_sharp.mrc
+Opened cryosparc_P17_J792_volume_map_sharp.mrc as #183, grid size 520,520,520,
+pixel 0.95, shown at level 0.153, step 4, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J792_volume_mask_fsc.mrc
+Opened cryosparc_P17_J792_volume_mask_fsc.mrc as #184, grid size 520,520,520,
+pixel 0.95, shown at level 5e-05, step 4, values float32
+> hide #!182 models
+> volume #183 step 1
+> volume #183 level 0.3916
+> lighting soft
+> lighting full
+> volume #184 step 1
+> volume #184 level 1
+> volume #184 color #b2b2ff80
+> volume #184 level 0
+> volume #184 level 0.03512
+> open /Users/cvetkom/Downloads/cryosparc_P17_J760_mask(1).mrc
+Opened cryosparc_P17_J760_mask(1).mrc as #185, grid size 520,520,520, pixel
+.95, shown at level 5e-05, step 4, values float32
+> volume #185 step 1
+> volume #185 color #ffb2ff7f
+> volume #185 level 1
+[Repeated 1 time(s)]
+> open /Users/cvetkom/Downloads/cryosparc_P17_J757_volume_map.mrc
+Opened cryosparc_P17_J757_volume_map.mrc as #186, grid size 520,520,520, pixel
+.95, shown at level 0.0189, step 4, values float32
+> volume #186 level 0.07565
+> volume #186 step 1
+> hide #!183 models
+> hide #!185 models
+> volume #186 level 0.1989
+> volume #186 level 0.1509
+> open /Users/cvetkom/Downloads/cryosparc_P17_J792_volume_map.mrc
+Opened cryosparc_P17_J792_volume_map.mrc as #187, grid size 520,520,520, pixel
+.95, shown at level 0.0388, step 4, values float32
+> hide #!183 models
+> hide #!186 models
+> volume #187 level 0.0929
+> volume #187 step 1
+> volume #187 level 0.2473
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!186 models
+> volume #186 level 0.1781
+> hide #!186 models
+> show #!186 models
+> hide #!186 models
+> show #!186 models
+> volume #186 level 0.2261
+> hide #!186 models
+> show #!186 models
+> hide #!186 models
+> show #!184 models
+> show #!185 models
+> volume #184 level 1
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!183 models
+> hide #!183 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J795_007_volume_map.mrc
+Opened cryosparc_P17_J795_007_volume_map.mrc as #188, grid size 520,520,520,
+pixel 0.95, shown at level 0.0131, step 4, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J795_007_volume_map_sharp.mrc
+Opened cryosparc_P17_J795_007_volume_map_sharp.mrc as #189, grid size
+,520,520, pixel 0.95, shown at level 0.0597, step 4, values float32
+> hide #!184 models
+> hide #!187 models
+> volume #188 level 0.1056
+> volume #188 step 1
+> volume #188 level 0.2671
+> volume #188 level 0.2362
+> volume #189 level 0.3385
+> volume #189 step 1
+> close #188-189
+> close #185
+> close #184
+> open /Users/cvetkom/Downloads/cryosparc_P17_J797_009_volume_map_sharp.mrc
+Opened cryosparc_P17_J797_009_volume_map_sharp.mrc as #184, grid size
+,520,520, pixel 0.95, shown at level 0.213, step 4, values float32
+> volume #184 level 0.4718
+> volume #184 step 1
+> volume #184 level 0.7484
+> volume #184 level 0.846
+> show #!183 models
+> hide #!183 models
+> show #!183 models
+> hide #!183 models
+> show #!183 models
+> hide #!183 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J797_009_volume_map.mrc
+Opened cryosparc_P17_J797_009_volume_map.mrc as #185, grid size 520,520,520,
+pixel 0.95, shown at level 0.0436, step 4, values float32
+> hide #!185 models
+> show #!185 models
+> hide #!184 models
+> volume #185 level 0.2092
+> volume #185 step 1
+> volume #185 level 0.2795
+> lighting soft
+> volume #185 level 0.2092
+> volume #185 level 0.08268
+> volume #185 level 0.1858
+> volume #185 level 0.1904
+> volume #185 level 0.2279
+> open /Users/cvetkom/Downloads/cryosparc_P17_J760_mask(1).mrc
+Opened cryosparc_P17_J760_mask(1).mrc as #188, grid size 520,520,520, pixel
+.95, shown at level 5e-05, step 4, values float32
+> volume #188 step 1
+> volume #188 level 0.9982
+> volume #188 color #ffffb280
+> volume #188 color #ffffb266
+> volume #185 level 0.2607
+> show #!183 models
+> hide #!183 models
+> show #!183 models
+> show #!182 models
+> hide #!182 models
+> show #!181 models
+> hide #!181 models
+> show #!181 models
+> hide #!181 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!183 models
+> volume #185 level 0.256
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!180 models
+> hide #!180 models
+> show #!177 models
+> hide #!177 models
+> show #!178 models
+> hide #!178 models
+> show #!179 models
+> hide #!179 models
+> show #!180 models
+> show #!182 models
+> hide #!182 models
+> close #180
+> show #!181 models
+> hide #!181 models
+> show #!179 models
+> hide #!179 models
+> show #!181 models
+> hide #!181 models
+> show #!182 models
+> show #!181 models
+> hide #!181 models
+> show #!181 models
+> hide #!181 models
+> show #!181 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!181 models
+> show #!181 models
+> hide #!181 models
+> show #!181 models
+> hide #!182 models
+> show #!179 models
+> hide #!179 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!181 models
+> show #!183 models
+> hide #!183 models
+> show #!184 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!184 models
+> volume #185 level 0.2841
+> show #!184 models
+> volume #184 level 0.7159
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!185 models
+> show #!185 models
+> hide #!182 models
+> volume #185 level 0.3076
+> open /Users/cvetkom/Downloads/cryosparc_P17_J802_009_volume_map.mrc
+Opened cryosparc_P17_J802_009_volume_map.mrc as #180, grid size 520,520,520,
+pixel 0.95, shown at level 0.0442, step 4, values float32
+> hide #!185 models
+> volume #180 level 0.09552
+> volume #180 step 1
+> volume #180 level 0.2625
+> show #!182 models
+> hide #!182 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!180 models
+> show #!180 models
+> hide #!185 models
+> volume #180 level 0.2996
+> open /Users/cvetkom/Downloads/cryosparc_P17_J802_009_volume_map_sharp.mrc
+Opened cryosparc_P17_J802_009_volume_map_sharp.mrc as #189, grid size
+,520,520, pixel 0.95, shown at level 0.217, step 4, values float32
+> volume #189 step 1
+> volume #189 level 0.3
+> volume #189 level 0.7605
+> hide #!189 models
+> show #!185 models
+> volume #185 level 0.31
+> volume #180 level 0.31
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> select add #180
+models selected
+> color #180.1 cornflower blue
+> select subtract #180
+Nothing selected
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> show #!185 models
+> hide #!185 models
+> hide #!180 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J803_005_volume_map.mrc
+Opened cryosparc_P17_J803_005_volume_map.mrc as #190, grid size 588,588,588,
+pixel 0.95, shown at level 0.109, step 4, values float32
+> volume #190 level 0.1683
+> volume #190 step 1
+> volume #190 level 0.1911
+> volume #190 level 0.3013
+> open /Users/cvetkom/Downloads/cryosparc_P17_J803_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J803_005_volume_map_sharp.mrc as #191, grid size
+,588,588, pixel 0.95, shown at level 0.211, step 4, values float32
+> volume #191 level 0.2508
+> volume #191 step 1
+> volume #191 level 0.4399
+> volume #191 color #005493
+> volume #191 color #009193
+> select add #191
+models selected
+> ui tool show "Color Actions"
+> color sel medium blue
+> color sel light sea green
+> select subtract #191
+Nothing selected
+> volume #191 level 0.3926
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> show #!181 models
+> hide #!181 models
+> hide #!191 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> volume #191 level 0.39
+> hide #!182 models
+> show #!182 models
+> hide #!191 models
+> show #!191 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> show #!182 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> volume #182 level 0.39
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!182 models
+> show #!182 models
+> hide #!182 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J811_volume_map.mrc
+Opened cryosparc_P17_J811_volume_map.mrc as #192, grid size 520,520,520, pixel
+.95, shown at level 0.00828, step 4, values float32
+> hide #!191 models
+> volume #192 level 0.03286
+> volume #192 step 1
+> volume #192 color #4f8f00
+> volume #192 color #009051
+> volume #192 level 0.07832
+> volume #192 level 0.1052
+> volume #192 level 0.1
+> volume #192 level 0.3
+> volume #192 level 0.15
+> volume #192 level 0.12
+> volume #192 level 0.1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J813_mask.mrc
+Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
+shown at level 5e-05, step 4, values float32
+> volume #193 step 1
+> volume #193 color #e5bf9980
+> volume #193 color #e5bf9967
+> volume #193 color #e5bf9966
+> volume #193 level 1
+> volume #192 level 0.1186
+> volume #193 level 0.5009
+> volume #193 level 1
+> volume #192 level 0.1434
+> volume #192 level 0.1217
+> close #193
+> open /Users/cvetkom/Downloads/cryosparc_P17_J813_mask.mrc
+Opened cryosparc_P17_J813_mask.mrc as #193, grid size 520,520,520, pixel 0.95,
+shown at level 5e-05, step 4, values float32
+> volume #193 level 1
+> volume #193 step 1
+> volume #193 color #99bfe574
+> volume #193 color #99bfe567
+> volume #193 color #99bfe566
+> volume #192 level 0.1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J812_volume_map.mrc
+Opened cryosparc_P17_J812_volume_map.mrc as #194, grid size 520,520,520, pixel
+.95, shown at level 0.0198, step 4, values float32
+> volume #194 level 0.05264
+> volume #194 step 1
+> volume #194 level 0.09845
+> volume #194 level 0.1
+> volume #194 level 0.12
+> close #194
+> show #!189 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J805_008_volume_map.mrc
+Opened cryosparc_P17_J805_008_volume_map.mrc as #194, grid size 520,520,520,
+pixel 0.95, shown at level 0.0442, step 4, values float32
+> hide #!189 models
+> volume #194 level 0.2318
+> volume #194 step 1
+> volume #194 level 0.1158
+> volume #194 level 0.3478
+> open /Users/cvetkom/Downloads/cryosparc_P17_J817_class_00_00116_volume.mrc
+Opened cryosparc_P17_J817_class_00_00116_volume.mrc as #195, grid size
+,336,336, pixel 1.47, shown at level 0.0447, step 2, values float32
+> hide #!194 models
+> volume #195 level 0.2559
+> volume #195 step 1
+> volume #195 level 0.2828
+> open /Users/cvetkom/Downloads/cryosparc_P17_J817_class_04_00116_volume.mrc
+Opened cryosparc_P17_J817_class_04_00116_volume.mrc as #196, grid size
+,336,336, pixel 1.47, shown at level 0.0135, step 2, values float32
+> volume #196 step 1
+> volume #196 level 0.1881
+> volume #196 level 0.2658
+> volume #196 level 0.2887
+> open /Users/cvetkom/Downloads/cryosparc_P17_J819_005_volume_map.mrc
+Opened cryosparc_P17_J819_005_volume_map.mrc as #197, grid size 588,588,588,
+pixel 0.95, shown at level 0.108, step 4, values float32
+> hide #!195 models
+> hide #!196 models
+> volume #197 level 0.1961
+> volume #197 step 1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J819_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #198, grid size
+,588,588, pixel 0.95, shown at level 0.207, step 4, values float32
+> volume #198 level 0.3147
+> volume #198 step 1
+> volume #198 level 0.4907
+> volume #198 level 0.46
+> volume #198 level 0.4
+> volume #198 level 0.36
+> volume #198 level 0.46
+> open /Users/cvetkom/Downloads/cryosparc_P17_J822_volume_map.mrc
+Opened cryosparc_P17_J822_volume_map.mrc as #199, grid size 588,588,588, pixel
+.95, shown at level 0.121, step 4, values float32
+> hide #!199 models
+> show #!199 models
+> hide #!198 models
+> volume #199 step 1
+> volume #199 level 0.12
+> volume #199 level 0.15
+> volume #199 level 0.16
+> volume #199 level 0.15
+> open /Users/cvetkom/Downloads/cryosparc_P17_J823_mask.mrc
+Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
+shown at level 1, step 4, values float32
+> volume #200 step 1
+> volume #200 color #b2ffb283
+> volume #200 color #b2ffb26c
+> volume #200 color #b2ffb26b
+> volume #200 level 1
+> close #200
+> open /Users/cvetkom/Downloads/cryosparc_P17_J823_mask.mrc
+Opened cryosparc_P17_J823_mask.mrc as #200, grid size 588,588,588, pixel 0.95,
+shown at level 1, step 4, values float32
+> color #200 #e5bf996b models
+> color #200 #e5bf9968 models
+> color #200 #e5bf9967 models
+> color #200 #e5bf9966 models
+> volume #200 step 1
+> volume #200 level 1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J824_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J824_005_volume_map_sharp.mrc as #201, grid size
+,588,588, pixel 0.95, shown at level 0.191, step 4, values float32
+> hide #!200 models
+> hide #!199 models
+> volume #201 level 0.4868
+> volume #201 step 1
+> volume #201 level 0.46
+> volume #201 level 0.4
+> volume #201 level 0.38
+> volume #201 level 0.3
+> volume #201 level 0.32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class001.mrc
+Opened Cl3D_j718_run_it025_class001.mrc as #202, grid size 520,520,520, pixel
+.95, shown at level 7.31e-07, step 4, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class002.mrc
+Opened Cl3D_j718_run_it025_class002.mrc as #203, grid size 520,520,520, pixel
+.95, shown at level 6.19e-07, step 4, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class003.mrc
+Opened Cl3D_j718_run_it025_class003.mrc as #204, grid size 520,520,520, pixel
+.95, shown at level 5.74e-07, step 4, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class004.mrc
+Opened Cl3D_j718_run_it025_class004.mrc as #205, grid size 520,520,520, pixel
+.95, shown at level 1.81e-06, step 4, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class005.mrc
+Opened Cl3D_j718_run_it025_class005.mrc as #206, grid size 520,520,520, pixel
+.95, shown at level 5.25e-07, step 4, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Cl3D_job718/Cl3D_j718_run_it025_class006.mrc
+Opened Cl3D_j718_run_it025_class006.mrc as #207, grid size 520,520,520, pixel
+.95, shown at level 2.64e-07, step 4, values float32
+> hide #!201 models
+> hide #!203 models
+> hide #!204 models
+> hide #!205 models
+> hide #!206 models
+> hide #!207 models
+> volume #202 step 1
+> volume #202 level 0.001537
+> volume #203 step 1
+> volume #203 level 0.00429
+> hide #!203 models
+> show #!205 models
+> volume #205 step 1
+> volume #205 level 0.006238
+> volume #205 level 0.007973
+> hide #!205 models
+> show #!205 models
+> hide #!205 models
+> volume #206 step 1
+> volume #206 level 0.003432
+> volume #206 level 0.004328
+> volume #202 level 0.001682
+> show #!205 models
+> hide #!205 models
+> show #!205 models
+> hide #!205 models
+> volume #202 level 0.001267
+> volume #203 level 0.004002
+> volume #204 step 1
+> volume #204 level 0.004153
+> volume #204 level 0.003947
+> volume #206 level 0.004481
+> volume #207 step 1
+> volume #207 level 0.00211
+> hide #!207 models
+> show #!205 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J828_volume_map.mrc
+Opened cryosparc_P17_J828_volume_map.mrc as #208, grid size 588,588,588, pixel
+.95, shown at level 0.14, step 4, values float32
+> hide #!205 models
+> volume #208 step 1
+> volume #208 level 0.1685
+> volume #208 level 0.1611
+> volume #208 level 0.08448
+> open /Users/cvetkom/Downloads/cryosparc_P17_J829_class_00_final_volume.mrc
+Opened cryosparc_P17_J829_class_00_final_volume.mrc as #209, grid size
+,192,192, pixel 2.91, shown at level 0.585, step 1, values float32
+> hide #!208 models
+> volume #209 level 0.5
+> volume #209 level 0.4
+> volume #209 level 0.45
+> volume #209 level 0.5
+> open /Users/cvetkom/Downloads/cryosparc_P17_J830_mask.mrc
+Opened cryosparc_P17_J830_mask.mrc as #210, grid size 192,192,192, pixel 2.91,
+shown at level 1, step 1, values float32
+> volume #210 color #e5bf9975
+> volume #210 color #e5bf9967
+> volume #210 color #e5bf9966
+> volume #210 level 1
+[Repeated 1 time(s)]
+> hide #!210 models
+> hide #!209 models
+> show #!201 models
+> hide #!201 models
+> show #!201 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J825_006_volume_map_sharp.mrc
+Opened cryosparc_P17_J825_006_volume_map_sharp.mrc as #211, grid size
+,588,588, pixel 0.95, shown at level 0.189, step 4, values float32
+> volume #211 step 1
+> volume #211 level 0.3194
+> volume #211 level 0.32
+> hide #!201 models
+> show #!201 models
+> hide #!201 models
+> show #!201 models
+> hide #!211 models
+> show #!211 models
+> hide #!211 models
+> show #!211 models
+> color #211 #ff40ffff models
+> color #211 #7a81ffff models
+> hide #!201 models
+> show #!201 models
+> hide #!211 models
+> show #!211 models
+> hide #!211 models
+> show #!211 models
+> show #!202 models
+> hide #!201 models
+> hide #!202 models
+> volume #211 level 0.35
+> show #!201 models
+> hide #!211 models
+> volume #201 level 0.35
+> open /Users/cvetkom/Downloads/cryosparc_P17_J831_007_volume_map_sharp.mrc
+Opened cryosparc_P17_J831_007_volume_map_sharp.mrc as #212, grid size
+,588,588, pixel 0.95, shown at level 0.148, step 4, values float32
+> hide #!201 models
+> volume #212 level 0.4011
+> volume #212 step 1
+> show #!201 models
+> hide #!201 models
+> show #!211 models
+> hide #!211 models
+> show #!211 models
+> select add #211
+models selected
+> ui mousemode right "rotate selected models"
+Drag select of 211 cryosparc_P17_J825_006_volume_map_sharp.mrc , 212
+cryosparc_P17_J831_007_volume_map_sharp.mrc
+> select subtract #212
+models selected
+> view matrix models
+> #211,0.99974,0.0073342,0.021665,-7.9265,-0.0059368,0.99794,-0.063871,19.839,-0.022089,0.063726,0.99772,-10.804
+> view matrix models
+> #211,-0.83053,-0.50843,-0.22743,701.17,-0.55206,0.80558,0.21509,144.3,0.073856,0.30419,-0.94974,435.51
+> select subtract #211
+Nothing selected
+> ui tool show "Fit in Map"
+> fitmap #211 inMap #212
+Fit map cryosparc_P17_J825_006_volume_map_sharp.mrc in map
+cryosparc_P17_J831_007_volume_map_sharp.mrc using 491366 points
+correlation = 0.5456, correlation about mean = 0.05943, overlap = 5.974e+04
+steps = 436, shift = 6.8, angle = 10.9 degrees
+Position of cryosparc_P17_J825_006_volume_map_sharp.mrc (#211) relative to
+cryosparc_P17_J831_007_volume_map_sharp.mrc (#212) coordinates:
+Matrix rotation and translation
+-0.89957058 -0.40667531 -0.15933603 680.38831906
+-0.42615436 0.89716922 0.11610278 108.46539449
+.09573525 0.17234438 -0.98037349 475.76940193
+Axis 0.21472534 -0.97383892 -0.07436926
+Axis point 336.07482386 0.00000000 256.67979639
+Rotation angle (degrees) 172.47482888
+Shift along axis 5.08617368
+Correlation = 0.5456, Correlation about mean = 0.05943, Overlap = 5.974e+04
+> fitmap #211 inMap #212
+Fit map cryosparc_P17_J825_006_volume_map_sharp.mrc in map
+cryosparc_P17_J831_007_volume_map_sharp.mrc using 491366 points
+correlation = 0.5457, correlation about mean = 0.0594, overlap = 5.974e+04
+steps = 44, shift = 0.0378, angle = 0.0389 degrees
+Position of cryosparc_P17_J825_006_volume_map_sharp.mrc (#211) relative to
+cryosparc_P17_J831_007_volume_map_sharp.mrc (#212) coordinates:
+Matrix rotation and translation
+-0.89980651 -0.40634880 -0.15883608 680.25943553
+-0.42572683 0.89739120 0.11595559 108.32590029
+.09541969 0.17195838 -0.98047203 475.96728322
+Axis 0.21451210 -0.97389690 -0.07422527
+Axis point 336.02953423 0.00000000 256.71123961
+Rotation angle (degrees) 172.49947586
+Shift along axis 5.09681985
+> select add #211
+models selected
+> view matrix models
+> #211,-0.90089,-0.40799,-0.14811,678.04,-0.41938,0.90616,0.054752,121.11,0.11187,0.11144,-0.98745,489.99
+> volume #211 level 0.4
+> select subtract #211
+Nothing selected
+> fitmap #211 inMap #212
+Fit map cryosparc_P17_J825_006_volume_map_sharp.mrc in map
+cryosparc_P17_J831_007_volume_map_sharp.mrc using 381853 points
+correlation = 0.9767, correlation about mean = 0.8803, overlap = 1.862e+05
+steps = 388, shift = 8.54, angle = 19 degrees
+Position of cryosparc_P17_J825_006_volume_map_sharp.mrc (#211) relative to
+cryosparc_P17_J831_007_volume_map_sharp.mrc (#212) coordinates:
+Matrix rotation and translation
+-0.97678811 -0.20990860 -0.04270100 623.15903654
+-0.20103231 0.96714269 -0.15563105 99.70859450
+.07396625 -0.14343428 -0.98689189 576.21341964
+Axis 0.10368016 -0.99174448 0.07545400
+Axis point 308.25071118 0.00000000 301.13328663
+Rotation angle (degrees) 176.62796126
+Shift along axis 9.20139044
+> hide #!212 models
+> show #!212 models
+> hide #!212 models
+> show #!212 models
+> hide #!212 models
+> show #!212 models
+> hide #!212 models
+> show #!212 models
+> hide #!212 models
+> show #!212 models
+> hide #!212 models
+> show #!212 models
+> hide #!212 models
+> show #!212 models
+> hide #!212 models
+> show #!212 models
+> hide #!212 models
+> show #!212 models
+> hide #!212 models
+> show #!212 models
+> hide #!212 models
+> show #!212 models
+> hide #!211 models
+> volume #212 level 0.4
+> volume #212 level 0.38
+> volume #212 level 0.35
+> open /Users/cvetkom/Downloads/cryosparc_P17_J831_007_volume_mask_refine.mrc
+Opened cryosparc_P17_J831_007_volume_mask_refine.mrc as #213, grid size
+,588,588, pixel 0.95, shown at level 1, step 4, values float32
+> volume #213 color #b2b2b259
+> volume #213 step 1
+> volume #213 level 1
+> volume #212 level 0.2391
+> close #211
+> open /Users/cvetkom/Downloads/cryosparc_P17_J843_008_volume_map_sharp.mrc
+Opened cryosparc_P17_J843_008_volume_map_sharp.mrc as #211, grid size
+,520,520, pixel 0.95, shown at level 0.249, step 4, values float32
+> hide #!211 models
+> hide #!212 models
+> hide #!213 models
+> show #!211 models
+> volume #211 level 0.7129
+> volume #211 step 1
+> volume #211 level 0.5829
+> volume #211 level 0.56
+> volume #211 level 0.55
+> volume #211 level 0.5
+> show #!194 models
+> hide #!194 models
+> show #!189 models
+> hide #!189 models
+> show #!189 models
+> hide #!189 models
+> show #!189 models
+> hide #!189 models
+> volume #211 level 0.55
+> show #!189 models
+> hide #!189 models
+> show #!189 models
+> volume #189 level 0.6
+> hide #!189 models
+> show #!189 models
+> hide #!189 models
+> ui mousemode right zoom
+> hide #!211 models
+> show #!210 models
+> hide #!210 models
+> show #!202 models
+> hide #!202 models
+> show #!203 models
+> hide #!203 models
+> show #!204 models
+> hide #!204 models
+> show #!205 models
+> hide #!205 models
+> show #!206 models
+> hide #!206 models
+> show #!207 models
+> close #202-207
+> show #!176 models
+> hide #!176 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> show #!130 models
+> hide #!129 models
+> hide #!130 models
+> show #!131 models
+> hide #!131 models
+> show #!132 models
+> hide #!132 models
+> show #!133 models
+> show #!134 models
+> show #!135 models
+> hide #!134 models
+> hide #!133 models
+> show #!133 models
+> hide #!135 models
+> show #!134 models
+> hide #!134 models
+> show #!134 models
+> hide #!134 models
+> show #!134 models
+> hide #!134 models
+> hide #!133 models
+> show #!133 models
+> show #!134 models
+> hide #!134 models
+> hide #!133 models
+> show #!129 models
+> show #!130 models
+> hide #!129 models
+> hide #!130 models
+> show #!131 models
+> hide #!131 models
+> show #!131 models
+> hide #!131 models
+> show #!132 models
+> hide #!132 models
+> show #!133 models
+> show #!134 models
+> hide #!133 models
+> show #!133 models
+> hide #!133 models
+> hide #!134 models
+> show #!110 models
+> show #!111 models
+> hide #!110 models
+> show #!110 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> hide #!110 models
+> show #!110 models
+> show #!111 models
+> hide #!110 models
+> hide #!111 models
+> show #!112 models
+> show #!120 models
+> hide #!120 models
+> show #!133 models
+> hide #!133 models
+> show #!133 models
+> hide #!112 models
+> show #!112 models
+> hide #!133 models
+> show #!134 models
+> hide #!112 models
+> show #!113 models
+> hide #!113 models
+> show #!113 models
+> hide #!113 models
+> show #!110 models
+> hide #!110 models
+> show #!111 models
+> hide #!111 models
+> show #!112 models
+> hide #!112 models
+> show #!113 models
+> hide #!113 models
+> show #!114 models
+> hide #!114 models
+> show #!115 models
+> hide #!115 models
+> show #!115 models
+> hide #!115 models
+> show #!115 models
+> hide #!115 models
+> hide #!134 models
+> show #!110 models
+> show #!111 models
+> hide #!110 models
+> show #!110 models
+> hide #!111 models
+> show #!71 models
+> hide #!71 models
+> show #!130 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> hide #!130 models
+> show #!110 models
+> show #!98 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!98 models
+> show #!98 models
+> hide #!110 models
+> hide #!98 models
+> show #!105 models
+> show #!106 models
+> hide #!105 models
+> hide #!106 models
+> show #!117 models
+> show #!118 models
+> hide #!117 models
+> hide #!118 models
+> show #!74 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!74 models
+> show #!74 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!74 models
+> hide #!75 models
+> show #!70 models
+> show #!71 models
+> hide #!70 models
+> show #!70 models
+> hide #!70 models
+> show #!70 models
+> hide #!71 models
+> show #!72 models
+> hide #!72 models
+> show #!73 models
+> hide #!73 models
+> show #!73 models
+> hide #!73 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!70 models
+> show #!75 models
+> hide #!74 models
+> hide #!75 models
+> show #!75 models
+> show #!74 models
+> hide #!74 models
+> hide #!75 models
+> show #!74 models
+> hide #!74 models
+> show #!75 models
+> hide #!75 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> show #!98 models
+> hide #!98 models
+> hide #!130 models
+> show #!130 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!130 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> show #!129 models
+> show #!130 models
+> hide #!98 models
+> hide #!99 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!129 models
+> show #!129 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!129 models
+> show #!139 models
+> hide #!139 models
+> show #!139 models
+> hide #!139 models
+> show #!139 models
+> hide #!130 models
+> show #!138 models
+> hide #!139 models
+> show #!143 models
+> hide #!143 models
+> show #!143 models
+> hide #!138 models
+> hide #!143 models
+> show #!141 models
+> show #!147 models
+> hide #!147 models
+> show #!147 models
+> hide #!141 models
+> show #!141 models
+> hide #!141 models
+> hide #!147 models
+> show #!140 models
+> hide #!140 models
+> show #!145 models
+> show #!146 models
+> hide #!146 models
+> show #!146 models
+> hide #!145 models
+> hide #!146 models
+> show #!148 models
+> hide #!148 models
+> show #!157 models
+> hide #!157 models
+> show #!161 models
+> hide #!161 models
+> show #!174 models
+> hide #!174 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J721_006_volume_map.mrc
+Opened cryosparc_P17_J721_006_volume_map.mrc as #202, grid size 294,294,294,
+pixel 1.9, shown at level 0.346, step 2, values float32
+> volume #202 step 1
+> volume #202 level 0.3331
+> show #!157 models
+> hide #!157 models
+> show #!157 models
+> hide #!157 models
+> show #!161 models
+> volume #161 level 0.32
+> volume #161 level 0.34
+> hide #!161 models
+> show #!160 models
+> hide #!160 models
+> show #!159 models
+> show #!161 models
+> hide #!161 models
+> show #!161 models
+> hide #!161 models
+> hide #!159 models
+> show #!159 models
+> hide #!159 models
+> show #!160 models
+> show #!173 models
+> show #!175 models
+> show #!157 models
+> hide #!157 models
+> hide #!160 models
+> volume #173 level 0.3031
+> volume #173 level 0.3465
+> show #!175 models
+> hide #!173 models
+> volume #175 level 0.3281
+> hide #!175 models
+> show #!172 models
+> hide #!172 models
+> close #155-156,159-160,173,175-176
+> show #!157 models
+> show #!174 models
+> hide #!174 models
+> show #!174 models
+> volume #174 level 0.3294
+> hide #!174 models
+> show #!174 models
+> hide #!174 models
+> show #!174 models
+> hide #!174 models
+> show #!174 models
+> hide #!174 models
+> show #!174 models
+> hide #!174 models
+> hide #!157 models
+> show #!161 models
+> show #!141 models
+> hide #!141 models
+> show #!141 models
+> hide #!161 models
+> show #!161 models
+> hide #!161 models
+> show #!161 models
+> select add #161
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #161,-0.80087,-0.4765,-0.3627,729.62,0.10949,-0.71198,0.69361,276.28,-0.58874,0.51578,0.62238,115.15
+> view matrix models
+> #161,-0.84255,0.43705,-0.31481,469.51,-0.49419,-0.85972,0.12908,627.85,-0.21423,0.26433,0.94034,2.6659
+> view matrix models
+> #161,-0.91542,-0.17496,-0.36248,675.94,0.17298,-0.98418,0.038186,498.42,-0.36343,-0.027746,0.93121,129.94
+> view matrix models
+> #161,-0.95897,-0.26467,-0.1016,649.01,0.27072,-0.9613,-0.051053,486.58,-0.084153,-0.076463,0.99351,49.911
+> view matrix models
+> #161,-0.99187,0.12321,0.03177,514.81,-0.12543,-0.98874,-0.081553,613.22,0.021365,-0.084875,0.99616,22.011
+> ui mousemode right zoom
+> select clear
+> hide #!161 models
+> show #!161 models
+> fitmap #161 inMap #141
+Fit map cryosparc_P17_J697_006_volume_map.mrc z flip in map
+cryosparc_P17_J685_007_volume_map.mrc using 269413 points
+correlation = 0.9961, correlation about mean = 0.9593, overlap = 9.415e+04
+steps = 112, shift = 3.83, angle = 9.13 degrees
+Position of cryosparc_P17_J697_006_volume_map.mrc z flip (#161) relative to
+cryosparc_P17_J685_007_volume_map.mrc (#141) coordinates:
+Matrix rotation and translation
+-0.99974072 -0.02276472 -0.00050563 565.44941758
+.02276965 -0.99929232 -0.02994005 559.04447071
+.00017631 -0.02994380 0.99955157 8.32772983
+Axis -0.00008235 -0.01497460 0.99988787
+Axis point 279.54196619 282.80415641 0.00000000
+Rotation angle (degrees) 178.69527744
+Shift along axis -0.09123841
+> hide #!141 models
+> show #!141 models
+> volume #161 level 0.36
+> hide #!141 models
+> show #!141 models
+> hide #!141 models
+> show #!141 models
+> hide #!141 models
+> show #!141 models
+> hide #!141 models
+> show #!141 models
+> hide #!141 models
+> show #!141 models
+> hide #!141 models
+> show #!141 models
+> hide #!141 models
+> show #!141 models
+> hide #!141 models
+> show #!141 models
+> show #!147 models
+> hide #!141 models
+> show #!141 models
+> hide #!141 models
+> show #!147 models
+> hide #!147 models
+> show #!147 models
+> hide #!161 models
+> show #!161 models
+> hide #!161 models
+> show #!141 models
+> select add #147
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #147,0.75391,-0.62474,-0.20327,302.4,-0.65039,-0.66601,-0.36528,749.91,0.092824,0.40759,-0.90843,455.15
+> view matrix models
+> #147,-0.31245,-0.67282,-0.67059,759.97,-0.54055,0.70643,-0.45691,373.58,0.78114,0.21972,-0.58441,212.49
+> view matrix models
+> #147,-0.90083,-0.32948,-0.28274,711.29,-0.41209,0.85388,0.3179,56.872,0.13669,0.40289,-0.90498,443.04
+> view matrix models
+> #147,-0.99864,0.030742,-0.042093,565.93,0.029267,0.99895,0.035202,-18.858,0.043131,0.033922,-0.99849,598.86
+> ui mousemode right "translate selected models"
+> view matrix models
+> #147,-0.99864,0.030742,-0.042093,560.75,0.029267,0.99895,0.035202,-44.757,0.043131,0.033922,-0.99849,550.76
+> view matrix models
+> #147,-0.99864,0.030742,-0.042093,571.25,0.029267,0.99895,0.035202,-21.366,0.043131,0.033922,-0.99849,539.43
+> select subtract #147
+Nothing selected
+> fitmap #147 inMap #141
+Fit map cryosparc_P17_J690_006_volume_map.mrc in map
+cryosparc_P17_J685_007_volume_map.mrc using 254434 points
+correlation = 0.9983, correlation about mean = 0.9814, overlap = 9.297e+04
+steps = 84, shift = 10.7, angle = 2.98 degrees
+Position of cryosparc_P17_J690_006_volume_map.mrc (#147) relative to
+cryosparc_P17_J685_007_volume_map.mrc (#141) coordinates:
+Matrix rotation and translation
+-0.99966375 0.02590789 -0.00108426 552.09827323
+.02590403 0.99965851 0.00344015 -9.28972053
+.00117301 0.00341091 -0.99999349 555.06217083
+Axis -0.01295398 -0.99991463 -0.00171281
+Axis point 275.95266832 0.00000000 277.69485205
+Rotation angle (degrees) 179.93532851
+Shift along axis 1.18634199
+> hide #!147 models
+> show #!147 models
+> hide #!147 models
+> show #!147 models
+> hide #!147 models
+> show #!147 models
+> hide #!141 models
+> show #!157 models
+> hide #!157 models
+> show #!161 models
+> hide #!161 models
+> show #!161 models
+> color #161 #00fa92ff models
+> hide #!161 models
+> show #!161 models
+> hide #!147 models
+> show #!147 models
+> hide #!147 models
+> show #!147 models
+> hide #!161 models
+> hide #!147 models
+> show #!32 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!34 models
+> show #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!34 models
+> show #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!34 models
+> hide #!32 models
+> show #!32 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> ui mousemode right zoom
+> lighting full
+> lighting soft
+> lighting simple
+> lighting full
+> hide #!32 models
+> show #!32 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!95 models
+> hide #!95 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J517_006_volume_map_zflip.mrc
+Opened cryosparc_P17_J517_006_volume_map_zflip.mrc as #155, grid size
+,588,588, pixel 0.95, shown at level 0.158, step 4, values float32
+> volume #155 step 1
+> lighting soft
+> show #!179 models
+> hide #!179 models
+> show #!179 models
+> hide #!179 models
+> show #!179 models
+> select add #155
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #155,-0.98089,0.19377,-0.017464,502.92,0.10481,0.60192,0.79165,-107.18,0.16391,0.77469,-0.61072,122.66
+> view matrix models
+> #155,-0.25052,0.96798,-0.015979,76.052,0.96671,0.24923,-0.057953,-41.024,-0.052115,-0.029966,-0.99819,507.99
+> view matrix models
+> #155,0.96775,0.17696,-0.17931,1.7558,0.20922,-0.96102,0.18073,460.27,-0.14034,-0.21242,-0.96705,577.47
+> view matrix models
+> #155,0.96767,0.091902,-0.2349,39.67,0.12427,-0.9841,0.12691,503.72,-0.2195,-0.152,-0.9637,581.47
+> view matrix models
+> #155,0.91176,0.40771,0.049574,-104.32,0.37999,-0.79159,-0.47852,523.82,-0.15586,0.45514,-0.87667,368.35
+> lighting simple
+> view matrix models
+> #155,0.92481,0.37946,0.027133,-94.419,0.34082,-0.79474,-0.50223,541.44,-0.16901,0.47372,-0.86431,363.7
+> view matrix models
+> #155,0.94675,0.28168,0.15598,-103.76,0.32196,-0.82268,-0.46855,546.56,-0.0036582,0.49382,-0.86956,312.94
+> view matrix models
+> #155,0.9947,0.045724,-0.092058,10.698,0.043566,-0.99873,-0.02532,567.43,-0.093098,0.021175,-0.99543,504.12
+> ui mousemode right "translate selected models"
+> view matrix models
+> #155,0.9947,0.045724,-0.092058,46.226,0.043566,-0.99873,-0.02532,564.24,-0.093098,0.021175,-0.99543,557.75
+> view matrix models
+> #155,0.9947,0.045724,-0.092058,13.547,0.043566,-0.99873,-0.02532,566.45,-0.093098,0.021175,-0.99543,563.81
+> select subtract #155
+Nothing selected
+> fitmap #155 inMap #179
+Fit map cryosparc_P17_J517_006_volume_map_zflip.mrc in map
+cryosparc_P17_J544_007_volume_map_zflip.mrc using 2026669 points
+correlation = 0.9972, correlation about mean = 0.9729, overlap = 1.474e+05
+steps = 220, shift = 19.3, angle = 6.44 degrees
+Position of cryosparc_P17_J517_006_volume_map_zflip.mrc (#155) relative to
+cryosparc_P17_J544_007_volume_map_zflip.mrc (#179) coordinates:
+Matrix rotation and translation
+.99982429 0.01272017 0.01376969 -7.71473943
+.01281628 -0.99989397 -0.00691402 556.62008375
+.01368028 0.00708928 -0.99988130 552.40010778
+Axis 0.99995607 0.00638455 0.00686279
+Axis point 0.00000000 277.36764127 277.20094376
+Rotation angle (degrees) 179.59881412
+Shift along axis -0.36962502
+> ui mousemode right zoom
+> lighting soft
+> hide #!179 models
+> show #!179 models
+> hide #!179 models
+> show #!179 models
+> show #!178 models
+> hide #!179 models
+> show #!179 models
+> hide #!178 models
+> volume #179 level 0.16
+> hide #!179 models
+> show #!179 models
+> hide #!179 models
+> open /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J851_volume_map.mrc
+Opened cryosparc_P17_J851_volume_map.mrc as #156, grid size 588,588,588, pixel
+.95, shown at level 0.179, step 4, values float32
+> open /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J854_volume_map.mrc
+Opened cryosparc_P17_J854_volume_map.mrc as #159, grid size 588,588,588, pixel
+.95, shown at level 0.178, step 4, values float32
+> hide #!156 models
+> show #!156 models
+> hide #!156 models
+> hide #!159 models
+> show #!159 models
+> show #!156 models
+> volume #156 step 1
+> volume #159 step 1
+> volume #156 level 0.15
+> volume #159 level 0.15
+> volume #156 level 0.12
+> volume #156 level 0.1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J857_mask.mrc
+Opened cryosparc_P17_J857_mask.mrc as #160, grid size 588,588,588, pixel 0.95,
+shown at level 1, step 4, values float32
+> volume #160 step 1
+> volume #160 color #b2ffb260
+> volume #160 color #b2ffb261
+> volume #160 level 1
+> volume #160 color #b2ffb270
+> volume #160 level 1
+> volume #156 level 0.08
+> volume #156 level 0.1
+> volume #156 level 0.9
+> volume #156 level 0.09
+> volume #156 level 0.08
+> open /Users/cvetkom/Downloads/cryosparc_P17_J858_007_volume_map.mrc
+Opened cryosparc_P17_J858_007_volume_map.mrc as #173, grid size 588,588,588,
+pixel 0.95, shown at level 0.154, step 4, values float32
+> volume #173 step 1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J866_class_00_00042_volume.mrc
+Opened cryosparc_P17_J866_class_00_00042_volume.mrc as #175, grid size
+,128,128, pixel 4.36, shown at level 1.71, step 1, values float32
+> volume #175 level 1.364
+> volume #175 level 1
+> volume #175 level 0.9
+> volume #175 level 0.8
+> volume #175 level 0.9
+> open /Users/cvetkom/Downloads/cryosparc_P17_J869_mask.mrc
+Opened cryosparc_P17_J869_mask.mrc as #176, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+> volume #176 color #cccc9964
+> volume #176 color #cccc9963
+> volume #176 level 1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J870_mask.mrc
+Opened cryosparc_P17_J870_mask.mrc as #203, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+> volume #203 color #b2b2b267
+> volume #203 color #b2b2b266
+> volume #203 level 1
+[Repeated 1 time(s)]
+> show #!213 models
+> hide #!213 models
+> show #!213 models
+> hide #!213 models
+> hide #!203 models
+> show #!203 models
+> hide #!203 models
+> show #!211 models
+> hide #!211 models
+> show #!212 models
+> hide #!212 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J867_007_volume_map.mrc
+Opened cryosparc_P17_J867_007_volume_map.mrc as #204, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 4, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J871_007_volume_map.mrc
+Opened cryosparc_P17_J871_007_volume_map.mrc as #205, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 4, values float32
+> volume #204 step 1
+> volume #205 step 1
+> volume #205 level 0.2369
+> volume #205 level 0.1513
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> show #!74 models
+> hide #!75 models
+> show #!75 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> hide #!75 models
+> volume #129 level 0.01525
+> volume #129 level 0.02295
+> volume #129 level 0.02195
+> volume #129 level 0.02859
+> volume #129 level 0.01548
+> volume #129 level 0.01394
+> volume #129 level 0.02201
+> volume #129 level 0.02491
+> volume #129 level 0.02207
+> volume #129 level 0.01258
+> volume #129 level 0.01323
+> show #!74 models
+> volume #129 level 0.014
+> hide #!74 models
+> show #!74 models
+> show #!75 models
+> hide #!74 models
+> show #!74 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!74 models
+> show #!74 models
+> hide #!75 models
+> show #!75 models
+> hide #!74 models
+> hide #!75 models
+> show #!98 models
+> show #!99 models
+> hide #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!99 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!99 models
+> hide #!99 models
+> show #!98 models
+> hide #!98 models
+> show #!99 models
+> hide #!99 models
+> show #!98 models
+> hide #!98 models
+> show #!99 models
+> hide #!99 models
+> show #!98 models
+> hide #!98 models
+> show #!99 models
+> hide #!99 models
+> show #!100 models
+> hide #!100 models
+> show #!100 models
+> hide #!100 models
+> show #!122 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!130 models
+> hide #!122 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!130 models
+> show #!130 models
+> hide #!123 models
+> show #!123 models
+> hide #!130 models
+> hide #!123 models
+> show #!122 models
+> show #!123 models
+> hide #!122 models
+> show #!122 models
+> show #!124 models
+> hide #!123 models
+> hide #!122 models
+> hide #!124 models
+> show #!124 models
+> show #!123 models
+> hide #!123 models
+> show #!122 models
+> hide #!122 models
+> hide #!124 models
+> show #!124 models
+> hide #!124 models
+> show #!125 models
+> hide #!125 models
+> show #!125 models
+> hide #!125 models
+> show #!126 models
+> show #!127 models
+> show #!134 models
+> show #!135 models
+> hide #!135 models
+> show #!128 models
+> hide #!128 models
+> show #!135 models
+> hide #!135 models
+> show #!133 models
+> hide #!127 models
+> hide #!126 models
+> show #!126 models
+> hide #!126 models
+> show #!126 models
+> hide #!126 models
+> show #!126 models
+> hide #!126 models
+> show #!127 models
+> hide #!127 models
+> show #!127 models
+> hide #!127 models
+> show #!127 models
+> hide #!127 models
+> show #!127 models
+> hide #!127 models
+> hide #!133 models
+> show #!133 models
+> hide #!133 models
+> show #!133 models
+> hide #!133 models
+> hide #!134 models
+> show #!129 models
+> show #!130 models
+> show #!131 models
+> hide #!131 models
+> show #!132 models
+> hide #!132 models
+> show #!132 models
+> hide #!132 models
+> show #!133 models
+> show #!134 models
+> show #!132 models
+> hide #!132 models
+> show #!131 models
+> hide #!131 models
+> hide #!133 models
+> hide #!134 models
+> show #!122 models
+> show #!123 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> hide #!130 models
+> show #!130 models
+> hide #!122 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> hide #!130 models
+> show #!129 models
+> show #!130 models
+> hide #!129 models
+> hide #!130 models
+> show #!133 models
+> show #!134 models
+> show #!104 models
+> hide #!104 models
+> show #!103 models
+> hide #!103 models
+> show #!103 models
+> show #!102 models
+> hide #!102 models
+> show #!104 models
+> hide #!104 models
+> show #!102 models
+> hide #!103 models
+> show #!103 models
+> hide #!102 models
+> show #!101 models
+> hide #!101 models
+> show #!100 models
+> hide #!100 models
+> show #!100 models
+> hide #!103 models
+> show #!103 models
+> hide #!100 models
+> show #!100 models
+> hide #!133 models
+> hide #!134 models
+> show #!134 models
+> hide #!134 models
+> hide #!100 models
+> show #!100 models
+> hide #!100 models
+> show #!100 models
+> hide #!100 models
+> show #!100 models
+> hide #!103 models
+> show #!103 models
+> hide #!103 models
+> show #!103 models
+> hide #!103 models
+> show #!103 models
+> hide #!100 models
+> hide #!103 models
+> show #!98 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> show #!100 models
+> hide #!100 models
+> show #!101 models
+> hide #!101 models
+> show #!102 models
+> hide #!102 models
+> show #!103 models
+> hide #!103 models
+> show #!104 models
+> hide #!104 models
+> show #!129 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J876_class_00_final_volume.mrc
+Opened cryosparc_P17_J876_class_00_final_volume.mrc as #206, grid size
+,192,192, pixel 2.91, shown at level 0.504, step 1, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J880_class_00_final_volume.mrc
+Opened cryosparc_P17_J880_class_00_final_volume.mrc as #207, grid size
+,192,192, pixel 2.91, shown at level 0.511, step 1, values float32
+> hide #!98 models
+> hide #!99 models
+> hide #!129 models
+> hide #!130 models
+> volume #206 level 0.3476
+> open /Users/cvetkom/Downloads/cryosparc_P17_J874_volume_map.mrc
+Opened cryosparc_P17_J874_volume_map.mrc as #214, grid size 294,294,294, pixel
+.9, shown at level 0.404, step 2, values float32
+> volume #214 step 1
+> volume #214 level 0.3304
+> open /Users/cvetkom/Downloads/cryosparc_P17_J882_volume_map.mrc
+Opened cryosparc_P17_J882_volume_map.mrc as #215, grid size 294,294,294, pixel
+.9, shown at level 0.4, step 2, values float32
+> volume #215 step 1
+> volume #215 level 0.347
+> volume #215 level 0.3003
+> open /Users/cvetkom/Downloads/cryosparc_P17_J878_class_00_00042_volume.mrc
+Opened cryosparc_P17_J878_class_00_00042_volume.mrc as #216, grid size
+,128,128, pixel 4.36, shown at level 0.839, step 1, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J878_class_01_00042_volume.mrc
+Opened cryosparc_P17_J878_class_01_00042_volume.mrc as #217, grid size
+,128,128, pixel 4.36, shown at level 1.37, step 1, values float32
+> volume #216 level 1.25
+> volume #217 level 1.171
+> volume #217 level 1
+> volume #217 level 0.9
+> volume #217 level 0.8
+> volume #217 level 0.85
+> volume #217 level 0.8
+> open /Users/cvetkom/Downloads/cryosparc_P17_J883_mask.mrc
+Opened cryosparc_P17_J883_mask.mrc as #218, grid size 128,128,128, pixel 4.36,
+shown at level 1, step 1, values float32
+> volume #218 color #cccc9967
+> volume #218 color #cccc9969
+> volume #218 level 1
+> volume #218 level 0.5107
+> volume #218 level 1
+> open /Users/cvetkom/Downloads/cryosparc_P17_J884_009_volume_map.mrc
+Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
+pixel 1.9, shown at level 0.347, step 2, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J885_008_volume_map.mrc
+Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
+pixel 1.9, shown at level 0.347, step 2, values float32
+> hide #!217 models
+> hide #!218 models
+> volume #219 step 1
+> volume #220 step 1
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job506_run_class001.mrc
+Opened Ref3D_job506_run_class001.mrc as #221, grid size 588,588,588, pixel
+.95, shown at level 0.00502, step 4, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job506_run_class001_NCP.mrc
+Opened Ref3D_job506_run_class001_NCP.mrc as #222, grid size 588,588,588, pixel
+.95, shown at level 0.00208, step 4, values float32
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/mask_job519.mrc
+Opened mask_job519.mrc as #223, grid size 588,588,588, pixel 0.95, shown at
+level 5e-05, step 4, values float32
+> hide #!218 models
+> hide #!220 models
+> volume #223 step 1
+> volume #223 level 0.9925
+> volume #223 color #ffb2ff80
+> volume #223 color #ffb2ff66
+> volume #222 step 1
+> volume #221 step 1
+> volume #222 level 0.002458
+> volume #222 level 0.003951
+> volume #222 level 0.004587
+> volume #222 level 0.005
+> volume #222 level 0.004508
+> volume #222 level 0.0045
+> volume #221 level 0.0045
+> hide #!223 models
+> hide #!221 models
+> show #!221 models
+> hide #!222 models
+> hide #!221 models
+> show #!222 models
+> ui tool show "Map Eraser"
+> hide #224 models
+> show #224 models
+> hide #!222 models
+Drag select of eraser sphere, 87 of 1000 triangles
+> select clear
+> show #!222 models
+> show #!221 models
+> hide #!221 models
+> show #!221 models
+> hide #!221 models
+> ui mousemode right zoom
+> select add #224
+model selected
+> ui mousemode right "translate selected models"
+> hide #224 models
+> show #224 models
+> hide #!222 models
+> show #!222 models
+> select subtract #224
+Nothing selected
+> select add #224
+model selected
+> select subtract #224
+Nothing selected
+> ui mousemode right zoom
+Drag select of eraser sphere, 27 of 1000 triangles
+> select #224
+model selected
+> select #224
+model selected
+> select clear
+> ui mousemode right "map eraser"
+> volume erase #222 center 235.13,229.91,259.65 radius 50.358
+Opened Ref3D_job506_run_class001_NCP.mrc copy as #225, grid size 588,588,588,
+pixel 0.95, shown at step 1, values float32
+> volume erase #225 center 240.34,217.6,249.39 radius 50.274
+> volume erase #225 center 249.31,217.92,185.58 radius 50.274
+> volume erase #225 center 254.34,196.31,201.83 radius 50.274
+> volume erase #225 center 244.51,226.1,178.85 radius 50.274
+> volume erase #225 center 266.29,219.21,231.39 radius 71.221
+> show #!222 models
+> hide #!222 models
+> show #!222 models
+> hide #!222 models
+> ui mousemode right zoom
+> vop gaussian #225 sdev 2.85
+Opened Ref3D_job506_run_class001_NCP.mrc copy gaussian as #224, grid size
+,588,588, pixel 0.95, shown at step 1, values float32
+> volume #224 level 0.004498
+> volume #224 level 0.004
+> volume #224 level 0.0045
+> save
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job506_run_class001_bareNCP.mrc
+> models #224
+> hide #!224 models
+> show #!224 models
+> show #!222 models
+> hide #!222 models
+> hide #!225 models
+> show #!222 models
+> hide #!222 models
+> show #!222 models
+> hide #!222 models
+> show #!222 models
+> hide #!222 models
+> show #!222 models
+> hide #!224 models
+> show #!224 models
+> hide #!224 models
+> show #!224 models
+> hide #!222 models
+> show #!222 models
+> hide #!222 models
+> show #!222 models
+> lighting full
+> hide #!222 models
+> show #!222 models
+> color #224 #d6d6d6ff models
+> color #224 darkgrey models
+> hide #!224 models
+> show #!224 models
+> hide #!222 models
+> show #!222 models
+> hide #!222 models
+> show #!222 models
+> hide #!222 models
+> show #!222 models
+> hide #!222 models
+> show #!222 models
+> hide #!222 models
+> show #!222 models
+> hide #!222 models
+> hide #!224 models
+> show #!222 models
+> show #!223 models
+> show #!221 models
+> volume #223 level 0.5133
+> volume #223 level 1
+> hide #!223 models
+> show #!223 models
+> hide #!223 models
+> show #!224 models
+> hide #!222 models
+> hide #!221 models
+> show #!221 models
+> hide #!221 models
+> show #!221 models
+> hide #!221 models
+> show #!221 models
+> hide #!221 models
+> show #!221 models
+> open /Volumes/lab-
+> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/MaskCreate/job744/mask.mrc
+Opened mask.mrc as #226, grid size 588,588,588, pixel 0.95, shown at level
+e-05, step 4, values float32
+> hide #!224 models
+> show #!224 models
+> hide #!221 models
+> volume #226 step 1
+> volume #226 color #e5bf9966
+> volume #226 level 1
+> volume #226 level 0.3859
+> volume #226 level 0.5044
+> hide #!224 models
+> show #!221 models
+> volume #226 level 1
+> hide #!226 models
+> show #!226 models
+> volume #226 level 1
+> show #!223 models
+> hide #!223 models
+> show #!223 models
+> hide #!223 models
+> show #!223 models
+> hide #!223 models
+> show #!223 models
+> hide #!223 models
+> show #!223 models
+> hide #!223 models
+> show #!223 models
+> hide #!223 models
+> volume #226 level 1
+> hide #!221 models
+> hide #!226 models
+> show #!219 models
+Error processing trigger "graphics update":
+You deleted or moved a volume file that is still open in ChimeraX.
+/Users/cvetkom/Downloads/cryosparc_P17_J884_009_volume_map.mrc
+To allow fast initial display of volume data ChimeraX does not read all data
+from the file when it is first opened, and will later read more data when
+needed. ChimeraX got an error trying to read the above file.
+> close #219-220
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J884_009_volume_map.mrc
+Opened cryosparc_P17_J884_009_volume_map.mrc as #219, grid size 294,294,294,
+pixel 1.9, shown at level 0.347, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J885_008_volume_map.mrc
+Opened cryosparc_P17_J885_008_volume_map.mrc as #220, grid size 294,294,294,
+pixel 1.9, shown at level 0.347, step 2, values float32
+> volume #219 step 1
+> volume #220 step 1
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J888_009_volume_map.mrc
+Opened cryosparc_P17_J888_009_volume_map.mrc as #227, grid size 294,294,294,
+pixel 1.9, shown at level 0.356, step 2, values float32
+> volume #227 step 1
+> volume #219 level 0.4485
+> volume #219 level 0.4625
+> volume #219 step 2
+> volume #219 step 1
+> show #!213 models
+> hide #!213 models
+> volume #227 step 2
+> volume #227 step 1
+> close #225
+> close #226
+> hide #!219 models
+> show #!219 models
+> volume #219 step 2
+> volume #219 step 4
+> volume #219 step 1
+> volume #219 step 2
+> volume #219 level 0.4261
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
+\u2014\u2014\u2014 End of log from Thu Jul 11 13:31:37 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> hide #!219 models
+> show #!227 models
+> hide #!227 models
+> open
+> /Users/cvetkom/Downloads/cryosparc_P17_J984_class_00_00062_volume_sharp.mrc
+Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc as #225, grid size
+,128,128, pixel 3.27, shown at level 0.37, step 1, values float32
+> open /Users/cvetkom/Downloads/cryosparc_P17_J967_class_00_00400_volume.mrc
+Opened cryosparc_P17_J967_class_00_00400_volume.mrc as #226, grid size
+,128,128, pixel 3.27, shown at level 0.384, step 1, values float32
+> open
+> /Users/cvetkom/Downloads/cryosparc_P17_J981_class_00_00062_volume_sharp.mrc
+Opened cryosparc_P17_J981_class_00_00062_volume_sharp.mrc as #228, grid size
+,128,128, pixel 3.27, shown at level 0.327, step 1, values float32
+> show #!227 models
+> hide #!227 models
+> hide #!225 models
+> hide #!228 models
+> volume #226 level 1.133
+> volume #226 level 1.3
+> volume #226 level 1.35
+> lighting soft
+> volume #226 color darkgrey
+> volume #226 level 1.4
+> volume #226 level 1.45
+> volume #225 level 2.008
+> show #!225 models
+> hide #!225 models
+> show #!225 models
+> hide #!226 models
+> show #!226 models
+> hide #!226 models
+> show #!226 models
+> hide #!226 models
+> show #!228 models
+> volume #228 level 1.823
+> open /Users/cvetkom/Downloads/cryosparc_P17_J967_class_00_final_volume.mrc
+Opened cryosparc_P17_J967_class_00_final_volume.mrc as #229, grid size
+,192,192, pixel 2.18, shown at level 0.197, step 1, values float32
+> close #226
+> volume #229 level 1.053
+> volume #229 level 1
+> volume #229 level 0.9
+> volume #229 level 0.8
+> show #!228 models
+> show #!227 models
+> hide #!227 models
+> show #!225 models
+> hide #!229 models
+> show #!229 models
+> hide #!228 models
+> hide #!229 models
+> show #!229 models
+> volume #225 level 1.9
+> volume #225 level 1.8
+> hide #!229 models
+> show #!229 models
+> volume #225 level 1.6
+> show #!211 models
+> hide #!211 models
+> show #!211 models
+> hide #!211 models
+> show #!198 models
+> hide #!198 models
+> show #!197 models
+> hide #!197 models
+> show #!191 models
+> hide #!191 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J842_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #226, grid size
+,588,588, pixel 0.95, shown at level 0.15, step 4, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J845_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #230, grid size
+,588,588, pixel 0.95, shown at level 0.142, step 4, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J846_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #231, grid size
+,588,588, pixel 0.95, shown at level 0.14, step 4, values float32
+> hide #!225 models
+> volume #226 level 0.2956
+> volume #226 step 1
+> volume #226 level 0.334
+> show #!230 models
+> hide #!226 models
+> volume #226 level 0.33
+> show #!226 models
+> hide #!230 models
+> hide #!226 models
+> show #!230 models
+> volume #230 step 1
+> volume #230 level 0.33
+> show #!226 models
+> hide #!226 models
+> show #!226 models
+> hide #!226 models
+> show #!226 models
+> hide #!226 models
+> show #!226 models
+> hide #!226 models
+> show #!226 models
+> hide #!226 models
+> show #!226 models
+> hide #!226 models
+> volume #230 level 0.32
+> volume #230 level 0.3
+> show #!226 models
+> hide #!226 models
+> show #!226 models
+> hide #!226 models
+> show #!231 models
+> hide #!230 models
+> volume #231 step 2
+> volume #231 step 1
+> volume #231 level 0.3
+> show #!191 models
+> hide #!191 models
+> show #!190 models
+> show #!191 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!198 models
+> hide #!191 models
+> show #!191 models
+> hide #!198 models
+> hide #!191 models
+> open 1ID3 fromDatabase pdb format mmcif
+id3 title:
+Crystal structure of the yeast nucleosome core particle reveals fundamental
+differences In inter-nucleosome interactions [more info...]
+Chain information for 1id3 #232
+---
+Chain | Description | UniProt
+A E | HISTONE H3 | H3_YEAST 1-135
+B F | HISTONE H4 | H4_YEAST 1-102
+C G | HISTONE H2A.1 | H2A1_YEAST 1-131
+D H | HISTONE H2B.2 | H2B2_YEAST 1-130
+I J | PALINDROMIC 146BP DNA FRAGMENT |
+Non-standard residues in 1id3 #232
+---
+MN \u2014 manganese (II) ion
+> hide #!232 models
+> show #!232 models
+> select add #232
+atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
+> view sel
+> select subtract #232
+Nothing selected
+> show #!228 models
+> hide #!228 models
+> show #!225 models
+> hide #!225 models
+> lighting simple
+> show #!229 models
+> hide #!229 models
+> show #!225 models
+> show #!228 models
+> hide #!225 models
+> show #!225 models
+> hide #!225 models
+> show #!225 models
+> hide #!225 models
+> show #!225 models
+> hide #!225 models
+> show #!225 models
+> hide #!225 models
+> show #!225 models
+> hide #!225 models
+> show #!225 models
+> hide #!225 models
+> show #!225 models
+> hide #!228 models
+> select add #232
+atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
+> ui mousemode right "rotate selected models"
+> ui mousemode right "translate selected models"
+> view matrix models #232,1,0,0,194.77,0,1,0,198.7,0,0,1,241.66
+> select add #225
+atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 7 models selected
+> view sel
+> select subtract #225
+atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #232,0.45362,0.62002,-0.64016,176.82,-0.86856,0.46844,-0.16176,188.02,0.19958,0.62939,0.75102,238.14
+> view matrix models
+> #232,0.73516,0.67582,-0.053002,205.68,-0.43197,0.40677,-0.80495,150.64,-0.52244,0.61466,0.59097,235.27
+> view matrix models
+> #232,0.74922,0.65491,0.098772,212.99,-0.3682,0.53581,-0.75982,154.67,-0.55054,0.53291,0.64258,236.74
+> view matrix models
+> #232,0.63725,0.62725,-0.44773,185.38,-0.56763,-0.01092,-0.82321,143.6,-0.52125,0.77874,0.34909,225.69
+> ui mousemode right "translate selected models"
+> view matrix models
+> #232,0.63725,0.62725,-0.44773,108.34,-0.56763,-0.01092,-0.82321,126.58,-0.52125,0.77874,0.34909,223.48
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #232,0.69009,0.70479,0.16445,140.62,-0.26062,0.454,-0.85204,130.7,-0.67517,0.54512,0.49698,228.24
+> view matrix models
+> #232,0.021212,0.98524,0.16984,150.87,-0.50552,0.15714,-0.84839,127.69,-0.86256,-0.067863,0.50139,219.42
+> view matrix models
+> #232,0.026211,0.99233,-0.12082,136.06,-0.53573,-0.088094,-0.83978,124.17,-0.84398,0.086736,0.52931,223.35
+> view matrix models
+> #232,0.0051654,0.11484,-0.99337,76.495,-0.63253,-0.76903,-0.092196,151.55,-0.77452,0.62881,0.068669,208.5
+> view matrix models
+> #232,0.026817,-0.97752,0.20912,119.22,-0.36995,0.18463,0.91052,217.22,-0.92866,-0.10178,-0.35669,175.39
+> view matrix models
+> #232,-0.0985,-0.93943,0.32829,126.94,0.94539,0.014666,0.32562,174.18,-0.31071,0.34244,0.88668,241.92
+> view matrix models
+> #232,0.23695,-0.92136,0.30814,123.63,0.84083,0.035592,-0.54013,130.99,0.48669,0.38708,0.78314,231.21
+> view matrix models
+> #232,0.37181,-0.91507,0.15625,114.91,0.42362,0.017477,-0.90567,115.18,0.82602,0.40293,0.39414,208.93
+> view matrix models
+> #232,0.30529,-0.94633,-0.10613,101.45,0.56154,0.26891,-0.78253,124.73,0.76907,0.1793,0.6135,216.78
+> view matrix models
+> #232,0.059237,0.85249,0.51938,166.21,0.47573,-0.48152,0.73609,190.34,0.8776,0.20348,-0.43407,162.69
+> view matrix models
+> #232,0.24626,-0.51664,-0.82003,72.694,0.61898,0.73489,-0.27712,158.16,0.7458,-0.43934,0.50076,200.59
+> view matrix models
+> #232,-0.067706,-0.98402,0.16471,117.56,0.51804,-0.17576,-0.83711,114.66,0.85268,0.028649,0.52165,208.85
+> volume flip #225
+Opened cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip as #233, grid
+size 128,128,128, pixel 3.27, shown at step 1, values float32
+> view matrix models
+> #232,-0.086674,-0.98325,0.16032,117.49,0.60367,-0.17985,-0.77669,117.02,0.79251,0.02946,0.60914,213.81
+> view matrix models
+> #232,-0.20892,-0.97186,0.10878,115.99,0.81932,-0.11321,0.56205,185.07,-0.53392,0.20655,0.81992,237.89
+> view matrix models
+> #232,-0.0034667,-0.99986,-0.016272,107.52,0.52919,-0.015641,0.84836,203.66,-0.8485,-0.0056699,0.52917,221.79
+> view matrix models
+> #232,0.10405,-0.99333,-0.049687,105.09,0.51074,0.010501,0.85967,204.82,-0.85341,-0.11483,0.50843,218.9
+> view matrix models
+> #232,0.155,-0.97565,0.1552,115.49,0.4679,0.21087,0.85826,208.52,-0.87008,-0.060414,0.48919,218.98
+> view matrix models
+> #232,0.045605,-0.97983,0.19456,118.28,0.53868,0.18814,0.82123,205.68,-0.84127,0.067353,0.5364,223.36
+> ui mousemode right "translate selected models"
+> view matrix models
+> #232,0.045605,-0.97983,0.19456,194.24,0.53868,0.18814,0.82123,258.89,-0.84127,0.067353,0.5364,231.26
+> view matrix models
+> #232,0.045605,-0.97983,0.19456,195.08,0.53868,0.18814,0.82123,259.08,-0.84127,0.067353,0.5364,236.86
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #232,-0.039543,-0.99451,0.096893,190.48,-0.23842,0.10356,0.96562,271.04,-0.97036,0.015082,-0.24121,197.13
+> view matrix models
+> #232,-0.078672,-0.98952,0.12105,192.1,-0.5971,0.14401,0.78913,265.46,-0.7983,-0.010198,-0.60217,176.87
+> view matrix models
+> #232,-0.14713,-0.98779,0.051262,189.09,-0.8147,0.15042,0.56004,255.52,-0.56091,0.040637,-0.82688,164.4
+> select subtract #232
+Nothing selected
+> ui tool show "Fit in Map"
+> fitmap #232 inMap #233
+Fit molecule 1id3 (#232) to map
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 12124
+atoms
+average map value = 1.802, steps = 72
+shifted from previous position = 12.2
+rotated from previous position = 11.2 degrees
+atoms outside contour = 5403, contour level = 1.6
+Position of 1id3 (#232) relative to
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
+Matrix rotation and translation
+-0.03585182 -0.99591182 0.08291139 194.40297797
+-0.72260858 0.08314376 0.68623899 250.19258695
+-0.69032709 -0.03530956 -0.72263528 174.98991176
+Axis -0.66054809 0.70786809 0.25019790
+Axis point 245.81431621 -0.00000000 -10.35559013
+Rotation angle (degrees) 146.89506394
+Shift along axis 92.47294040
+> volume #233 level 1.5
+> volume #233 level 1.4
+> ui mousemode right "translate selected models"
+> select add #232
+atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
+> view matrix models
+> #232,-0.035852,-0.99591,0.082911,187.84,-0.72261,0.083144,0.68624,334.95,-0.69033,-0.03531,-0.72264,195.33
+> lighting soft
+> view matrix models
+> #232,-0.035852,-0.99591,0.082911,189.25,-0.72261,0.083144,0.68624,329.81,-0.69033,-0.03531,-0.72264,193.67
+> lighting simple
+> view matrix models
+> #232,-0.035852,-0.99591,0.082911,207.89,-0.72261,0.083144,0.68624,254.31,-0.69033,-0.03531,-0.72264,174.46
+> view matrix models
+> #232,-0.035852,-0.99591,0.082911,196.79,-0.72261,0.083144,0.68624,255.92,-0.69033,-0.03531,-0.72264,174.52
+> fitmap #232 inMap #233
+Fit molecule 1id3 (#232) to map
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 12124
+atoms
+average map value = 1.802, steps = 52
+shifted from previous position = 6.21
+rotated from previous position = 0.0558 degrees
+atoms outside contour = 4425, contour level = 1.4
+Position of 1id3 (#232) relative to
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
+Matrix rotation and translation
+-0.03529330 -0.99599473 0.08215154 194.42252609
+-0.72248530 0.08222358 0.68647963 250.18011940
+-0.69048489 -0.03512516 -0.72249349 174.98679362
+Axis -0.66080361 0.70753542 0.25046400
+Axis point 245.92146757 -0.00000000 -10.42218197
+Rotation angle (degrees) 146.90659877
+Shift along axis 92.36408147
+> fitmap #232 inMap #233
+Fit molecule 1id3 (#232) to map
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 12124
+atoms
+average map value = 1.802, steps = 48
+shifted from previous position = 0.0262
+rotated from previous position = 0.0179 degrees
+atoms outside contour = 4427, contour level = 1.4
+Position of 1id3 (#232) relative to
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
+Matrix rotation and translation
+-0.03522647 -0.99601286 0.08196018 194.43601851
+-0.72265585 0.08203483 0.68632267 250.16027535
+-0.69030980 -0.03505228 -0.72266432 174.97347823
+Axis -0.66086507 0.70749095 0.25042747
+Axis point 245.92434501 0.00000000 -10.39497167
+Rotation angle (degrees) 146.92196206
+Shift along axis 92.30832410
+> select subtract #232
+Nothing selected
+> hide #!232 atoms
+> show #!232 cartoons
+> hide #!233 models
+> show #!233 models
+> fitmap #232 inMap #233
+Fit molecule 1id3 (#232) to map
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 12124
+atoms
+average map value = 1.802, steps = 44
+shifted from previous position = 0.00249
+rotated from previous position = 0.0128 degrees
+atoms outside contour = 4428, contour level = 1.4
+Position of 1id3 (#232) relative to
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
+Matrix rotation and translation
+-0.03534401 -0.99599682 0.08210439 194.44302789
+-0.72273427 0.08221501 0.68621853 250.15752046
+-0.69022169 -0.03508594 -0.72274684 174.96686637
+Axis -0.66081898 0.70756214 0.25034793
+Axis point 245.90230259 0.00000000 -10.37331191
+Rotation angle (degrees) 146.92300591
+Shift along axis 92.31293996
+> fitmap #232 inMap #233
+Fit molecule 1id3 (#232) to map
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 12124
+atoms
+average map value = 1.802, steps = 48
+shifted from previous position = 0.0672
+rotated from previous position = 0.0319 degrees
+atoms outside contour = 4424, contour level = 1.4
+Position of 1id3 (#232) relative to
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
+Matrix rotation and translation
+-0.03562336 -0.99595084 0.08254033 194.40523233
+-0.72285407 0.08271076 0.68603274 250.17963983
+-0.69008186 -0.03522582 -0.72287355 174.97000524
+Axis -0.66069357 0.70774412 0.25016449
+Axis point 245.83818539 0.00000000 -10.32676146
+Rotation angle (degrees) 146.91829753
+Shift along axis 92.39216339
+> volume #233 color #b2b2b2db
+> volume #233 color #b2b2b2b0
+> volume #233 color #b2b2b29a
+> volume #233 color #b2b2b299
+> volume #233 color #b2b2b2b2
+> volume #233 color #b2b2b2cc
+> combine #232
+> hide #!232 models
+> hide #!234 models
+> show #!234 models
+> select #234/I
+atoms, 3354 bonds, 3 pseudobonds, 162 residues, 2 models selected
+> delete atoms (#!234 & sel)
+> delete bonds (#!234 & sel)
+> select #234/J
+atoms, 3354 bonds, 6 pseudobonds, 160 residues, 2 models selected
+> delete atoms (#!234 & sel)
+> delete bonds (#!234 & sel)
+> hide #!233 models
+> show #!233 models
+> fitmap #234 inMap #233
+Fit molecule copy of 1id3 (#234) to map
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) using 6114
+atoms
+average map value = 1.618, steps = 48
+shifted from previous position = 0.869
+rotated from previous position = 6.47 degrees
+atoms outside contour = 2277, contour level = 1.4
+Position of copy of 1id3 (#234) relative to
+cryosparc_P17_J984_class_00_00062_volume_sharp.mrc z flip (#233) coordinates:
+Matrix rotation and translation
+-0.05927763 -0.99809265 0.01724050 190.79692871
+-0.66015313 0.05215041 0.74931847 251.66034038
+-0.74878836 0.03303645 -0.66198534 180.19394497
+Axis -0.65007489 0.69522355 0.30670320
+Axis point 244.94027053 -0.00000000 -21.53118005
+Rotation angle (degrees) 146.56966321
+Shift along axis 106.19396109
+> volume #233 color #b2b2b280
+> volume #233 color #b2b2b29a
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!234 models
+> hide #!233 models
+> show #!233 models
+> hide #!232 models
+> hide #!233 models
+> show #!129 models
+> select add #129
+models selected
+> view clip false
+> select subtract #129
+Nothing selected
+> show #!130 models
+> show #!227 models
+> hide #!227 models
+> show #!227 models
+> hide #!227 models
+> show #!227 models
+> hide #!227 models
+> volume flip #227
+Opened cryosparc_P17_J888_009_volume_map.mrc z flip as #235, grid size
+,294,294, pixel 1.9, shown at step 1, values float32
+> select add #235
+models selected
+> ui mousemode right "move picked models"
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #235,0.84663,0.46913,0.25127,-169.59,0.42608,-0.88042,0.20812,364.8,0.31886,-0.069133,-0.94528,519.57
+> view matrix models
+> #235,-0.53578,-0.80769,-0.24613,731.78,-0.84162,0.48737,0.23271,310.31,-0.067998,0.33183,-0.94089,508.65
+> view matrix models
+> #235,-0.9965,-0.022294,-0.080596,581.12,-0.043426,0.96162,0.27092,-58.716,0.071463,0.27347,-0.95922,492.67
+> ui mousemode right "translate selected models"
+> view matrix models
+> #235,-0.9965,-0.022294,-0.080596,577.57,-0.043426,0.96162,0.27092,-52.189,0.071463,0.27347,-0.95922,460.39
+> volume #235 step 2
+> select subtract #235
+Nothing selected
+> fitmap #235 inMap #130
+Fit map cryosparc_P17_J888_009_volume_map.mrc z flip in map
+Cl3D_j591_run_it025_class002.mrc using 31742 points
+correlation = 0.9449, correlation about mean = 0.3834, overlap = 384.9
+steps = 216, shift = 20, angle = 24.3 degrees
+Position of cryosparc_P17_J888_009_volume_map.mrc z flip (#235) relative to
+Cl3D_j591_run_it025_class002.mrc (#130) coordinates:
+Matrix rotation and translation
+-0.97670485 -0.09877980 -0.19049983 628.35061820
+-0.19630370 0.76986862 0.60726203 -34.18266636
+.08667462 0.63051159 -0.77132526 290.90888037
+Axis 0.07887912 -0.94037367 -0.33087073
+Axis point 301.47094386 0.00000000 176.26702948
+Rotation angle (degrees) 171.52518698
+Shift along axis -14.54501139
+> hide #!130 models
+> show #!130 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> hide #!130 models
+> show #!98 models
+> show #!99 models
+> show #!219 models
+> hide #!219 models
+> volume flip #219
+Opened cryosparc_P17_J884_009_volume_map.mrc z flip as #236, grid size
+,294,294, pixel 1.9, shown at step 1, values float32
+> select add #236
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,-0.14,0.86518,0.48153,-32.729,-0.98201,-0.059076,-0.17936,602.39,-0.12673,-0.49797,0.85788,204
+> view matrix models
+> #236,-0.95021,0.22201,0.21868,433.84,-0.29489,-0.86749,-0.40063,679.42,0.10076,-0.44517,0.88976,117.62
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,-0.95021,0.22201,0.21868,442.55,-0.29489,-0.86749,-0.40063,714.68,0.10076,-0.44517,0.88976,125.94
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,-0.96826,0.24636,0.042262,487.62,-0.23836,-0.85916,-0.4528,710.28,-0.07524,-0.4485,0.89061,176.2
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,-0.96826,0.24636,0.042262,471.31,-0.23836,-0.85916,-0.4528,704.57,-0.07524,-0.4485,0.89061,178.79
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> select clear
+> fitmap #236 inMap #98
+Fit map cryosparc_P17_J884_009_volume_map.mrc z flip in map
+Cl3D_j581_run_it025_class001.mrc using 185363 points
+correlation = 0.8766, correlation about mean = 0.02403, overlap = 2112
+steps = 192, shift = 22.6, angle = 21.2 degrees
+Position of cryosparc_P17_J884_009_volume_map.mrc z flip (#236) relative to
+Cl3D_j581_run_it025_class001.mrc (#98) coordinates:
+Matrix rotation and translation
+-0.84354066 0.50422936 0.18491053 314.97189258
+-0.50932699 -0.64184531 -0.57325441 772.53341394
+-0.17036775 -0.57774333 0.79824024 267.14568387
+Axis -0.00417951 0.33079007 -0.94369511
+Axis point 276.01471701 384.47498501 0.00000000
+Rotation angle (degrees) 147.51935105
+Shift along axis 2.12587651
+> hide #!98 models
+> hide #!99 models
+> volume flip #236
+Opened cryosparc_P17_J884_009_volume_map.mrc z flip z flip as #237, grid size
+,294,294, pixel 1.9, shown at step 1, values float32
+> close #236
+> show #!98 models
+> show #!99 models
+> select add #237
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #237,0.96723,0.12731,-0.21969,22.54,0.15273,-0.9829,0.10285,476.95,-0.20284,-0.13303,-0.97013,678.92
+> view matrix models
+> #237,0.98911,0.12697,-0.074375,-26.233,0.1345,-0.98512,0.10698,481.46,-0.059685,-0.11582,-0.99148,640.32
+> view matrix models
+> #237,0.99344,0.076053,-0.08539,-10.83,0.10378,-0.91318,0.39411,386.84,-0.048004,-0.40039,-0.91509,689.4
+> ui mousemode right "translate selected models"
+> view matrix models
+> #237,0.99344,0.076053,-0.08539,-17.742,0.10378,-0.91318,0.39411,419.91,-0.048004,-0.40039,-0.91509,662.61
+> view matrix models
+> #237,0.99344,0.076053,-0.08539,-17.954,0.10378,-0.91318,0.39411,412.57,-0.048004,-0.40039,-0.91509,657.54
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #237,0.99498,0.052431,-0.085289,-12.206,0.089013,-0.85322,0.5139,365.78,-0.045827,-0.51891,-0.8536,670.02
+> ui mousemode right "translate selected models"
+> view matrix models
+> #237,0.99498,0.052431,-0.085289,4.4691,0.089013,-0.85322,0.5139,363.94,-0.045827,-0.51891,-0.8536,680.57
+> select subtract #237
+Nothing selected
+> fitmap #237 inMap #98
+Fit map cryosparc_P17_J884_009_volume_map.mrc z flip z flip in map
+Cl3D_j581_run_it025_class001.mrc using 185363 points
+correlation = 0.9464, correlation about mean = 0.3043, overlap = 2607
+steps = 148, shift = 5.24, angle = 12.2 degrees
+Position of cryosparc_P17_J884_009_volume_map.mrc z flip z flip (#237)
+relative to Cl3D_j581_run_it025_class001.mrc (#98) coordinates:
+Matrix rotation and translation
+.95506772 0.17454310 -0.23954199 25.26355402
+.28049806 -0.79336127 0.54027653 283.68421592
+-0.09574180 -0.58319174 -0.80667274 694.76834568
+Axis -0.98759585 -0.12640897 0.09314076
+Axis point 0.00000000 249.94675701 303.67322404
+Rotation angle (degrees) 145.33414419
+Shift along axis 3.90083895
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> hide #!99 models
+> volume #237 step 2
+> volume #237 level 0.3935
+> volume #237 level 0.3609
+> volume #237 level 0.3342
+> show #!98 models
+> show #!97 models
+> hide #!97 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> hide #!98 models
+> show #!98 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> hide #!99 models
+> show #!129 models
+> show #!130 models
+> hide #!129 models
+> hide #!130 models
+> show #!173 models
+> show #!205 models
+> hide #!173 models
+> ui mousemode right zoom
+> lighting soft
+> show #!204 models
+> hide #!205 models
+> show #!205 models
+> hide #!204 models
+> show #!204 models
+> show #!206 models
+> hide #!205 models
+> hide #!206 models
+> hide #!204 models
+> show #!204 models
+> show #!205 models
+> hide #!204 models
+> hide #!205 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> show #!228 models
+> hide #!228 models
+> show #!225 models
+> hide #!225 models
+> show #!233 models
+> show #!232 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> hide #!233 models
+> hide #!232 models
+> show #!225 models
+> show #!233 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> color #233 #b2b2b2b7 models
+> color #233 #b2b2b2c0 models
+> color #233 #b2b2b2c6 models
+> color #233 #b2b2b2ca models
+> color #233 #b2b2b2cb models
+> color #233 #b2b2b2cc models
+> color #233 #b2b2b2ff models
+> color #233 #b2b2b2f3 models
+> color #233 #b2b2b2ff models
+> color #233 #b2b2b2ee models
+> color #233 #b2b2b2a5 models
+> color #233 #b2b2b2ff models
+> color #233 #b2b2b283 models
+> color #233 #b2b2b298 models
+> color #233 #b2b2b2ff models
+[Repeated 2 time(s)]
+> color #233 #b2b2b216 models
+> color #233 #b2b2b22a models
+> color #233 #b2b2b268 models
+> color #233 #b2b2b24e models
+> color #233 #b2b2b27c models
+> color #233 #b2b2b236 models
+> color #233 #b2b2b280 models
+> color #233 #b2b2b2ff models
+> hide #!233 models
+> show #!233 models
+> select #234/A
+atoms, 813 bonds, 102 residues, 1 model selected
+> volume flip #236sel #234/A,E
+Missing or invalid "volumes" argument: only initial part "#236" of atom
+specifier valid
+> select #234/A,E
+atoms, 1626 bonds, 205 residues, 1 model selected
+> color sel orange
+> select #234/B,F
+atoms, 1326 bonds, 173 residues, 1 model selected
+> color sel orange red
+> select clear
+> show #!233 models
+> hide #!237 models
+> color #233 #b2b2b272 models
+> color #233 #b2b2b27c models
+> show #!179 models
+> hide #!179 models
+> show #!178 models
+> hide #!178 models
+> show #!179 models
+> hide #!179 models
+> combine #179
+No structures specified
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J544_007_volume_map_zflip.mrc
+Opened cryosparc_P17_J544_007_volume_map_zflip.mrc as #236, grid size
+,588,588, pixel 0.95, shown at level 0.158, step 4, values float32
+> select add #236
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,-0.012453,0.9963,-0.085041,38.532,-0.99954,-0.014744,-0.026367,562,-0.027524,0.084674,0.99603,-14.052
+> view matrix models
+> #236,0.059878,0.99536,-0.075321,15.571,-0.99446,0.066013,0.081795,504.47,0.086388,0.070006,0.9938,-41.09
+> view matrix models
+> #236,0.76783,0.50486,-0.39441,52.38,-0.29922,0.82696,0.47602,-20.228,0.56648,-0.24749,0.78603,-22.96
+> lighting simple
+> view matrix models
+> #236,-0.88103,0.27074,-0.38793,573.03,-0.025569,0.79159,0.61052,-129.36,0.47237,0.5478,-0.69049,254.3
+> view matrix models
+> #236,-0.16658,-0.56618,-0.80728,733.71,-0.98446,0.049393,0.16849,478.79,-0.055524,0.8228,-0.56561,287.22
+> view matrix models
+> #236,0.4492,-0.45163,-0.77088,519.64,-0.80916,-0.57146,-0.13671,694.91,-0.37879,0.68517,-0.62214,432.45
+> view matrix models
+> #236,0.65993,-0.46974,-0.58638,407.54,-0.74905,-0.47202,-0.46488,754.94,-0.058416,0.74602,-0.66336,339.76
+> view matrix models
+> #236,0.53079,-0.4452,-0.72115,479.45,-0.83669,-0.41075,-0.36226,730.28,-0.13493,0.79566,-0.59052,324.57
+> view matrix models
+> #236,0.35401,-0.88851,0.29195,328.65,-0.68389,-0.033001,0.72884,240.28,-0.63794,-0.45768,-0.61932,813.79
+> view matrix models
+> #236,0.42906,-0.90235,0.040822,390.9,-0.42585,-0.16222,0.89013,152.48,-0.79659,-0.3993,-0.45387,789.83
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.42906,-0.90235,0.040822,224.14,-0.42585,-0.16222,0.89013,22.814,-0.79659,-0.3993,-0.45387,720.65
+> view matrix models
+> #236,0.42906,-0.90235,0.040822,264.42,-0.42585,-0.16222,0.89013,-12.91,-0.79659,-0.3993,-0.45387,709.48
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,0.35817,-0.93201,-0.055435,322.64,-0.41443,-0.21191,0.88507,-1.0118,-0.83664,-0.29403,-0.46215,694.69
+> view matrix models
+> #236,0.67931,-0.62117,-0.39075,254.89,-0.16273,-0.64672,0.74516,91.098,-0.71558,-0.44261,-0.54041,726.03
+> view matrix models
+> #236,0.71295,-0.55192,-0.43253,239.94,-0.10993,-0.69717,0.70842,101.7,-0.69254,-0.45753,-0.55772,729.13
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.71295,-0.55192,-0.43253,297.54,-0.10993,-0.69717,0.70842,100.6,-0.69254,-0.45753,-0.55772,732.73
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,0.68046,-0.63817,-0.36017,307.11,0.13892,-0.37025,0.91849,-123.81,-0.7195,-0.67503,-0.16328,674.54
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.68046,-0.63817,-0.36017,294.76,0.13892,-0.37025,0.91849,-125.98,-0.7195,-0.67503,-0.16328,621.96
+> view matrix models
+> #236,0.68046,-0.63817,-0.36017,302.19,0.13892,-0.37025,0.91849,-125.89,-0.7195,-0.67503,-0.16328,622.96
+> view matrix models
+> #236,0.68046,-0.63817,-0.36017,303.09,0.13892,-0.37025,0.91849,-124.21,-0.7195,-0.67503,-0.16328,623.52
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,0.68673,-0.57216,-0.44837,311.32,0.2108,-0.43355,0.87613,-113.66,-0.69568,-0.69618,-0.17711,627
+> view matrix models
+> #236,0.6869,-0.56458,-0.45762,312.14,0.21863,-0.43999,0.87099,-112.46,-0.69308,-0.69833,-0.1788,627.39
+> view matrix models
+> #236,0.68383,-0.61388,-0.39437,306.37,0.16624,-0.39519,0.90343,-120.29,-0.71045,-0.68336,-0.16819,624.81
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.68383,-0.61388,-0.39437,314.45,0.16624,-0.39519,0.90343,-114.46,-0.71045,-0.68336,-0.16819,626.72
+> view matrix models
+> #236,0.68383,-0.61388,-0.39437,313.59,0.16624,-0.39519,0.90343,-113.76,-0.71045,-0.68336,-0.16819,626.96
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,0.68659,-0.57615,-0.44344,318.1,0.20666,-0.4301,0.87881,-107.76,-0.69705,-0.69503,-0.17624,628.94
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.68659,-0.57615,-0.44344,327.07,0.20666,-0.4301,0.87881,-108.47,-0.69705,-0.69503,-0.17624,628.68
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,0.63818,-0.60887,-0.47118,358.2,0.24341,-0.42105,0.87377,-119.57,-0.7304,-0.67231,-0.1205,614.18
+> view matrix models
+> #236,0.63577,-0.5548,-0.53665,364.9,0.29495,-0.46787,0.83313,-108.37,-0.7133,-0.68796,-0.13382,617.88
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.63577,-0.5548,-0.53665,372.36,0.29495,-0.46787,0.83313,-107.39,-0.7133,-0.68796,-0.13382,618.18
+> hide #!234 models
+> hide #!233 models
+> show #!233 models
+> color #233 #b2b2b2ff models
+> select subtract #236
+Nothing selected
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> volume #236 step 1
+> volume #236 level 0.1732
+> volume #236 color #009193
+[Repeated 1 time(s)]
+> select add #236
+models selected
+> view matrix models
+> #236,0.63577,-0.5548,-0.53665,371.67,0.29495,-0.46787,0.83313,-109.23,-0.7133,-0.68796,-0.13382,606.22
+> hide #!236 models
+> show #!236 models
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,0.64925,-0.56021,-0.51443,362.37,0.19972,-0.52706,0.82603,-64.458,-0.73388,-0.63904,-0.23031,629.16
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.64925,-0.56021,-0.51443,360.82,0.19972,-0.52706,0.82603,-64.722,-0.73388,-0.63904,-0.23031,636.2
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,0.65709,-0.56493,-0.49909,355.08,0.13448,-0.56361,0.81502,-33.193,-0.74172,-0.60266,-0.29436,648.75
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.65709,-0.56493,-0.49909,353.84,0.13448,-0.56361,0.81502,-29.68,-0.74172,-0.60266,-0.29436,652.83
+> select subtract #236
+Nothing selected
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> ui mousemode right "rotate selected models"
+> select add #236
+models selected
+> view matrix models
+> #236,0.66843,-0.53922,-0.5123,347.9,0.2468,-0.48895,0.83667,-87.981,-0.70163,-0.68569,-0.19375,632.36
+> select subtract #236
+Nothing selected
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!236 models
+> show #!236 models
+> select add #236
+models selected
+> view matrix models
+> #236,0.6648,-0.54898,-0.50663,349.76,0.17003,-0.54919,0.81822,-44.49,-0.72742,-0.63009,-0.27176,649.12
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.6648,-0.54898,-0.50663,348.92,0.17003,-0.54919,0.81822,-46.742,-0.72742,-0.63009,-0.27176,656.36
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,0.66754,-0.54182,-0.5107,347.51,0.22647,-0.50565,0.83248,-78.738,-0.70929,-0.67138,-0.21483,644.51
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.66754,-0.54182,-0.5107,347.63,0.22647,-0.50565,0.83248,-82.762,-0.70929,-0.67138,-0.21483,639.69
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,0.67038,-0.53268,-0.51657,346.22,0.29731,-0.44502,0.84473,-122.74,-0.67985,-0.71987,-0.13996,620.98
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.67038,-0.53268,-0.51657,347.56,0.29731,-0.44502,0.84473,-116.97,-0.67985,-0.71987,-0.13996,611.3
+> select subtract #236
+Nothing selected
+> select add #236
+models selected
+> view matrix models
+> #236,0.67038,-0.53268,-0.51657,347.92,0.29731,-0.44502,0.84473,-119.74,-0.67985,-0.71987,-0.13996,610.38
+> select subtract #236
+Nothing selected
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> select add #236
+models selected
+> view matrix models
+> #236,0.67038,-0.53268,-0.51657,348.46,0.29731,-0.44502,0.84473,-117.4,-0.67985,-0.71987,-0.13996,603.72
+> select subtract #236
+Nothing selected
+> hide #!233 models
+> show #!233 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> ui mousemode right "rotate selected models"
+> select add #236
+models selected
+> view matrix models
+> #236,0.66305,-0.53587,-0.5227,353.3,0.32847,-0.41917,0.84641,-133.6,-0.67266,-0.7329,-0.10191,593.24
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.66305,-0.53587,-0.5227,353.67,0.32847,-0.41917,0.84641,-133.02,-0.67266,-0.7329,-0.10191,590.06
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #236,0.68404,-0.53709,-0.49359,338.97,0.31215,-0.39604,0.86355,-140.12,-0.65928,-0.74477,-0.10325,589.96
+> view matrix models
+> #236,0.68758,-0.51714,-0.50971,337.68,0.32634,-0.40699,0.85315,-137.85,-0.64864,-0.75294,-0.11107,591.67
+> view matrix models
+> #236,0.68393,-0.51897,-0.51275,340.15,0.34156,-0.39327,0.85363,-145.94,-0.64466,-0.75895,-0.091709,586.07
+> hide #!233 models
+> show #!233 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> select subtract #236
+Nothing selected
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!233 models
+> show #!233 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!236 models
+> show #!236 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!236 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> show #!235 models
+> hide #!235 models
+> ui tool show Matchmaker
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> hide #!232 models
+> show #!234 models
+> select #234/C,G
+atoms, 1700 bonds, 2 pseudobonds, 231 residues, 2 models selected
+> color (#!234 & sel) light gray
+> select clear
+> select #234/D,H
+atoms, 1494 bonds, 1 pseudobond, 203 residues, 2 models selected
+> color (#!234 & sel) dim gray
+> select clear
+> show #!236 models
+> hide #!236 models
+> show #!233 models
+> hide #!233 models
+> show #!235 models
+> hide #!235 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> color #233 #b2b2b2cb models
+> color #233 #b2b2b2be models
+> color #233 #b2b2b2c0 models
+> color #233 #b2b2b2bf models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> lighting soft
+[Repeated 1 time(s)]
+> lighting full
+> lighting simple
+> lighting full
+[Repeated 1 time(s)]
+> lighting soft
+> lighting full
+[Repeated 6 time(s)]
+> color #233 #b2b2b2ed models
+> color #233 #b2b2b2ff models
+> lighting soft
+> show #!236 models
+> select add #236
+models selected
+> ui mousemode right "translate selected models"
+> view matrix models
+> #236,0.68393,-0.51897,-0.51275,340.34,0.34156,-0.39327,0.85363,-144.79,-0.64466,-0.75895,-0.091709,589.32
+> select subtract #236
+Nothing selected
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!234 models
+> show #!234 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!234 models
+> show #!234 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> ui mousemode right zoom
+> hide #!233 models
+> hide #!236 models
+> show #!98 models
+> show #!99 models
+> show #!129 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!130 models
+> show #!130 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> hide #!99 models
+> hide #!129 models
+> hide #!130 models
+> show #!98 models
+> show #!99 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!130 models
+> hide #!130 models
+> show #!129 models
+> hide #!129 models
+> show #!130 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> hide #!98 models
+> hide #!99 models
+> show #!173 models
+> volume flip #173
+Opened cryosparc_P17_J858_007_volume_map.mrc z flip as #238, grid size
+,588,588, pixel 0.95, shown at step 1, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J864_007_volume_map.mrc
+Opened cryosparc_P17_J864_007_volume_map.mrc as #239, grid size 588,588,588,
+pixel 0.95, shown at level 0.153, step 4, values float32
+> volume #239 step 1
+> show #!173 models
+Error processing trigger "graphics update":
+You deleted or moved a volume file that is still open in ChimeraX.
+/Users/cvetkom/Downloads/cryosparc_P17_J858_007_volume_map.mrc
+To allow fast initial display of volume data ChimeraX does not read all data
+from the file when it is first opened, and will later read more data when
+needed. ChimeraX got an error trying to read the above file.
+> hide #!173 models
+> show #!173 models
+> hide #!173 models
+> show #!173 models
+> hide #!173 models
+> show #!173 models
+> hide #!173 models
+> volume flip #239
+Opened cryosparc_P17_J864_007_volume_map.mrc z flip as #240, grid size
+,588,588, pixel 0.95, shown at step 1, values float32
+> hide #!240 models
+> show #!240 models
+> show #!239 models
+> hide #!239 models
+> hide #!240 models
+> show #!240 models
+> close #238
+> volume #240 level 0.1562
+> hide #!240 models
+> show #!240 models
+> select add #240
+models selected
+> select subtract #240
+Nothing selected
+> view #240 clip false
+No displayed objects specified.
+> show #!237 models
+> hide #!237 models
+> close #237
+> hide #!240 models
+> show #!240 models
+> close #240
+> show #!239 models
+> volume flip #239
+Opened cryosparc_P17_J864_007_volume_map.mrc z flip as #237, grid size
+,588,588, pixel 0.95, shown at step 1, values float32
+> hide #!237 models
+> show #!237 models
+> show #!233 models
+> hide #!233 models
+> hide #!237 models
+> show #!237 models
+> close #237
+> show #!233 models
+> save
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc
+> models #233
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!235 models
+> show #!236 models
+> show #!234 models
+> hide #!234 models
+> show #!233 models
+> hide #!233 models
+> hide #!235 models
+> hide #!236 models
+> show #!235 models
+> hide #!235 models
+> show #!235 models
+> close #235
+> volume flip #239
+Opened cryosparc_P17_J864_007_volume_map.mrc z flip as #235, grid size
+,588,588, pixel 0.95, shown at step 1, values float32
+> hide #!235 models
+> show #!235 models
+> close #235
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
+\u2014\u2014\u2014 End of log from Thu Jul 18 17:16:17 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> show #!236 models
+> hide #!236 models
+> show #!233 models
+> show #!236 models
+> hide #!236 models
+> hide #!233 models
+> show #!239 models
+> lighting simple
+> volume flip #239
+Opened cryosparc_P17_J864_007_volume_map.mrc z flip as #235, grid size
+,588,588, pixel 0.95, shown at step 1, values float32
+> save
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J864_007_volume_map_zflip.mrc
+> models #235
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240711_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_mix.cxs
+[Repeated 1 time(s)]
+\u2014\u2014\u2014 End of log from Thu Jul 18 19:11:33 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> show #!236 models
+> hide #!236 models
+> hide #!235 models
+> show #!236 models
+> show #!233 models
+> hide #!236 models
+> hide #!233 models
+> open /Users/cvetkom/Documents/AlphaFold/Mrc1_Ctf4CTD/ranked_0.pdb
+Chain information for ranked_0.pdb #237
+---
+Chain | Description
+A | No description available
+B C D | No description available
+> open /Users/cvetkom/Documents/AlphaFold/Mrc1_Ctf4CTD/ranked_1.pdb
+Chain information for ranked_1.pdb #238
+---
+Chain | Description
+A | No description available
+B C D | No description available
+> open /Users/cvetkom/Documents/AlphaFold/Mrc1_Ctf4CTD/ranked_2.pdb
+Chain information for ranked_2.pdb #240
+---
+Chain | Description
+A | No description available
+B C D | No description available
+> open /Users/cvetkom/Documents/AlphaFold/Mrc1_Ctf4CTD/ranked_3.pdb
+Chain information for ranked_3.pdb #241
+---
+Chain | Description
+A | No description available
+B C D | No description available
+> open /Users/cvetkom/Documents/AlphaFold/Mrc1_Ctf4CTD/ranked_4.pdb
+Chain information for ranked_4.pdb #242
+---
+Chain | Description
+A | No description available
+B C D | No description available
+> hide #237 models
+> show #237 models
+> view #237 clip false
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!235 models
+> hide #!235 models
+> select add #237
+atoms, 39489 bonds, 2467 residues, 1 model selected
+> cofr sel
+> select subtract #237
+Nothing selected
+> select add #237
+atoms, 39489 bonds, 2467 residues, 1 model selected
+> select subtract #237
+Nothing selected
+> hide #238 models
+> hide #240 models
+> hide #241 models
+> hide #242 models
+> show #238 models
+> hide #238 models
+> show #238 models
+> hide #238 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> show #238 models
+> hide #238 models
+> show #240 models
+> ui tool show Matchmaker
+> hide #240 models
+> show #237 models
+> hide #237 models
+> show #!211 models
+> select add #211
+models selected
+> cofr sel
+> view sel
+> select subtract #211
+Nothing selected
+> show #!221 models
+> hide #!221 models
+> show #!177 models
+> hide #!177 models
+> show #!191 models
+> hide #!211 models
+> show #!211 models
+> hide #!211 models
+> show #!211 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> show #!197 models
+> hide #!197 models
+> show #!198 models
+> hide #!191 models
+> show #!191 models
+> hide #!198 models
+> hide #!191 models
+> show #!191 models
+> select add #191
+models selected
+> select subtract #191
+Nothing selected
+> select add #211
+models selected
+Drag select of 211 cryosparc_P17_J843_008_volume_map_sharp.mrc
+> ui mousemode right "translate selected models"
+> select #211
+models selected
+> view matrix models #211,1,0,0,23.591,0,1,0,56.577,0,0,1,-51.52
+> view matrix models #211,1,0,0,22.768,0,1,0,47.717,0,0,1,-59.573
+> ui tool show "Fit in Map"
+> fitmap #211 inMap #191
+Fit map cryosparc_P17_J843_008_volume_map_sharp.mrc in map
+cryosparc_P17_J803_005_volume_map_sharp.mrc using 95383 points
+correlation = 0.8844, correlation about mean = 0.6114, overlap = 1.144e+05
+steps = 204, shift = 6.18, angle = 0.216 degrees
+Position of cryosparc_P17_J843_008_volume_map_sharp.mrc (#211) relative to
+cryosparc_P17_J803_005_volume_map_sharp.mrc (#191) coordinates:
+Matrix rotation and translation
+.99999559 -0.00221335 -0.00198223 26.85415332
+.00221794 0.99999485 0.00231772 45.03607037
+.00197709 -0.00232210 0.99999535 -64.65124874
+Axis -0.61542026 -0.52516117 0.58776156
+Axis point 0.00000000 -8050.27859560 -1735.24699520
+Rotation angle (degrees) 0.21598457
+Shift along axis -78.17730413
+> select subtract #211
+Nothing selected
+> hide #!191 models
+> show #!191 models
+> ui mousemode right zoom
+[Repeated 1 time(s)]
+> lighting soft
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> show #!198 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> hide #!198 models
+> hide #!211 models
+> show #!190 models
+> show #!226 models
+> hide #!226 models
+> show #!226 models
+> color #226 #9437ffff models
+> lighting simple
+> hide #!190 models
+> show #!190 models
+> select add #226
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #226,-0.69587,-0.71701,-0.040702,705.69,-0.14519,0.19596,-0.9698,554.35,0.70334,-0.66895,-0.24047,350.03
+> view matrix models
+> #226,-0.55466,-0.80613,-0.20617,738.49,-0.80542,0.58236,-0.11025,383.62,0.20894,0.1049,-0.97229,500.26
+> view matrix models
+> #226,-0.93544,-0.34201,0.089373,633.42,-0.33939,0.93964,0.043527,102.84,-0.098865,0.010385,-0.99505,623.13
+> ui mousemode right "translate selected models"
+> view matrix models
+> #226,-0.93544,-0.34201,0.089373,607.14,-0.33939,0.93964,0.043527,107.99,-0.098865,0.010385,-0.99505,615.3
+> view matrix models
+> #226,-0.93544,-0.34201,0.089373,604.94,-0.33939,0.93964,0.043527,90.344,-0.098865,0.010385,-0.99505,582.38
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #226,-0.92949,-0.35318,0.10634,601.2,-0.35497,0.93487,0.0022278,108.57,-0.1002,-0.035677,-0.99433,595.25
+> ui mousemode right "translate selected models"
+> view matrix models
+> #226,-0.92949,-0.35318,0.10634,600.67,-0.35497,0.93487,0.0022278,112.16,-0.1002,-0.035677,-0.99433,599.08
+> view matrix models
+> #226,-0.92949,-0.35318,0.10634,604.71,-0.35497,0.93487,0.0022278,115.64,-0.1002,-0.035677,-0.99433,597.23
+> fitmap #226 inMap #190
+Fit map cryosparc_P17_J842_005_volume_map_sharp.mrc in map
+cryosparc_P17_J803_005_volume_map.mrc using 488089 points
+correlation = 0.9693, correlation about mean = 0.8115, overlap = 1.318e+05
+steps = 208, shift = 8.45, angle = 11.9 degrees
+Position of cryosparc_P17_J842_005_volume_map_sharp.mrc (#226) relative to
+cryosparc_P17_J803_005_volume_map.mrc (#190) coordinates:
+Matrix rotation and translation
+-0.97649779 -0.20178090 0.07573987 585.60429131
+-0.21091477 0.96696460 -0.14315876 117.19127531
+-0.04435107 -0.15576887 -0.98679737 611.32765515
+Axis -0.10413305 0.99169911 -0.07542663
+Axis point 308.30518170 0.00000000 301.15926555
+Rotation angle (degrees) 176.52872801
+Shift along axis 9.12733602
+> select subtract #226
+Nothing selected
+> hide #!190 models
+> show #!191 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> show #!190 models
+> hide #!226 models
+> show #!230 models
+> show #!231 models
+> select add #230
+models selected
+> select add #231
+models selected
+> view matrix models
+> #230,1,0,0,6.1821,0,1,0,2.3092,0,0,1,0.16596,#231,1,0,0,6.1821,0,1,0,2.3092,0,0,1,0.16596
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #230,-0.89534,0.44297,-0.046301,393.57,0.44479,0.88392,-0.14437,-39.265,-0.023027,-0.14986,-0.98844,641.69,#231,-0.89534,0.44297,-0.046301,393.57,0.44479,0.88392,-0.14437,-39.265,-0.023027,-0.14986,-0.98844,641.69
+> ui mousemode right "translate selected models"
+> view matrix models
+> #230,-0.89534,0.44297,-0.046301,320.22,0.44479,0.88392,-0.14437,-44.069,-0.023027,-0.14986,-0.98844,639.1,#231,-0.89534,0.44297,-0.046301,320.22,0.44479,0.88392,-0.14437,-44.069,-0.023027,-0.14986,-0.98844,639.1
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #230,-0.91848,0.23415,0.31871,274.41,0.27736,0.95585,0.097055,-92.686,-0.28191,0.17754,-0.94287,602.62,#231,-0.91848,0.23415,0.31871,274.41,0.27736,0.95585,0.097055,-92.686,-0.28191,0.17754,-0.94287,602.62
+> ui mousemode right "translate selected models"
+> view matrix models
+> #230,-0.91848,0.23415,0.31871,357.45,0.27736,0.95585,0.097055,-82.118,-0.28191,0.17754,-0.94287,602.24,#231,-0.91848,0.23415,0.31871,357.45,0.27736,0.95585,0.097055,-82.118,-0.28191,0.17754,-0.94287,602.24
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #230,-0.9953,-0.08301,0.049969,545.27,-0.075504,0.9877,0.13689,-11.072,-0.060718,0.13247,-0.98933,571.06,#231,-0.9953,-0.08301,0.049969,545.27,-0.075504,0.9877,0.13689,-11.072,-0.060718,0.13247,-0.98933,571.06
+> ui mousemode right "translate selected models"
+> view matrix models
+> #230,-0.9953,-0.08301,0.049969,559.93,-0.075504,0.9877,0.13689,-6.7949,-0.060718,0.13247,-0.98933,569.44,#231,-0.9953,-0.08301,0.049969,559.93,-0.075504,0.9877,0.13689,-6.7949,-0.060718,0.13247,-0.98933,569.44
+> view matrix models
+> #230,-0.9953,-0.08301,0.049969,568.3,-0.075504,0.9877,0.13689,-40.558,-0.060718,0.13247,-0.98933,526.44,#231,-0.9953,-0.08301,0.049969,568.3,-0.075504,0.9877,0.13689,-40.558,-0.060718,0.13247,-0.98933,526.44
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #230,-0.99234,-0.11444,0.046504,577.22,-0.10693,0.9843,0.14046,-32.528,-0.061848,0.13441,-0.98899,526.1,#231,-0.99234,-0.11444,0.046504,577.22,-0.10693,0.9843,0.14046,-32.528,-0.061848,0.13441,-0.98899,526.1
+> view matrix models
+> #230,-0.98137,-0.13006,0.14143,550.27,-0.15125,0.97687,-0.15114,68.276,-0.1185,-0.16971,-0.97834,621.31,#231,-0.98137,-0.13006,0.14143,550.27,-0.15125,0.97687,-0.15114,68.276,-0.1185,-0.16971,-0.97834,621.31
+> ui mousemode right "translate selected models"
+> view matrix models
+> #230,-0.98137,-0.13006,0.14143,541.12,-0.15125,0.97687,-0.15114,98.697,-0.1185,-0.16971,-0.97834,633.01,#231,-0.98137,-0.13006,0.14143,541.12,-0.15125,0.97687,-0.15114,98.697,-0.1185,-0.16971,-0.97834,633.01
+> fitmap #230 inMap #190
+Fit map cryosparc_P17_J845_005_volume_map_sharp.mrc in map
+cryosparc_P17_J803_005_volume_map.mrc using 572767 points
+correlation = 0.9702, correlation about mean = 0.8247, overlap = 1.352e+05
+steps = 108, shift = 7.64, angle = 5.67 degrees
+Position of cryosparc_P17_J845_005_volume_map_sharp.mrc (#230) relative to
+cryosparc_P17_J803_005_volume_map.mrc (#190) coordinates:
+Matrix rotation and translation
+-0.97635603 -0.20284331 0.07472287 586.20276261
+-0.21174871 0.96698095 -0.14181092 117.11563644
+-0.04349020 -0.15428042 -0.98706949 610.85909501
+Axis -0.10460810 0.99170348 -0.07470851
+Axis point 308.47483717 0.00000000 301.01098483
+Rotation angle (degrees) 176.58308850
+Shift along axis 9.18605482
+> fitmap #231 inMap #190
+Fit map cryosparc_P17_J846_005_volume_map_sharp.mrc in map
+cryosparc_P17_J803_005_volume_map.mrc using 570393 points
+correlation = 0.9715, correlation about mean = 0.8289, overlap = 1.331e+05
+steps = 120, shift = 7.62, angle = 5.66 degrees
+Position of cryosparc_P17_J846_005_volume_map_sharp.mrc (#231) relative to
+cryosparc_P17_J803_005_volume_map.mrc (#190) coordinates:
+Matrix rotation and translation
+-0.97634464 -0.20282850 0.07491170 586.12671435
+-0.21175571 0.96700450 -0.14163978 117.05949264
+-0.04371137 -0.15415222 -0.98707974 610.90239310
+Axis -0.10460616 0.99170937 -0.07463300
+Axis point 308.46618437 0.00000000 300.99661437
+Rotation angle (degrees) 176.57124371
+Shift along axis 9.18305466
+> select subtract #231
+models selected
+> select subtract #230
+Nothing selected
+> hide #!231 models
+> show #!231 models
+> hide #!231 models
+> hide #!230 models
+> show #!230 models
+> hide #!230 models
+> show #!177 models
+> select add #177
+atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
+> view matrix models #177,1,0,0,79.796,0,1,0,51.72,0,0,1,-8.0933
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #177,0.69184,0.051639,0.7202,1.2453,0.39268,0.81013,-0.4353,88.033,-0.60594,0.58396,0.54021,85.465
+> view matrix models
+> #177,0.68848,0.040322,0.72414,3.3706,0.40239,0.80944,-0.42765,84.826,-0.60339,0.58581,0.54106,84.445
+> ui mousemode right "translate selected models"
+> view matrix models
+> #177,0.68848,0.040322,0.72414,-24.721,0.40239,0.80944,-0.42765,124.91,-0.60339,0.58581,0.54106,181.95
+> fitmap #177 inMap #190
+Fit molecule 6skl (#177) to map cryosparc_P17_J803_005_volume_map.mrc (#190)
+using 118220 atoms
+average map value = 0.2974, steps = 296
+shifted from previous position = 36.4
+rotated from previous position = 17.9 degrees
+atoms outside contour = 74597, contour level = 0.30132
+Position of 6skl (#177) relative to cryosparc_P17_J803_005_volume_map.mrc
+(#190) coordinates:
+Matrix rotation and translation
+.46579535 -0.09937691 0.87929456 48.24974596
+.51662113 0.83728469 -0.17904461 61.91426409
+-0.71842697 0.53766029 0.44134352 233.27290342
+Axis 0.38609415 0.86070423 0.33184263
+Axis point 168.02643327 0.00000000 112.77870008
+Rotation angle (degrees) 68.14791182
+Shift along axis 149.32870821
+> select subtract #177
+Nothing selected
+> ui mousemode right zoom
+> select add #177
+atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
+> hide (#!177 & sel) target a
+> cartoon (#!177 & sel)
+> select subtract #177
+Nothing selected
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!191 models
+> hide #!177 models
+> show #!177 models
+> fitmap #177 inMap #191
+Fit molecule 6skl (#177) to map cryosparc_P17_J803_005_volume_map_sharp.mrc
+(#191) using 118220 atoms
+average map value = 0.3767, steps = 56
+shifted from previous position = 0.0922
+rotated from previous position = 0.0581 degrees
+atoms outside contour = 80226, contour level = 0.39
+Position of 6skl (#177) relative to
+cryosparc_P17_J803_005_volume_map_sharp.mrc (#191) coordinates:
+Matrix rotation and translation
+.46578087 -0.09837126 0.87941531 48.10212088
+.51628561 0.83733279 -0.17978591 62.07532586
+-0.71867751 0.53777030 0.44080126 233.33404225
+Axis 0.38651030 0.86080969 0.33108377
+Axis point 168.00088480 0.00000000 112.96763857
+Rotation angle (degrees) 68.16361025
+Shift along axis 149.28012082
+> hide #!177 models
+> show #!177 models
+> hide #!191 models
+> show #!191 models
+> hide #!191 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
+> show #237 models
+> hide #237 models
+> show #237 models
+> matchmaker #237/B to #177/H pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain H (#177) with ranked_0.pdb, chain B (#237), sequence
+alignment score = 2258
+RMSD between 412 pruned atom pairs is 0.645 angstroms; (across all 425 pairs:
+.877)
+> hide #237 models
+> show #237 models
+> show #238 models
+> matchmaker #238/B to #177/H pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain H (#177) with ranked_1.pdb, chain B (#238), sequence
+alignment score = 2254.4
+RMSD between 411 pruned atom pairs is 0.626 angstroms; (across all 425 pairs:
+.888)
+> matchmaker #240/B to #177/H pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain H (#177) with ranked_2.pdb, chain B (#240), sequence
+alignment score = 2264.6
+RMSD between 414 pruned atom pairs is 0.635 angstroms; (across all 425 pairs:
+.838)
+> show #240 models
+> hide #240 models
+> hide #237 models
+> hide #238 models
+> show #240 models
+> hide #!177 models
+> matchmaker #240/C to #177/H pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain H (#177) with ranked_2.pdb, chain C (#240), sequence
+alignment score = 2261.6
+RMSD between 413 pruned atom pairs is 0.630 angstroms; (across all 425 pairs:
+.840)
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #240 models
+> show #241 models
+> matchmaker #242/B to #177/H pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain H (#177) with ranked_4.pdb, chain B (#242), sequence
+alignment score = 2243.6
+RMSD between 412 pruned atom pairs is 0.623 angstroms; (across all 425 pairs:
+.828)
+> show #242 models
+> matchmaker #241/B to #177/H pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain H (#177) with ranked_3.pdb, chain B (#241), sequence
+alignment score = 2265.2
+RMSD between 410 pruned atom pairs is 0.661 angstroms; (across all 425 pairs:
+.961)
+> hide #242 models
+> hide #241 models
+> show #242 models
+> hide #242 models
+> show #241 models
+> show #242 models
+> hide #241 models
+> hide #242 models
+> show #237 models
+> hide #!177 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!177 models
+> hide #!177 models
+> select #237/A#238/A#240/A#241/A#242/A
+atoms, 87105 bonds, 5480 residues, 5 models selected
+> select #237/B#238/B#240/B#241/B#242/B
+atoms, 36780 bonds, 2285 residues, 5 models selected
+> ui tool show "Color Actions"
+> color sel lime green
+> select #237/C#238/C#240/C#241/C#242/C
+atoms, 36780 bonds, 2285 residues, 5 models selected
+> color sel lime green
+> select #237/D#238/D#240/D#241/D#242/D
+atoms, 36780 bonds, 2285 residues, 5 models selected
+> color sel lime green
+> select #237/A#238/A#240/A#241/A#242/A
+atoms, 87105 bonds, 5480 residues, 5 models selected
+> show #!177 models
+> color sel medium blue
+> color sel dark blue
+> color sel medium blue
+[Repeated 1 time(s)]
+> color sel purple
+> color sel blue
+> color sel medium blue
+[Repeated 1 time(s)]
+> select clear
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #!190 models
+> hide #!190 models
+> show #238 models
+> hide #238 models
+> show #238 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #238 models
+> show #238 models
+> hide #238 models
+> show #238 models
+> hide #238 models
+> hide #237 models
+> show #240 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #240 models
+> show #240 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> hide #240 models
+> show #241 models
+> show #240 models
+> hide #240 models
+> show #240 models
+> hide #240 models
+> show #240 models
+> hide #240 models
+> show #242 models
+> hide #242 models
+> show #242 models
+> hide #241 models
+> show #241 models
+> hide #241 models
+> show #241 models
+> hide #242 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #241 models
+> show #241 models
+> hide #241 models
+> show #241 models
+> hide #237 models
+> hide #241 models
+> show #237 models
+> hide #237 models
+> show #238 models
+> show #237 models
+> hide #238 models
+> show #238 models
+> hide #237 models
+> hide #238 models
+> show #240 models
+> show #237 models
+> hide #237 models
+> hide #240 models
+> show #237 models
+> hide #237 models
+> show #238 models
+> hide #238 models
+> show #!239 models
+> hide #!239 models
+> show #240 models
+> hide #240 models
+> show #237 models
+> hide #237 models
+> show #238 models
+> hide #238 models
+> show #237 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #237/A
+Alignment identifier is 237/A
+> select #237/A:746
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #237/A:746-757
+atoms, 193 bonds, 12 residues, 1 model selected
+> show sel target ab
+> style sel ball
+Changed 193 atom styles
+> style sel sphere
+Changed 193 atom styles
+> style sel ball
+Changed 193 atom styles
+> select ~sel & ##selected
+atoms, 39296 bonds, 2455 residues, 1 model selected
+> hide sel target a
+> cartoon hide sel
+> select #237/A#238/A#240/A#241/A#242/A
+atoms, 87105 bonds, 5480 residues, 5 models selected
+> ui tool show "Color Actions"
+> color sel cornflower blue
+> color sel royal blue
+> select clear
+> show #238 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> hide #238 models
+> show #240 models
+> show #237 models
+> hide #240 models
+> show #240 models
+> hide #240 models
+> show #240 models
+> hide #240 models
+> hide #!177 models
+> select add #237
+atoms, 39489 bonds, 2467 residues, 1 model selected
+> select subtract #237
+Nothing selected
+> select add #237
+atoms, 39489 bonds, 2467 residues, 1 model selected
+> show sel target ab
+> hide sel target a
+> cartoon sel
+> ui tool show "Show Sequence Viewer"
+> sequence chain #237/A
+Alignment identifier is 237/A
+> select subtract #237
+Nothing selected
+> select #237/A:746-747
+atoms, 22 bonds, 2 residues, 1 model selected
+> select #237/A:746-757
+atoms, 193 bonds, 12 residues, 1 model selected
+> select #237/A:744
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #237/A:744-759
+atoms, 255 bonds, 16 residues, 1 model selected
+> show sel target ab
+> combine #237
+> hide #237 models
+> show #237 models
+> hide #243 models
+> select #237/A:743
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #237/A:1-743
+atoms, 11702 bonds, 743 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select #237/A:761
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #237/A:761-1096
+atoms, 5441 bonds, 336 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select #237/A:744
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #237/A
+atoms, 276 bonds, 17 residues, 1 model selected
+> show sel target ab
+> style sel ball
+Changed 274 atom styles
+> select clear
+> show #!211 models
+> lighting soft
+> color #211 #ffffb27e models
+> color #211 #ffffb2c3 models
+> color #211 #ffffb2ad models
+> color #211 #ffffb29d models
+> color #211 #ffffb28e models
+> color #211 #ffffb28f models
+> lighting full
+> lighting simple
+> set bgColor white
+> set bgColor #ffffff00
+> graphics silhouettes true
+> color #211 #ffffb2b0 models
+> color #211 #ffffb2d5 models
+> color #211 #ffffb2ec models
+> color #211 #ffffb2ca models
+> color #211 #ffffb227 models
+> color #211 #ffffb290 models
+> color #211 #ffffb2b1 models
+> color #211 #ffffb282 models
+> color #211 #ffffb2ff models
+> lighting soft
+> volume #211 level 0.6913
+> volume #211 level 0.65
+> show #!230 models
+> hide #!230 models
+> show #!230 models
+> hide #!230 models
+> show #!230 models
+> hide #!230 models
+> show #!230 models
+> hide #!230 models
+> show #!230 models
+> hide #!230 models
+> show #!230 models
+> hide #!230 models
+> show #!230 models
+> hide #!230 models
+> show #!230 models
+> show #!231 models
+> hide #!230 models
+> hide #!231 models
+> show #!231 models
+> hide #!231 models
+> show #!231 models
+> hide #!231 models
+> show #!231 models
+> hide #!231 models
+> show #!231 models
+> hide #!231 models
+> show #!231 models
+> hide #!231 models
+> show #!231 models
+> color #231 #b2ffb2d9 models
+> color #231 #b2ffb2c1 models
+> color #231 #b2ffb2a3 models
+> color #231 #b2ffb27f models
+> color #231 #b2ffb26e models
+> color #231 #b2ffb2ff models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> hide #!231 models
+> show #!231 models
+> hide #!231 models
+> show #!231 models
+> hide #!231 models
+> show #!231 models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> hide #!231 models
+> show #!231 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> set bgColor black
+> set bgColor transparent
+> ui tool show "Fit in Map"
+> show #243 models
+> hide #243 models
+> show #237 models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> hide #!231 models
+> show #!231 models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> fitmap #237 inMap #231
+Fit molecule ranked_0.pdb (#237) to map
+cryosparc_P17_J846_005_volume_map_sharp.mrc (#231) using 22081 atoms
+average map value = 0.3487, steps = 116
+shifted from previous position = 1.47
+rotated from previous position = 1.84 degrees
+atoms outside contour = 10270, contour level = 0.3
+Position of ranked_0.pdb (#237) relative to
+cryosparc_P17_J846_005_volume_map_sharp.mrc (#231) coordinates:
+Matrix rotation and translation
+.07105997 -0.95640246 -0.28327514 285.99602561
+.71998545 0.24572901 -0.64902865 297.83602531
+.69034152 -0.15783402 0.70605736 373.36846355
+Axis 0.24561334 -0.48684010 0.83824865
+Axis point -161.36898166 394.59093851 0.00000000
+Rotation angle (degrees) 89.34548655
+Shift along axis 238.22153124
+> hide #237 models
+> show #237 models
+> color #231 #b2ffb283 models
+> set bgColor white
+> set bgColor #ffffff00
+> color #231 #b2ffb282 models
+> color #231 #b2ffb292 models
+> color #231 #b2ffb2ae models
+> color #231 #b2ffb2bd models
+> color #231 #b2ffb295 models
+> lighting full
+> lighting simple
+> color #231 #b2ffb2ff models
+> color #231 #b2ffb29d models
+> color #231 #b2ffb2d4 models
+> color #231 #b2ffb2af models
+> color #231 #b2ffb2ff models
+> lighting soft
+> lighting full
+> lighting soft
+> hide #237 models
+> set bgColor black
+> set bgColor transparent
+> hide #!231 models
+> show #!230 models
+> show #!231 models
+> hide #!231 models
+> show #!231 models
+> hide #!231 models
+> show #!226 models
+> hide #!230 models
+> show #!231 models
+> hide #!226 models
+> hide #!231 models
+> show #!211 models
+> show #!232 models
+> hide #!232 models
+> hide #!211 models
+> show #!235 models
+> hide #!235 models
+> show #!233 models
+> show #!232 models
+> show #!236 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!232 models
+> show #!232 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> show #!236 models
+> hide #!232 models
+> hide #!233 models
+> show #!233 models
+> hide #!236 models
+> select add #233
+models selected
+> cofr sel
+> select subtract #233
+Nothing selected
+> show #!236 models
+> show #!232 models
+> hide #!232 models
+> show #!234 models
+> hide #!234 models
+> show #!232 models
+> show #!231 models
+> hide #!231 models
+> show #!230 models
+> hide #!230 models
+> show #!231 models
+> hide #!231 models
+> hide #!236 models
+> show #!236 models
+> show #!234 models
+> hide #!234 models
+> hide #!236 models
+> color #233 #b2b2b2b0 models
+> hide #!233 models
+> hide #!232 models
+> show #!191 models
+> hide #!191 models
+> show #!211 models
+> hide #!211 models
+> show #!231 models
+> show #!177 models
+> hide #!177 models
+> show #237 models
+> hide #237 models
+> hide #!231 models
+> show #!233 models
+> color #233 #b2b2b2ff models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> open /Volumes/lab-
+> costaa/working/Milos/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Refine3D/job814/run_class001.mrc
+Opened run_class001.mrc as #244, grid size 588,588,588, pixel 0.95, shown at
+level 0.00486, step 4, values float32
+> close #244
+> hide #!236 models
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> lighting shadows true intensity 0.5
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> lighting soft
+> lighting full
+> lighting soft
+> lighting full
+> show #!236 models
+> lighting soft
+> lighting simple
+> lighting full
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> hide #!236 models
+> show #!236 models
+> hide #!233 models
+> show #!233 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
+\u2014\u2014\u2014 End of log from Wed Jul 24 16:21:27 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> hide #!236 models
+> hide #!233 models
+> show #!98 models
+> lighting simple
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!100 models
+> hide #!100 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> hide #!99 models
+> show #!99 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!99 models
+> show #!99 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> show #!98 models
+> hide #!98 models
+> hide #!99 models
+> show #!32 models
+> show #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> hide #!34 models
+> show #!129 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!129 models
+> hide #!130 models
+> show #!74 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!74 models
+> show #!75 models
+> hide #!75 models
+> hide #!74 models
+> show #!110 models
+> show #!111 models
+> hide #!110 models
+> show #!110 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> hide #!110 models
+> show #!122 models
+> show #!129 models
+> hide #!122 models
+> show #!122 models
+> hide #!129 models
+> show #!129 models
+> hide #!129 models
+> show #!129 models
+> hide #!122 models
+> show #!122 models
+> hide #!129 models
+> show #!123 models
+> hide #!122 models
+> hide #!123 models
+> show #!123 models
+> show #!124 models
+> hide #!124 models
+> show #!122 models
+> hide #!122 models
+> show #!130 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!130 models
+> hide #!123 models
+> show #!123 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!110 models
+> show #!110 models
+> hide #!123 models
+> show #!123 models
+> hide #!110 models
+> show #!110 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!123 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!34 models
+> show #!32 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!112 models
+> hide #!112 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!110 models
+> show #!110 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!110 models
+> hide #!111 models
+> hide #!32 models
+> hide #!34 models
+> show #!123 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!129 models
+> hide #!129 models
+> show #!130 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!75 models
+> show #!75 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> hide #!74 models
+> show #!74 models
+> show #!122 models
+> hide #!122 models
+> show #!122 models
+> hide #!122 models
+> show #!122 models
+> hide #!122 models
+> show #!122 models
+> hide #!122 models
+> show #!122 models
+> hide #!122 models
+> show #!122 models
+> hide #!122 models
+> show #!122 models
+> hide #!122 models
+> show #!122 models
+> hide #!123 models
+> show #!123 models
+> hide #!122 models
+> hide #!74 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!123 models
+> show #!123 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!123 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!130 models
+> show #!130 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> show #!75 models
+> hide #!75 models
+> hide #!130 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J368_007_volume_map.mrc
+Opened cryosparc_P17_J368_007_volume_map.mrc as #244, grid size 294,294,294,
+pixel 1.9, shown at level 0.37, step 2, values float32
+> lighting simple
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #244 step 1
+> volume #244 level 0.344
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J685_007_volume_map.mrc
+Opened cryosparc_P17_J685_007_volume_map.mrc as #245, grid size 294,294,294,
+pixel 1.9, shown at level 0.361, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J690_006_volume_map.mrc
+Opened cryosparc_P17_J690_006_volume_map.mrc as #246, grid size 294,294,294,
+pixel 1.9, shown at level 0.36, step 2, values float32
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #245 step 1
+> volume #245 level 0.3413
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #246 step 1
+> show #!245 models
+> hide #!245 models
+> show #!245 models
+> select add #245
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #245,0.24392,0.87788,0.4121,-128.61,0.92708,-0.086349,-0.36479,125.94,-0.28466,0.47103,-0.83493,401.32
+> view matrix models
+> #245,0.64106,-0.054068,-0.76558,302.83,0.031113,-0.99486,0.096313,510.77,-0.76686,-0.085561,-0.63609,638.94
+> view matrix models
+> #245,0.9162,-0.026949,-0.39982,128.81,0.14241,-0.91071,0.38773,385.27,-0.37456,-0.41217,-0.83055,665.84
+> view matrix models
+> #245,0.91682,-0.37423,-0.13924,159.29,-0.35009,-0.92108,0.17043,579.11,-0.19203,-0.1075,-0.97548,567.39
+> ui mousemode right "translate selected models"
+> view matrix models
+> #245,0.91682,-0.37423,-0.13924,163.24,-0.35009,-0.92108,0.17043,567.35,-0.19203,-0.1075,-0.97548,639.7
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #245,0.98493,-0.05987,-0.16227,64.254,-0.032068,-0.98512,0.16883,496.24,-0.16996,-0.16108,-0.9722,647.31
+> ui mousemode right "translate selected models"
+> view matrix models
+> #245,0.98493,-0.05987,-0.16227,72.788,-0.032068,-0.98512,0.16883,503.81,-0.16996,-0.16108,-0.9722,638.94
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #245,0.96022,0.026881,-0.27794,84.445,0.064645,-0.98972,0.12761,488.12,-0.27165,-0.1405,-0.95208,656.85
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #245,0.96845,0.06341,-0.24101,63.142,0.079191,-0.99527,0.056358,503.03,-0.23629,-0.073665,-0.96889,632.88
+> ui mousemode right "translate selected models"
+> view matrix models
+> #245,0.96845,0.06341,-0.24101,55.646,0.079191,-0.99527,0.056358,515.43,-0.23629,-0.073665,-0.96889,633.64
+> select subtract #245
+Nothing selected
+> hide #!245 models
+> show #!246 models
+> select add #246
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #246,-0.94249,-0.14738,0.29999,492.53,0.01794,-0.91854,-0.39491,640.24,0.33376,-0.36682,0.86836,47.073
+> view matrix models
+> #246,-0.98683,-0.012271,0.16129,511.21,-0.0067172,-0.99315,-0.11666,581.14,0.16162,-0.11621,0.97999,-7.5123
+> view matrix models
+> #246,-0.99462,-0.028395,0.099663,536.91,0.012491,-0.98757,-0.15671,586.65,0.10287,-0.15462,0.9826,18.639
+> select subtract #246
+Nothing selected
+> select add #246
+models selected
+> select subtract #246
+Nothing selected
+> show #!245 models
+> ui tool show "Fit in Map"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+[Repeated 1 time(s)]
+> fitmap #245 inMap #244
+Fit map cryosparc_P17_J685_007_volume_map.mrc in map
+cryosparc_P17_J368_007_volume_map.mrc using 271515 points
+correlation = 0.9949, correlation about mean = 0.9457, overlap = 9.464e+04
+steps = 188, shift = 2.56, angle = 15.2 degrees
+Position of cryosparc_P17_J685_007_volume_map.mrc (#245) relative to
+cryosparc_P17_J368_007_volume_map.mrc (#244) coordinates:
+Matrix rotation and translation
+.99981329 -0.01923951 0.00179460 4.69427957
+-0.01931352 -0.99208863 0.12404490 525.91853508
+-0.00060616 -0.12405640 -0.99227498 588.72614471
+Axis -0.99995314 0.00967608 -0.00029828
+Axis point 0.00000000 281.31245766 277.98752927
+Rotation angle (degrees) 172.87372921
+Shift along axis 0.21916772
+> fitmap #246 inMap #244
+Fit map cryosparc_P17_J690_006_volume_map.mrc in map
+cryosparc_P17_J368_007_volume_map.mrc using 254434 points
+correlation = 0.9952, correlation about mean = 0.9446, overlap = 9.256e+04
+steps = 120, shift = 8.54, angle = 6.45 degrees
+Position of cryosparc_P17_J690_006_volume_map.mrc (#246) relative to
+cryosparc_P17_J368_007_volume_map.mrc (#244) coordinates:
+Matrix rotation and translation
+-0.99997157 0.00691924 -0.00299642 557.81739805
+-0.00648161 -0.99184550 -0.12728119 593.36152310
+-0.00385267 -0.12725815 0.99186215 38.74337635
+Axis 0.00171577 0.06376541 -0.99796344
+Axis point 279.94000643 296.98029450 0.00000000
+Rotation angle (degrees) 179.61530751
+Shift along axis 0.12855455
+> hide #!246 models
+> hide #!244 models
+> show #!246 models
+> ui mousemode right zoom
+> lighting soft
+> hide #!245 models
+> show #!245 models
+> hide #!246 models
+> show #!246 models
+> hide #!246 models
+> show #!246 models
+> hide #!246 models
+> show #!246 models
+> hide #!245 models
+> show #!245 models
+> hide #!246 models
+> hide #!245 models
+> show #!244 models
+> show #!246 models
+> hide #!246 models
+> show #!246 models
+> hide #!244 models
+> show #!244 models
+> hide #!244 models
+> show #!244 models
+> volume #244 level 0.36
+> hide #!246 models
+> show #!246 models
+> hide #!246 models
+> show #!246 models
+> hide #!244 models
+> show #!244 models
+> hide #!244 models
+> show #!244 models
+> hide #!246 models
+> show #!246 models
+> hide #!244 models
+> show #!245 models
+> show #!244 models
+> hide #!246 models
+> hide #!245 models
+> show #!245 models
+> volume #245 level 0.36
+> hide #!244 models
+> show #!246 models
+> hide #!246 models
+> show #!246 models
+> hide #!245 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J697_006_volume_map.mrc
+Opened cryosparc_P17_J697_006_volume_map.mrc as #247, grid size 294,294,294,
+pixel 1.9, shown at level 0.358, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J712_007_volume_map.mrc
+Opened cryosparc_P17_J712_007_volume_map.mrc as #248, grid size 294,294,294,
+pixel 1.9, shown at level 0.349, step 2, values float32
+> hide #!246 models
+> show #!246 models
+> hide #!246 models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #247 step 1
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #248 step 1
+> volume #247 level 0.36
+> volume #248 level 0.36
+> close #248
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J362_007_volume_map.mrc
+Opened cryosparc_P17_J362_007_volume_map.mrc as #248, grid size 294,294,294,
+pixel 1.9, shown at level 0.368, step 2, values float32
+> hide #!247 models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #248 step 1
+> volume #248 level 0.36
+> show #!244 models
+> hide #!248 models
+> show #!248 models
+> hide #!244 models
+> show #!244 models
+> hide #!248 models
+> show #!248 models
+> hide #!244 models
+> hide #!248 models
+> show #!248 models
+> show #!246 models
+> show #!247 models
+> hide #!247 models
+> hide #!248 models
+> show #!248 models
+> hide #!248 models
+> show #!248 models
+> hide #!246 models
+> show #!246 models
+> hide #!248 models
+> hide #!246 models
+> show #!98 models
+> show #!110 models
+> show #!32 models
+> hide #!32 models
+> show #!32 models
+> show #!34 models
+> hide #!32 models
+> hide #!98 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> show #!99 models
+> hide #!110 models
+> show #!111 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> show #!219 models
+> show #!220 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> hide #!99 models
+> show #!99 models
+> hide #!99 models
+> hide #!34 models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #219 step 1
+> volume #220 level 0.35
+> volume #219 level 0.35
+> volume #219 step 2
+> volume #219 step 1
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #220 step 2
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1103_006_volume_map.mrc
+Opened cryosparc_P17_J1103_006_volume_map.mrc as #249, grid size 294,294,294,
+pixel 1.9, shown at level 0.358, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1105_008_volume_map.mrc
+Opened cryosparc_P17_J1105_008_volume_map.mrc as #250, grid size 294,294,294,
+pixel 1.9, shown at level 0.362, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1106_006_volume_map.mrc
+Opened cryosparc_P17_J1106_006_volume_map.mrc as #251, grid size 294,294,294,
+pixel 1.9, shown at level 0.357, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1107_006_volume_map.mrc
+Opened cryosparc_P17_J1107_006_volume_map.mrc as #252, grid size 294,294,294,
+pixel 1.9, shown at level 0.356, step 2, values float32
+> hide #!219 models
+> hide #!220 models
+> hide #!249 models
+> hide #!250 models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #251 step 1
+> volume #251 level 0.3333
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #252 step 1
+> volume #252 level 0.33
+> volume #252 level 0.35
+> volume #252 level 0.34
+> hide #!252 models
+> show #!32 models
+> show #!33 models
+> hide #!33 models
+> show #!33 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!33 models
+> show #!33 models
+> hide #!33 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!34 models
+> show #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!34 models
+> show #!34 models
+> hide #!32 models
+> hide #!34 models
+> show #!98 models
+> show #!99 models
+> hide #!99 models
+> hide #!98 models
+> show #!99 models
+> show #!98 models
+> hide #!99 models
+> hide #!98 models
+> show #!99 models
+> hide #!99 models
+> show #!110 models
+> show #!111 models
+> hide #!110 models
+> show #!110 models
+> hide #!111 models
+> show #!111 models
+> hide #!111 models
+> hide #!110 models
+> show #!246 models
+> hide #!246 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240718_CMGC4MCT_Fpl20MN_krios_II_merged_3Dclasses_concensus_Ctf4Mrc1_mix.cxs
+\u2014\u2014\u2014 End of log from Tue Jul 30 11:34:25 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> show #!232 models
+> hide #!232 models
+> show #!234 models
+> show #!236 models
+> lighting simple
+> close #1-18
+> close #22-27,32-75
+> close #98-135
+> close #85-90
+> show #!244 models
+> hide #!244 models
+> close #244-252
+> show #!19 models
+> hide #!19 models
+> open 8XGC fromDatabase pdb format mmcif
+xgc title:
+Structure of yeast replisome associated with FACT and histone hexamer,
+Composite map [more info...]
+Chain information for 8xgc #1
+---
+Chain | Description | UniProt
+| DNA replication licensing factor MCM2 | A0A6A5Q1S9_YEASX 1-868
+| DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
+| DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
+| Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
+| DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
+| DNA replication licensing factor MCM7 | A0A8H4BTB2_YEASX 1-845
+| DNA polymerase epsilon catalytic subunit A | DPOE_YEAST 1-2222
+| DNA polymerase epsilon subunit B | DPB2_YEAST 1-689
+A | DNA replication complex GINS protein PSF1 | PSF1_YEAST 1-208
+B | DNA replication complex GINS protein PSF2 |
+C | DNA replication complex GINS protein PSF3 | PSF3_YEAST 1-194
+D | DNA replication complex GINS protein SLD5 | SLD5_YEAST 1-294
+E | Cell division control protein 45 | CDC45_YEAST 1-650
+F G H | DNA polymerase alpha-binding protein | CTF4_YEAST 1-927
+I | Topoisomerase 1-associated factor 1 | TOF1_YEAST 1-1238
+J | Chromosome segregation in meiosis protein 3 | CSM3_YEAST 1-317
+K | Mediator of replication checkpoint protein 1 | MRC1_YEAST 1-1096
+L | FACT complex subunit SPT16 | SPT16_YEAST 1-1035
+M | FACT complex subunit POB3 | POB3_YEAST 1-552
+N R | Histone H3 | A0A6A5Q536_YEASX 1-136
+O S | Histone H4 | H4_YEAST 1-103
+P | Histone H2A.1 | H2A1_YEAST 1-132
+Q | Histone H2B.2 | H2B2_YEAST 1-131
+X | DNA (51-MER) |
+Y | DNA (39-MER) |
+Non-standard residues in 8xgc #1
+---
+ADP \u2014 adenosine-5'-diphosphate
+ZN \u2014 zinc ion
+> select add #1
+atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
+> hide (#!1 & sel) target a
+> cartoon (#!1 & sel)
+> cartoon style (#!1 & sel) modeHelix tube sides 20
+> select clear
+> select add #1
+atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
+> ui mousemode right "translate selected models"
+> view matrix models #1,1,0,0,47.645,0,1,0,-186.91,0,0,1,-225.38
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #1,0.58597,0.26748,0.76491,-77.764,-0.68071,0.6746,0.28556,-31.019,-0.43963,-0.68802,0.57737,101.42
+> view matrix models
+> #1,-0.63049,-0.77581,0.02448,555.31,-0.40378,0.30088,-0.86396,224.99,0.66291,-0.5546,-0.50296,59.311
+> view matrix models
+> #1,-0.60522,-0.79563,-0.026037,564.5,-0.4515,0.37002,-0.81194,209.77,0.65563,-0.47965,-0.58317,61.313
+> view matrix models
+> #1,-0.51594,-0.8087,-0.28251,600.78,-0.65671,0.58517,-0.47573,138.81,0.55003,-0.059923,-0.83299,45.531
+> view matrix models
+> #1,-0.75431,-0.62553,0.19933,513.87,-0.20404,-0.065216,-0.97679,283.54,0.62401,-0.77747,-0.078442,28.164
+> view matrix models
+> #1,0.75405,0.27605,-0.59599,163.26,0.6559,-0.26853,0.70547,-200.8,0.034703,-0.92287,-0.38355,247.17
+> view matrix models
+> #1,0.73033,0.35167,-0.58562,150.07,0.68309,-0.37214,0.62842,-168.74,0.0030683,-0.85898,-0.51201,266.6
+> view matrix models
+> #1,0.72602,0.36576,-0.58233,147.32,0.68766,-0.39043,0.61212,-162.48,-0.0034657,-0.84486,-0.53498,269.69
+> select subtract #1
+Nothing selected
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> select add #177
+atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
+> ui mousemode right "translate selected models"
+> view matrix models
+> #177,0.46578,-0.098371,0.87942,92.221,0.51629,0.83733,-0.17979,-43.763,-0.71868,0.53777,0.4408,171.47
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #177,-0.49891,-0.69823,-0.51339,651.92,-0.83168,0.55231,0.057061,237.03,0.24371,0.45544,-0.85626,230.01
+> view matrix models
+> #177,0.26698,-0.55614,-0.78704,521.35,-0.5875,0.55345,-0.59037,305.23,0.76392,0.62,-0.17897,-27.896
+> ui mousemode right "translate selected models"
+> view matrix models
+> #177,0.26698,-0.55614,-0.78704,529.97,-0.5875,0.55345,-0.59037,261.16,0.76392,0.62,-0.17897,-91.066
+> view matrix models
+> #177,0.26698,-0.55614,-0.78704,447.11,-0.5875,0.55345,-0.59037,192.81,0.76392,0.62,-0.17897,-38.287
+> select subtract #177
+Nothing selected
+> ui tool show "Fit in Map"
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> fitmap #177 inMap #236
+Fit molecule 6skl (#177) to map cryosparc_P17_J544_007_volume_map_zflip.mrc
+(#236) using 118220 atoms
+average map value = 0.2679, steps = 436
+shifted from previous position = 21.5
+rotated from previous position = 40.5 degrees
+atoms outside contour = 24734, contour level = 0.17324
+Position of 6skl (#177) relative to
+cryosparc_P17_J544_007_volume_map_zflip.mrc (#236) coordinates:
+Matrix rotation and translation
+-0.51563097 -0.12952906 -0.84696336 558.27691744
+-0.84526058 -0.08486257 0.52757265 364.76426350
+-0.14021148 0.98793753 -0.06572804 118.82779302
+Axis 0.41616323 -0.63889353 -0.64701099
+Axis point 390.84775709 -13.99098898 0.00000000
+Rotation angle (degrees) 146.41962992
+Shift along axis -77.59409021
+> hide #!236 models
+> show #!236 models
+> hide #!236 models
+> show #!236 models
+> hide #!234 models
+> show #!234 models
+> show #!232 models
+> hide #!234 models
+> show #!233 models
+> hide #!236 models
+> ui mousemode right zoom
+> ui tool show Matchmaker
+> matchmaker #1/E to #177/E pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain E (#177) with 8xgc, chain E (#1), sequence alignment
+score = 3091.5
+RMSD between 562 pruned atom pairs is 0.577 angstroms; (across all 562 pairs:
+.577)
+> hide #!233 models
+> hide #!232 models
+> select add #177
+atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
+> cartoon style (#!177 & sel) modeHelix tube sides 20
+> select subtract #177
+Nothing selected
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> matchmaker #!1 to #177
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain X (#177) with 8xgc, chain I (#1), sequence alignment
+score = 5322.6
+RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
+.839)
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> matchmaker #1/I to #177/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain X (#177) with 8xgc, chain I (#1), sequence alignment
+score = 5322.6
+RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
+.839)
+> hide #!177 models
+> show #!177 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #237 models
+> hide #237 models
+> show #243 models
+> hide #243 models
+> show #243 models
+> hide #243 models
+> show #237 models
+> show #!234 models
+> hide #!234 models
+> show #243 models
+> hide #243 models
+> show #243 models
+> hide #243 models
+> combine #237
+> hide #237 models
+> show #243 models
+> hide #243 models
+> show #243 models
+> hide #243 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> show #237 models
+> hide #237 models
+> hide #2 models
+> show #2 models
+> ui tool show Matchmaker
+> hide #2 models
+> close #2
+> open /Users/cvetkom/Documents/AlphaFold/yCsm3_Tof1_Oliver/yCsm3Tof1_AF.pdb
+Chain information for yCsm3Tof1_AF.pdb #2
+---
+Chain | Description
+A | No description available
+B | No description available
+> select add #2
+atoms, 25142 bonds, 1555 residues, 1 model selected
+> view sel
+> select clear
+> matchmaker #2/A to #177/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain X (#177) with yCsm3Tof1_AF.pdb, chain A (#2), sequence
+alignment score = 5355
+RMSD between 517 pruned atom pairs is 1.040 angstroms; (across all 665 pairs:
+.956)
+> hide #2 models
+> show #2 models
+> hide #2 models
+> show #2 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #2/A
+Alignment identifier is 2/A
+> select #2/A:612
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #2/A:612-643
+atoms, 528 bonds, 32 residues, 1 model selected
+> select #2/A:612-613
+atoms, 34 bonds, 2 residues, 1 model selected
+> select #2/A:613-657
+atoms, 731 bonds, 45 residues, 1 model selected
+> color sel blue
+> color sel orange red
+> select clear
+> hide #2 models
+> show #2 models
+> hide #2 models
+> show #2 models
+> show #!236 models
+> hide #!236 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc
+Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc as #3, grid size
+,440,440, pixel 0.95, shown at level 0.0283, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1206_003_volume_map_EMReady.mrc
+Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc as #4, grid size
+,440,440, pixel 0.95, shown at level 0.00374, step 2, values float32
+> open /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1207_map_sharp.mrc
+Opened cryosparc_P17_J1207_map_sharp.mrc as #5, grid size 440,440,440, pixel
+.95, shown at level 2.63e-06, step 2, values float32
+> open /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1210_map_sharp.mrc
+Opened cryosparc_P17_J1210_map_sharp.mrc as #6, grid size 440,440,440, pixel
+.95, shown at level 0.000291, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1268_002_volume_map_sharp.mrc
+Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #7, grid size
+,440,440, pixel 0.95, shown at level 0.0259, step 2, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1163_006_volume_map.mrc
+Opened cryosparc_P17_J1163_006_volume_map.mrc as #8, grid size 588,588,588,
+pixel 0.95, shown at level 0.155, step 4, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J864_007_volume_map_zflip.mrc
+Opened cryosparc_P17_J864_007_volume_map_zflip.mrc as #9, grid size
+,588,588, pixel 0.95, shown at level 0.153, step 4, values float32
+> hide #!9 models
+> hide #!8 models
+> hide #!7 models
+> hide #!6 models
+> hide #!5 models
+> hide #!4 models
+> hide #!3 models
+> hide #2 models
+> show #!236 models
+> show #!9 models
+> volume #9 step 1
+> select add #9
+models selected
+> ui mousemode right "translate selected models"
+> view matrix models #9,1,0,0,44.079,0,1,0,-129.91,0,0,1,33.561
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #9,-0.89241,-0.2853,-0.34957,745.33,-0.22047,0.95166,-0.21387,0.58537,0.39369,-0.11379,-0.91217,447.06
+> view matrix models
+> #9,-0.86115,-0.40726,-0.30424,765.4,-0.37668,0.9131,-0.15612,41.487,0.34138,-0.019841,-0.93972,437.48
+> ui mousemode right "translate selected models"
+> view matrix models
+> #9,-0.86115,-0.40726,-0.30424,699.37,-0.37668,0.9131,-0.15612,-44.304,0.34138,-0.019841,-0.93972,339.64
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #9,-0.93636,-0.11772,-0.33072,631.45,-0.22073,0.93,0.2939,-206.54,0.27297,0.34819,-0.8968,226.48
+> ui mousemode right zoom
+> fitmap #9 inMap #236
+Fit map cryosparc_P17_J864_007_volume_map_zflip.mrc in map
+cryosparc_P17_J544_007_volume_map_zflip.mrc using 2028136 points
+correlation = 0.9937, correlation about mean = 0.9426, overlap = 1.458e+05
+steps = 468, shift = 23.6, angle = 33.5 degrees
+Position of cryosparc_P17_J864_007_volume_map_zflip.mrc (#9) relative to
+cryosparc_P17_J544_007_volume_map_zflip.mrc (#236) coordinates:
+Matrix rotation and translation
+-0.96823974 -0.24332681 -0.05747924 633.07873275
+.10233189 -0.59543288 0.79686125 204.91238326
+-0.22812274 0.76567078 0.60142188 -52.82098481
+Axis -0.08064861 0.44122957 0.89376298
+Axis point 302.77781545 150.02897929 0.00000000
+Rotation angle (degrees) 168.85032375
+Shift along axis -7.85295761
+> select subtract #9
+Nothing selected
+> show #!8 models
+> volume #8 step 1
+> select add #8
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #8,0.83981,0.16349,-0.51768,159.04,-0.33783,0.90383,-0.26259,201.97,0.42496,0.39542,0.81428,-171.03
+> view matrix models
+> #8,-0.088093,0.71527,-0.69328,321.17,0.1227,0.69847,0.70504,-168.1,0.98853,-0.022959,-0.1493,82.529
+> view matrix models
+> #8,0.18202,-0.63889,-0.74746,635.26,0.31514,-0.68216,0.65981,172.32,-0.93143,-0.35565,0.077172,642.94
+> ui mousemode right "translate selected models"
+> view matrix models
+> #8,0.18202,-0.63889,-0.74746,569.25,0.31514,-0.68216,0.65981,-13.259,-0.93143,-0.35565,0.077172,525.18
+> view matrix models
+> #8,0.18202,-0.63889,-0.74746,562.71,0.31514,-0.68216,0.65981,-14.599,-0.93143,-0.35565,0.077172,487.95
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #8,0.49045,-0.55087,-0.67528,429.78,0.60915,-0.33743,0.71769,-209.84,-0.62321,-0.76334,0.17007,485.31
+> ui mousemode right "translate selected models"
+> view matrix models
+> #8,0.49045,-0.55087,-0.67528,444.24,0.60915,-0.33743,0.71769,-178.89,-0.62321,-0.76334,0.17007,497.07
+> fitmap #8 inMap #236
+Fit map cryosparc_P17_J1163_006_volume_map.mrc in map
+cryosparc_P17_J544_007_volume_map_zflip.mrc using 2031120 points
+correlation = 0.9907, correlation about mean = 0.9161, overlap = 1.477e+05
+steps = 368, shift = 21.9, angle = 21.5 degrees
+Position of cryosparc_P17_J1163_006_volume_map.mrc (#8) relative to
+cryosparc_P17_J544_007_volume_map_zflip.mrc (#236) coordinates:
+Matrix rotation and translation
+.99949009 -0.03184645 0.00231562 7.34723952
+.03147411 0.99482700 0.09658474 -35.10247418
+-0.00537952 -0.09646261 0.99532207 32.64947374
+Axis -0.94951030 0.03784884 0.31144447
+Axis point 0.00000000 313.97495420 380.98360453
+Rotation angle (degrees) 5.83455364
+Shift along axis 1.86363064
+> select add #8
+models selected
+> select subtract #8
+Nothing selected
+> lighting soft
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> color #8 silver models
+> hide #!8 models
+> show #!9 models
+> hide #!9 models
+> show #!8 models
+> hide #!8 models
+> show #!9 models
+> hide #!9 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J959_008_volume_map_zflip.mrc
+Opened cryosparc_P17_J959_008_volume_map_zflip.mrc as #10, grid size
+,588,588, pixel 0.95, shown at level 0.148, step 4, values float32
+> select add #10
+models selected
+> view matrix models #10,1,0,0,23.505,0,1,0,-15.929,0,0,1,-23.739
+> lighting simple
+> view matrix models #10,1,0,0,124.8,0,1,0,-99.812,0,0,1,-122.71
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #10,-0.42765,0.3857,-0.81752,672.45,0.75258,-0.34906,-0.55837,194.61,-0.50073,-0.85404,-0.141,572.88
+> view matrix models
+> #10,-0.5836,0.78463,0.2092,308.37,-0.51615,-0.15955,-0.84151,586.63,-0.62689,-0.59908,0.4981,352.72
+> view matrix models
+> #10,-0.66506,0.6951,0.273,334.38,-0.54368,-0.20005,-0.8151,596.53,-0.51196,-0.69052,0.51096,339.61
+> view matrix models
+> #10,-0.87025,-0.14082,0.47205,540.96,-0.24214,-0.71221,-0.65888,593.45,0.42898,-0.68769,0.58571,53.595
+> view matrix models
+> #10,-0.51532,-0.60142,0.61052,515.4,0.36144,-0.79846,-0.48148,393.16,0.77704,-0.027449,0.62885,-221.63
+> view matrix models
+> #10,-0.57269,-0.31806,0.75556,417.1,0.29571,-0.93976,-0.17146,353.87,0.76458,0.12523,0.63225,-257.33
+> ui mousemode right "translate selected models"
+> view matrix models
+> #10,-0.57269,-0.31806,0.75556,316.03,0.29571,-0.93976,-0.17146,301.69,0.76458,0.12523,0.63225,-291.73
+> view matrix models
+> #10,-0.57269,-0.31806,0.75556,307.58,0.29571,-0.93976,-0.17146,309.28,0.76458,0.12523,0.63225,-267.22
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #10,-0.69988,-0.20741,0.68348,337.07,0.084924,-0.97429,-0.2087,387.97,0.70919,-0.088019,0.6995,-218.61
+> ui mousemode right "translate selected models"
+> view matrix models
+> #10,-0.69988,-0.20741,0.68348,322.79,0.084924,-0.97429,-0.2087,374.73,0.70919,-0.088019,0.6995,-205.24
+> volume #10 step 1
+> fitmap #10 inMap #236
+Fit map cryosparc_P17_J959_008_volume_map_zflip.mrc in map
+cryosparc_P17_J544_007_volume_map_zflip.mrc using 2028921 points
+correlation = 0.9436, correlation about mean = 0.7528, overlap = 1.329e+05
+steps = 224, shift = 12.9, angle = 13.2 degrees
+Position of cryosparc_P17_J959_008_volume_map_zflip.mrc (#10) relative to
+cryosparc_P17_J544_007_volume_map_zflip.mrc (#236) coordinates:
+Matrix rotation and translation
+-0.96431898 -0.25440259 0.07326822 606.33395084
+-0.22036646 0.61794867 -0.75470396 377.39307444
+.14672264 -0.74392121 -0.65196143 620.81486733
+Axis 0.13202542 -0.89938569 0.41674293
+Axis point 323.81378637 0.00000000 404.72898510
+Rotation angle (degrees) 177.65962530
+Shift along axis -0.65022839
+> select add #10
+models selected
+> select subtract #10
+Nothing selected
+> color #10 #945200ff models
+> color #10 #941100ff models
+> color #10 #945200ff models
+> color #10 #ff9300ff models
+> color #10 #ff2600ff models
+> color #10 #ff7e79ff models
+> color #10 #fffc79ff models
+> color #10 #d4fb79ff models
+> color #10 #fffc79ff models
+> color #10 #d4fb79ff models
+> volume #10 level 0.1697
+> volume #10 level 0.1731
+> ui mousemode right zoom
+> lighting soft
+> hide #!10 models
+> show #!10 models
+> open
+> /Users/cvetkom/Documents/20240109_CMGC4MCT_Fpl20MN_ATPgS_krios2/Ref3D_job802_run_class001.mrc
+Opened Ref3D_job802_run_class001.mrc as #11, grid size 588,588,588, pixel
+.95, shown at level 0.00416, step 4, values float32
+> lighting simple
+> select add #11
+models selected
+> ui mousemode right "translate selected models"
+> view matrix models #11,1,0,0,-51.74,0,1,0,-84.314,0,0,1,-73.541
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #11,0.0036933,-0.45538,0.89029,72.314,-0.79632,0.53717,0.27807,170.48,-0.60486,-0.70998,-0.36065,684.31
+> view matrix models
+> #11,-0.90602,-0.026747,0.4224,361.01,-0.42311,0.032534,-0.90549,549.65,0.010478,-0.99911,-0.040793,487.81
+> view matrix models
+> #11,-0.90163,0.38295,-0.20102,445.5,0.0063584,-0.453,-0.89149,546.69,-0.43245,-0.80508,0.406,428.35
+> view matrix models
+> #11,-0.68901,-0.48447,0.53903,379.58,0.2377,-0.85366,-0.46343,452.94,0.68467,-0.19118,0.70333,-127.8
+> view matrix models
+> #11,-0.70406,-0.10147,0.70285,238.48,-0.37448,-0.78789,-0.48887,615.54,0.60338,-0.60739,0.51673,55.46
+> view matrix models
+> #11,-0.76623,0.05272,0.6404,236.16,-0.49162,-0.68984,-0.53144,636.65,0.41376,-0.72204,0.5545,125.83
+> ui mousemode right "translate selected models"
+> view matrix models
+> #11,-0.76623,0.05272,0.6404,261.62,-0.49162,-0.68984,-0.53144,557.66,0.41376,-0.72204,0.5545,116.13
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #11,-0.60221,0.45689,0.65467,110.25,-0.62773,-0.77766,-0.034707,467.75,0.49325,-0.43186,0.75511,-39.317
+> view matrix models
+> #11,-0.68577,0.26569,0.67759,174.57,-0.57475,-0.76886,-0.28021,524.85,0.44652,-0.58161,0.67996,33.93
+> volume #11 step 1
+> fitmap #11 inMap #236
+Fit map Ref3D_job802_run_class001.mrc in map
+cryosparc_P17_J544_007_volume_map_zflip.mrc using 2030281 points
+correlation = 0.9571, correlation about mean = 0.8205, overlap = 3535
+steps = 488, shift = 19.8, angle = 32.9 degrees
+Position of Ref3D_job802_run_class001.mrc (#11) relative to
+cryosparc_P17_J544_007_volume_map_zflip.mrc (#236) coordinates:
+Matrix rotation and translation
+-0.96450343 -0.25313673 0.07519943 605.61171904
+-0.21928378 0.60909585 -0.76217904 383.34466562
+.14713185 -0.75161431 -0.64298380 621.67767309
+Axis 0.13173116 -0.89692214 0.42211086
+Axis point 323.99781428 0.00000000 407.81801536
+Rotation angle (degrees) 177.70184669
+Shift along axis -1.63548244
+> hide #!10 models
+> select add #11
+models selected
+> select subtract #11
+Nothing selected
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> hide #!11 models
+> show #!7 models
+> hide #!7 models
+> show #!233 models
+> show #!3 models
+> volume #3 step 1
+> volume #3 level 0.2689
+> hide #!3 models
+> show #!3 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> fitmap #3 inMap #233
+Fit map cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc in map
+cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc using 171797 points
+correlation = 0.9986, correlation about mean = 0.9835, overlap = 1.873e+05
+steps = 64, shift = 2.32, angle = 0.05 degrees
+Position of cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) relative
+to cryosparc_P17_J984_clss_00_00062_volume_sharp_zflip.mrc (#233) coordinates:
+Matrix rotation and translation
+.99999969 -0.00055856 -0.00055446 0.28221116
+.00055877 0.99999977 0.00037517 -0.20830704
+.00055425 -0.00037548 0.99999978 -2.35151229
+Axis -0.43044636 -0.63576954 0.64071291
+Axis point 2074.34448759 -648.53479123 0.00000000
+Rotation angle (degrees) 0.04995831
+Shift along axis -1.49568576
+> volume #3 level 0.25
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!234 models
+> hide #!236 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> show #!232 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> hide #!232 models
+> show #!232 models
+> show #!234 models
+> select add #232
+atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
+> select add #234
+atoms, 19000 bonds, 223 pseudobonds, 1946 residues, 5 models selected
+> view matrix models
+> #232,-0.019001,-0.99844,0.052579,192.68,-0.84729,0.043998,0.5293,242.41,-0.53078,-0.034493,-0.84681,167.29,#234,-0.045299,-0.99887,-0.014131,189.08,-0.79838,0.027697,0.60152,244.8,-0.60045,0.03853,-0.79874,172.18
+> ui mousemode right "translate selected models"
+> view matrix models
+> #232,-0.019001,-0.99844,0.052579,192.71,-0.84729,0.043998,0.5293,242.76,-0.53078,-0.034493,-0.84681,167.34,#234,-0.045299,-0.99887,-0.014131,189.11,-0.79838,0.027697,0.60152,245.15,-0.60045,0.03853,-0.79874,172.22
+> select subtract #234
+atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
+> select subtract #232
+Nothing selected
+> hide #!234 models
+> show #!234 models
+> hide #!232 models
+> hide #!234 models
+> volume flip #4,5,6
+Opened cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip as #12, grid size
+,440,440, pixel 0.95, shown at step 1, values float32
+Opened cryosparc_P17_J1207_map_sharp.mrc z flip as #13, grid size 440,440,440,
+pixel 0.95, shown at step 1, values float32
+Opened cryosparc_P17_J1210_map_sharp.mrc z flip as #14, grid size 440,440,440,
+pixel 0.95, shown at step 1, values float32
+> hide #!13 models
+> volume #12 level 0.6868
+> hide #!14 models
+> volume #12 level 1.994
+> volume #12 level 2.112
+> hide #!12 models
+> show #!13 models
+> volume #13 level 0.04456
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!13 models
+> show #!14 models
+> volume #14 level 0.06454
+> volume #14 level 0.1669
+> hide #!14 models
+> show #!14 models
+> volume #14 level 0.2071
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> show #!7 models
+> volume #7 level 0.1489
+> volume #7 step 1
+> volume #7 level 0.2483
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> select add #7
+models selected
+> show #!3 models
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #7,0.95557,0.0046513,-0.29472,69.933,0.27535,0.34272,0.89818,-107.26,0.10519,-0.93943,0.32621,316.27
+> view matrix models
+> #7,0.91915,0.11688,-0.37617,70.997,0.39267,-0.1961,0.89853,-18.651,0.031252,-0.97359,-0.22614,454.39
+> view matrix models
+> #7,0.91426,0.13556,-0.38178,69.268,0.40482,-0.26848,0.87409,-0.87336,0.015992,-0.9537,-0.30034,468.92
+> view matrix models
+> #7,0.95579,-0.038803,-0.29149,78.32,0.26406,-0.32299,0.90882,32.378,-0.12941,-0.94561,-0.29846,496.89
+> view matrix models
+> #7,0.94972,0.029908,-0.31167,69.398,0.30564,-0.30453,0.90213,21.312,-0.067931,-0.95203,-0.29836,485.5
+> view matrix models
+> #7,0.9488,-0.094559,-0.30141,93.528,0.2555,-0.33137,0.90825,36.024,-0.18576,-0.93875,-0.29025,505.38
+> view matrix models
+> #7,0.95015,-0.094376,-0.29717,92.323,0.25152,-0.33129,0.90939,36.591,-0.18427,-0.9388,-0.29104,505.25
+> view matrix models
+> #7,0.95804,-0.094732,-0.27054,85.191,0.22599,-0.33099,0.91617,40.384,-0.17634,-0.93887,-0.29569,504.6
+> view matrix models
+> #7,0.9581,-0.19453,-0.21025,93.469,0.13432,-0.34319,0.92961,59.077,-0.25299,-0.9189,-0.30268,517.72
+> view matrix models
+> #7,0.95765,-0.21305,-0.19368,93.974,0.11202,-0.34399,0.93227,63.299,-0.26525,-0.91448,-0.30556,519.93
+> hide #!3 models
+> show #!3 models
+> view matrix models
+> #7,0.95696,-0.21706,-0.19263,94.734,0.10944,-0.34484,0.93226,64.012,-0.26878,-0.91322,-0.30625,520.54
+> view matrix models
+> #7,0.94815,-0.27392,-0.1612,101.89,0.14424,-0.081125,0.98621,-9.7554,-0.28322,-0.95833,-0.03741,476.68
+> view matrix models
+> #7,0.95414,-0.24037,-0.17843,97.229,0.16379,-0.079738,0.98327,-13.471,-0.25057,-0.9674,-0.036713,471.68
+> ui mousemode right "translate selected models"
+> view matrix models
+> #7,0.95414,-0.24037,-0.17843,96.447,0.16379,-0.079738,0.98327,-14.654,-0.25057,-0.9674,-0.036713,467.78
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #7,0.99024,-0.071411,-0.11966,41.263,0.11264,-0.095331,0.98905,-2.0232,-0.082036,-0.99288,-0.086357,448.67
+> view matrix models
+> #7,0.99499,-0.013505,-0.099097,23.84,0.096797,-0.11921,0.98814,6.4479,-0.025158,-0.99278,-0.1173,443.37
+> view matrix models
+> #7,0.996,0.01454,-0.088107,15.449,0.089245,-0.12802,0.98775,9.9368,0.0030827,-0.99167,-0.1288,439.71
+> view matrix models
+> #7,0.99258,0.11362,-0.043338,-13.986,0.055935,-0.11014,0.99234,12.115,0.10798,-0.9874,-0.11568,414.38
+> view matrix models
+> #7,0.99638,0.054238,-0.065393,2.2931,0.06993,-0.086471,0.9938,3.9549,0.048247,-0.99478,-0.089951,422.89
+> select subtract #7
+Nothing selected
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> fitmap #7 inMap #3
+Fit map cryosparc_P17_J1268_002_volume_map_sharp.mrc in map
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc using 184853 points
+correlation = 0.8964, correlation about mean = 0.4436, overlap = 2.415e+04
+steps = 140, shift = 3.54, angle = 8.85 degrees
+Position of cryosparc_P17_J1268_002_volume_map_sharp.mrc (#7) relative to
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) coordinates:
+Matrix rotation and translation
+.99817702 -0.04588002 0.03921297 3.35030958
+-0.04066443 -0.03114210 0.99868743 12.39857491
+-0.04459863 -0.99846141 -0.03295101 431.82063884
+Axis -0.99911720 0.04192858 0.00260921
+Axis point 0.00000000 215.36415158 209.87663468
+Rotation angle (degrees) 91.88869867
+Shift along axis -1.70078525
+> fitmap #7 inMap #3
+Fit map cryosparc_P17_J1268_002_volume_map_sharp.mrc in map
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc using 184853 points
+correlation = 0.8964, correlation about mean = 0.4436, overlap = 2.415e+04
+steps = 52, shift = 0.00236, angle = 0.00447 degrees
+Position of cryosparc_P17_J1268_002_volume_map_sharp.mrc (#7) relative to
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) coordinates:
+Matrix rotation and translation
+.99817611 -0.04587745 0.03923922 3.34208981
+-0.04068728 -0.03106753 0.99868882 12.38761501
+-0.04459824 -0.99846385 -0.03287749 431.80589646
+Axis -0.99911670 0.04194141 0.00259649
+Axis point 0.00000000 215.36687767 209.87412872
+Rotation angle (degrees) 91.88448023
+Shift along axis -1.69840331
+> hide #!7 models
+> show #!7 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> lighting soft
+> lighting full
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!3 models
+> volume #7 level 0.22
+> lighting simple
+> show #!5 models
+> hide #!5 models
+> show #!3 models
+> hide #!3 models
+> hide #!7 models
+> show #!3 models
+> close #144-146,148-154
+> show #!162 models
+> hide #!162 models
+> close #162-165
+> close #169-171
+> show #!12 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!13 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> volume #13 level 0.04
+> volume #13 level 0.02
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> hide #!13 models
+> show #!13 models
+> show #!14 models
+> hide #!13 models
+> volume #14 level 0.25
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!14 models
+> hide #!11 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> show #2 models
+> hide #2 models
+> show #!1 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #1/I
+Alignment identifier is 1/I
+> select #1/I:613
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/I:613-657
+atoms, 362 bonds, 45 residues, 1 model selected
+> color sel red
+> select add #1
+atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
+> select subtract #1
+Nothing selected
+> show #2 models
+> hide #!1 models
+> show #!1 models
+> hide #2 models
+> show #2 models
+> hide #!1 models
+> hide #2 models
+> show #2 models
+> hide #2 models
+> show #!19 models
+> hide #!19 models
+> close
+> #19-21,76-84,91-97,136-140,142-143,155-156,158-159,161,166-168,172-173,175-176
+> show #!178 models
+> hide #!178 models
+> show #!232 models
+> hide #!232 models
+> show #!234 models
+> hide #!234 models
+> show #!232 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!232 models
+> hide #!234 models
+> show #!233 models
+> hide #!233 models
+> close #180-231
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!1 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> color #9 #d6d6d6ff models
+> color #9 silver models
+> color #9 darkgrey models
+> color #9 #919191ff models
+> show #!8 models
+> hide #!9 models
+> show #!9 models
+> hide #!8 models
+> show #!8 models
+> hide #!9 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> show #2 models
+> hide #!8 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!8 models
+> show #!3 models
+> select add #8
+models selected
+> select subtract #8
+Nothing selected
+> select add #8
+models selected
+> ui tool show "Color Actions"
+> color sel light sea green
+> select subtract #8
+Nothing selected
+> hide #!8 models
+> show #!9 models
+> select add #9
+models selected
+> color sel steel blue
+> select subtract #9
+Nothing selected
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!9 models
+> hide #!3 models
+> show #!4 models
+> hide #!4 models
+> show #!12 models
+> hide #!12 models
+> show #!13 models
+> show #!14 models
+> hide #!13 models
+> show #!13 models
+> hide #!14 models
+> show #!12 models
+> hide #!12 models
+> show #!3 models
+> fitmap #13 inMap #3
+Fit map cryosparc_P17_J1207_map_sharp.mrc z flip in map
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc using 135754 points
+correlation = 0.8195, correlation about mean = 0.6657, overlap = 1.259e+04
+steps = 52, shift = 2.26, angle = 0.101 degrees
+Position of cryosparc_P17_J1207_map_sharp.mrc z flip (#13) relative to
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) coordinates:
+Matrix rotation and translation
+.99999956 -0.00066700 -0.00066264 0.29074301
+.00066701 0.99999978 0.00001245 -0.17783395
+.00066263 -0.00001289 0.99999978 -0.07194977
+Axis -0.01347599 -0.70471591 0.70936161
+Axis point 192.41646705 437.19131956 0.00000000
+Rotation angle (degrees) 0.05387447
+Shift along axis 0.07036596
+> hide #!13 models
+> show #!12 models
+> fitmap #12 inMap #3
+Fit map cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip in map
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc using 178682 points
+correlation = 0.9651, correlation about mean = 0.6584, overlap = 2.725e+05
+steps = 56, shift = 2.37, angle = 0.0731 degrees
+Position of cryosparc_P17_J1206_003_volume_map_EMReady.mrc z flip (#12)
+relative to cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3)
+coordinates:
+Matrix rotation and translation
+.99999939 0.00102607 0.00041428 -0.30090785
+-0.00102640 0.99999915 0.00080313 0.12472239
+-0.00041345 -0.00080355 0.99999959 0.19980920
+Axis -0.58749376 0.30266385 -0.75049695
+Axis point 102.26087289 256.35146195 0.00000000
+Rotation angle (degrees) 0.07834647
+Shift along axis 0.06457425
+> hide #!12 models
+> fitmap #14 inMap #3
+Fit map cryosparc_P17_J1210_map_sharp.mrc z flip in map
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc using 113255 points
+correlation = 0.9486, correlation about mean = 0.6387, overlap = 2.633e+04
+steps = 52, shift = 2.43, angle = 0.0525 degrees
+Position of cryosparc_P17_J1210_map_sharp.mrc z flip (#14) relative to
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) coordinates:
+Matrix rotation and translation
+.99999995 0.00019277 -0.00024648 0.02840578
+-0.00019280 0.99999997 -0.00012225 0.02141418
+.00024646 0.00012230 0.99999996 -0.18912634
+Axis 0.36395622 -0.73365042 -0.57384051
+Axis point 527.18097402 0.00000000 -37.18039835
+Rotation angle (degrees) 0.01924876
+Shift along axis 0.10315629
+> show #!14 models
+> hide #!14 models
+> show #!10 models
+> hide #!10 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!11 models
+> hide #!8 models
+> hide #!11 models
+> hide #2 models
+> hide #!3 models
+> show #!11 models
+> show #!7 models
+> combine #7
+No structures specified
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1268_002_volume_map_sharp.mrc
+Opened cryosparc_P17_J1268_002_volume_map_sharp.mrc as #15, grid size
+,440,440, pixel 0.95, shown at level 0.0259, step 2, values float32
+> volume #15 step 1
+> volume #15 level 0.22
+> select add #15
+models selected
+> ui mousemode right "translate selected models"
+> view matrix models #15,1,0,0,100.39,0,1,0,-46.513,0,0,1,45.903
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #15,0.80976,-0.45265,0.37335,153.4,0.3286,0.877,0.35057,-163.14,-0.48611,-0.1612,0.8589,208.93
+> view matrix models
+> #15,0.48179,-0.6745,0.5594,227.28,0.3403,0.73229,0.58987,-186.41,-0.80751,-0.093832,0.58234,319.83
+> view matrix models
+> #15,0.11088,-0.79909,0.5909,322.74,0.17639,0.60095,0.77958,-165.65,-0.97805,0.017785,0.20759,411.17
+> ui mousemode right "translate selected models"
+> view matrix models
+> #15,0.11088,-0.79909,0.5909,326.79,0.17639,0.60095,0.77958,-133.13,-0.97805,0.017785,0.20759,331.85
+> view matrix models
+> #15,0.11088,-0.79909,0.5909,305.76,0.17639,0.60095,0.77958,-140.24,-0.97805,0.017785,0.20759,332.58
+> view matrix models
+> #15,0.11088,-0.79909,0.5909,312.36,0.17639,0.60095,0.77958,-53.435,-0.97805,0.017785,0.20759,338.76
+> view matrix models
+> #15,0.11088,-0.79909,0.5909,308.51,0.17639,0.60095,0.77958,-56.402,-0.97805,0.017785,0.20759,338.76
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #15,-0.024164,-0.79613,0.60464,332.95,0.20877,0.58746,0.78186,-60.832,-0.97767,0.14512,0.15201,324.44
+> view matrix models
+> #15,-0.11821,-0.78529,0.60774,349.54,0.18703,0.58347,0.7903,-57.299,-0.97522,0.20709,0.077898,326.9
+> view matrix models
+> #15,-0.105,-0.78677,0.60825,347,0.20205,0.58199,0.78769,-59.555,-0.97373,0.2056,0.097857,322.7
+> view matrix models
+> #15,-0.19293,-0.90299,-0.3839,597.45,0.097707,-0.40698,0.90819,138.04,-0.97633,0.13771,0.16675,322.58
+> view matrix models
+> #15,-0.14742,-0.90868,-0.3906,590.6,0.015659,-0.39701,0.91768,150.99,-0.98895,0.12916,0.072754,346.69
+> view matrix models
+> #15,-0.22245,-0.89505,-0.38653,602.49,0.048703,-0.40617,0.9125,147.11,-0.97373,0.18416,0.13394,319.48
+> view matrix models
+> #15,-0.22402,-0.95714,-0.18358,572.78,0.083751,-0.20657,0.97484,86.116,-0.97098,0.20301,0.12644,316.65
+> ui mousemode right "translate selected models"
+> view matrix models
+> #15,-0.22402,-0.95714,-0.18358,576.09,0.083751,-0.20657,0.97484,-0.31383,-0.97098,0.20301,0.12644,309.91
+> view matrix models
+> #15,-0.22402,-0.95714,-0.18358,576.03,0.083751,-0.20657,0.97484,0.10503,-0.97098,0.20301,0.12644,306.13
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #15,-0.2138,-0.95931,-0.18443,574.53,0.10809,-0.21087,0.97152,-3.3553,-0.97088,0.18777,0.14877,304.52
+> view matrix models
+> #15,-0.23097,-0.97294,-0.0055806,543.26,0.1557,-0.042623,0.98688,-50.688,-0.96042,0.22707,0.16133,291.71
+> ui mousemode right "translate selected models"
+> view matrix models
+> #15,-0.23097,-0.97294,-0.0055806,539.65,0.1557,-0.042623,0.98688,-54.918,-0.96042,0.22707,0.16133,290.53
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #15,-0.28101,-0.95968,0.0065516,544.75,0.21102,-0.055129,0.97593,-61.509,-0.93622,0.27563,0.21801,263.72
+> hide #!15 models
+> show #!15 models
+> select subtract #15
+Nothing selected
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!7 models
+> show #!7 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!7 models
+> show #!7 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> select add #15
+models selected
+> view matrix models
+> #15,-0.25657,-0.95952,-0.11618,565.46,0.1776,-0.16496,0.97018,-31.028,-0.95007,0.22828,0.21274,277.33
+> view matrix models
+> #15,-0.2471,-0.95598,-0.15824,571.63,0.16674,-0.20281,0.96492,-19.967,-0.95454,0.21204,0.20951,282.24
+> select subtract #15
+Nothing selected
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!3 models
+> hide #!11 models
+> show #!177 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> show #243 models
+> hide #243 models
+> close #240-243
+> show #!239 models
+> hide #!239 models
+> close #239
+> close #237-238
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+\u2014\u2014\u2014 End of log from Tue Sep 3 13:30:10 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> hide #!3 models
+> show #!3 models
+> show #!232 models
+> hide #!232 models
+> show #!1 models
+> hide #!177 models
+> hide #!3 models
+> hide #!15 models
+> show #!9 models
+> hide #!9 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> color #8 #20b2aa8f models
+> set bgColor white
+> color #8 #20b2aaa3 models
+> color #8 #20b2aaab models
+> color #8 #20b2aaae models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> color #8 #20b2aa8a models
+> show #!232 models
+> hide #!8 models
+> show #!8 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #1/L
+Alignment identifier is 1/L
+> select clear
+> select #1/L:905-996
+atoms, 638 bonds, 1 pseudobond, 88 residues, 2 models selected
+> hide #!8 models
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> hide #!1 models
+> show #!1 models
+> show #!8 models
+> hide #!232 models
+> lighting soft
+> lighting full
+> lighting simple
+> hide #!1 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J535_003_volume_map_zflip.mrc
+Opened cryosparc_P17_J535_003_volume_map_zflip.mrc as #16, grid size
+,588,588, pixel 0.95, shown at level 0.0831, step 4, values float32
+> select add #8
+atoms, 638 bonds, 1 pseudobond, 88 residues, 6 models selected
+> cofr sel
+> select subtract #8
+atoms, 638 bonds, 1 pseudobond, 88 residues, 2 models selected
+> select add #8
+atoms, 638 bonds, 1 pseudobond, 88 residues, 6 models selected
+> view sel
+> select subtract #8
+atoms, 638 bonds, 1 pseudobond, 88 residues, 2 models selected
+> volume #16 step 1
+> volume #16 level 0.2325
+> select add #16
+atoms, 638 bonds, 1 pseudobond, 88 residues, 5 models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #1,-0.25096,-0.5068,-0.82472,635.54,0.24628,-0.85738,0.45193,125.51,-0.93614,-0.089699,0.33999,418.44,#16,0.38885,-0.060579,0.91931,48.211,-0.26865,0.94702,0.17604,66.153,-0.88126,-0.31542,0.35197,458.59
+> view matrix models
+> #1,-0.22215,-0.94943,-0.22187,455.62,0.42836,-0.29946,0.85254,-75.15,-0.87587,0.094354,0.47323,351.85,#16,-0.088966,0.51185,0.85446,2.4214,-0.38273,0.77443,-0.50376,264.06,-0.91957,-0.37184,0.127,524.01
+> view matrix models
+> #1,-0.38537,-0.9141,-0.12615,489.05,0.83574,-0.40371,0.37223,-86.716,-0.39118,0.038019,0.91953,35.134,#16,-0.26392,0.43198,0.8624,77.602,0.2312,0.89637,-0.37824,28.981,-0.93643,0.099556,-0.33645,444.31
+> view matrix models
+> #1,-0.1356,-0.57517,-0.80671,587.5,0.91613,-0.38283,0.11895,-42.958,-0.37725,-0.72292,0.57884,147.36,#16,0.44409,0.060297,0.89395,-3.9514,0.47456,0.83047,-0.29176,-31.753,-0.75999,0.5538,0.34018,134.84
+> view matrix models
+> #1,0.26845,-0.68107,-0.68124,397.8,0.89856,-0.077833,0.4319,-135.6,-0.34718,-0.72807,0.59108,132.33,#16,0.6063,0.40624,0.68364,-132.59,0.26507,0.70727,-0.65536,126.61,-0.74976,0.57856,0.32114,126.66
+> view matrix models
+> #1,0.38233,-0.62566,-0.67998,352.57,0.87609,0.011513,0.48201,-143.78,-0.29374,-0.78001,0.55254,124.4,#16,0.68689,0.42691,0.58816,-147.27,0.22309,0.64636,-0.72969,170.71,-0.69167,0.63243,0.34874,87.742
+> ui mousemode right "translate selected models"
+> view matrix models
+> #1,0.38233,-0.62566,-0.67998,380.63,0.87609,0.011513,0.48201,-254.96,-0.29374,-0.78001,0.55254,165.63,#16,0.68689,0.42691,0.58816,-119.21,0.22309,0.64636,-0.72969,59.535,-0.69167,0.63243,0.34874,128.97
+> view matrix models
+> #1,0.38233,-0.62566,-0.67998,289.1,0.87609,0.011513,0.48201,-274.53,-0.29374,-0.78001,0.55254,190.38,#16,0.68689,0.42691,0.58816,-210.74,0.22309,0.64636,-0.72969,39.961,-0.69167,0.63243,0.34874,153.72
+> view matrix models
+> #1,0.38233,-0.62566,-0.67998,298.14,0.87609,0.011513,0.48201,-272.93,-0.29374,-0.78001,0.55254,167.18,#16,0.68689,0.42691,0.58816,-201.7,0.22309,0.64636,-0.72969,41.57,-0.69167,0.63243,0.34874,130.51
+> view matrix models
+> #1,0.38233,-0.62566,-0.67998,282.73,0.87609,0.011513,0.48201,-276.94,-0.29374,-0.78001,0.55254,170.84,#16,0.68689,0.42691,0.58816,-217.11,0.22309,0.64636,-0.72969,37.554,-0.69167,0.63243,0.34874,134.18
+> view matrix models
+> #1,0.38233,-0.62566,-0.67998,281.94,0.87609,0.011513,0.48201,-275.2,-0.29374,-0.78001,0.55254,167.66,#16,0.68689,0.42691,0.58816,-217.9,0.22309,0.64636,-0.72969,39.291,-0.69167,0.63243,0.34874,130.99
+> select subtract #16
+atoms, 638 bonds, 1 pseudobond, 88 residues, 2 models selected
+> ui tool show "Fit in Map"
+> select add #1
+atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
+> select subtract #1
+Nothing selected
+> fitmap #16 inMap #8
+Fit map cryosparc_P17_J535_003_volume_map_zflip.mrc in map
+cryosparc_P17_J1163_006_volume_map.mrc using 276739 points
+correlation = 0.9612, correlation about mean = 0.5525, overlap = 1.969e+04
+steps = 164, shift = 2.78, angle = 15.9 degrees
+Position of cryosparc_P17_J535_003_volume_map_zflip.mrc (#16) relative to
+cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
+Matrix rotation and translation
+.99998050 -0.00425494 -0.00457199 0.73851682
+-0.00391421 -0.99738877 0.07211322 540.07003803
+-0.00486689 -0.07209391 -0.99738598 573.94195717
+Axis -0.99999512 0.00204496 0.00236281
+Axis point 0.00000000 280.39509902 277.22388946
+Rotation angle (degrees) 175.86516180
+Shift along axis 1.72202130
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!8 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> fitmap #3 inMap #16
+Fit map cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc in map
+cryosparc_P17_J535_003_volume_map_zflip.mrc using 193604 points
+correlation = 0.9176, correlation about mean = 0.2012, overlap = 2.042e+04
+steps = 124, shift = 8.42, angle = 17.5 degrees
+Position of cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) relative
+to cryosparc_P17_J535_003_volume_map_zflip.mrc (#16) coordinates:
+Matrix rotation and translation
+.58513310 0.56587388 -0.58086660 162.67581615
+.53803292 0.26503049 0.80017461 1.17881883
+.60674527 -0.78073400 -0.14938067 218.34134813
+Axis -0.79945189 -0.60056511 -0.01407893
+Axis point 0.00000000 55.92177713 150.33929755
+Rotation angle (degrees) 98.60424165
+Shift along axis -133.83346040
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> select add #16
+models selected
+> ui tool show "Color Actions"
+> color sel cornflower blue
+> color sel light sea green
+> color sel cornflower blue
+> color sel dark turquoise
+> color sel light sky blue
+[Repeated 1 time(s)]
+> color sel light blue
+> color sel light sky blue
+> color sel light blue
+> color sel light sky blue
+> color sel powder blue
+> color sel light steel blue
+> color sel pale turquoise
+> color sel light blue
+> color sel light sky blue
+> select subtract #16
+Nothing selected
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!8 models
+> show #!8 models
+> hide #!9 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> hide #!3 models
+> show #!8 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J655_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J655_005_volume_map_sharp.mrc as #17, grid size
+,588,588, pixel 0.95, shown at level 0.168, step 4, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J645_010_volume_map_sharp.mrc
+Opened cryosparc_P17_J645_010_volume_map_sharp.mrc as #18, grid size
+,588,588, pixel 0.95, shown at level 0.158, step 4, values float32
+> volume #18 level 0.2742
+> volume #18 step 1
+> volume #18 level 0.4422
+> volume #17 step 1
+> volume #17 level 0.4266
+> select add #17
+models selected
+> view matrix models #17,1,0,0,61.784,0,1,0,-62.478,0,0,1,-102.28
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #17,0.48945,0.25112,-0.83509,356.29,-0.79242,0.52783,-0.30572,377.6,0.36402,0.81137,0.45734,-292.7
+> view matrix models
+> #17,0.15791,0.038191,-0.98672,550.87,-0.45006,0.89221,-0.03749,107.36,0.87893,0.45,0.15807,-262.93
+> view matrix models
+> #17,-0.52223,0.57538,-0.62945,504.75,-0.48515,0.40657,0.77416,41.996,0.70136,0.70967,0.066821,-260.32
+> view matrix models
+> #17,-0.58537,-0.023225,-0.81043,736.95,-0.72536,0.46156,0.5107,164.54,0.3622,0.88681,-0.28703,-119.76
+> ui mousemode right "translate selected models"
+> view matrix models
+> #17,-0.58537,-0.023225,-0.81043,769.33,-0.72536,0.46156,0.5107,134.03,0.3622,0.88681,-0.28703,-184.13
+> view matrix models
+> #17,-0.58537,-0.023225,-0.81043,689.38,-0.72536,0.46156,0.5107,105.15,0.3622,0.88681,-0.28703,-37.942
+> view matrix models
+> #17,-0.58537,-0.023225,-0.81043,631.43,-0.72536,0.46156,0.5107,-28.227,0.3622,0.88681,-0.28703,-100.2
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #17,-0.3388,-0.27569,-0.89956,653.75,-0.79784,0.59094,0.11938,58.328,0.49867,0.75815,-0.42016,-69.159
+> ui mousemode right "translate selected models"
+> view matrix models
+> #17,-0.3388,-0.27569,-0.89956,660.19,-0.79784,0.59094,0.11938,89.728,0.49867,0.75815,-0.42016,-58.912
+> fitmap #17 inMap #8
+Fit map cryosparc_P17_J655_005_volume_map_sharp.mrc in map
+cryosparc_P17_J1163_006_volume_map.mrc using 286513 points
+correlation = 0.8688, correlation about mean = 0.2449, overlap = 8.66e+04
+steps = 256, shift = 11.4, angle = 20.7 degrees
+Position of cryosparc_P17_J655_005_volume_map_sharp.mrc (#17) relative to
+cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
+Matrix rotation and translation
+-0.95262622 -0.30211083 -0.03510445 642.60145687
+.17067519 -0.62654330 0.76046925 202.72382050
+-0.25174046 0.71845148 0.64842440 -51.92560179
+Axis -0.08053233 0.41521020 0.90615398
+Axis point 303.70069952 160.23700769 0.00000000
+Rotation angle (degrees) 164.87800612
+Shift along axis -14.62978716
+> select subtract #17
+Nothing selected
+> hide #!17 models
+> show #!17 models
+> show #!18 models
+> select add #18
+models selected
+> view matrix models #18,1,0,0,64.318,0,1,0,-54.342,0,0,1,-66.309
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #18,-0.21982,0.46975,-0.85499,506.62,-0.95518,0.074469,0.28649,397.56,0.19825,0.87965,0.43233,-216.22
+> view matrix models
+> #18,-0.94049,0.19544,-0.278,639.01,-0.33946,-0.50251,0.79514,246.97,0.015703,0.84219,0.53895,-181.2
+> view matrix models
+> #18,-0.54157,-0.62412,-0.56319,821.43,-0.82771,0.27878,0.487,253.66,-0.14694,0.7299,-0.66757,207.28
+> view matrix models
+> #18,-0.42526,-0.61847,-0.66079,811.74,-0.90422,0.2587,0.3398,319.03,-0.039206,0.742,-0.66925,173.54
+> view matrix models
+> #18,-0.94737,0.13657,-0.28954,659.99,-0.1521,0.60383,0.78247,-104.74,0.2817,0.78533,-0.55128,39.326
+> view matrix models
+> #18,-0.93716,-0.1073,-0.33199,734.43,-0.3217,0.63403,0.70321,-43.906,0.13504,0.76582,-0.62871,106.65
+> ui mousemode right "translate selected models"
+> view matrix models
+> #18,-0.93716,-0.1073,-0.33199,676.58,-0.3217,0.63403,0.70321,-192.92,0.13504,0.76582,-0.62871,39.473
+> view matrix models
+> #18,-0.93716,-0.1073,-0.33199,622.9,-0.3217,0.63403,0.70321,-192.02,0.13504,0.76582,-0.62871,103.22
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #18,-0.79577,-0.00053325,-0.6056,623.89,-0.55271,0.40935,0.72591,-70.483,0.24752,0.91238,-0.32605,-47.021
+> ui mousemode right "translate selected models"
+> view matrix models
+> #18,-0.79577,-0.00053325,-0.6056,629.43,-0.55271,0.40935,0.72591,-66.36,0.24752,0.91238,-0.32605,-58.769
+> fitmap #18 inMap #8
+Fit map cryosparc_P17_J645_010_volume_map_sharp.mrc in map
+cryosparc_P17_J1163_006_volume_map.mrc using 292439 points
+correlation = 0.7365, correlation about mean = 0.04959, overlap = 5.271e+04
+steps = 264, shift = 14.2, angle = 19.7 degrees
+Position of cryosparc_P17_J645_010_volume_map_sharp.mrc (#18) relative to
+cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
+Matrix rotation and translation
+-0.98450205 -0.17536898 0.00119668 603.21178623
+.16771790 -0.93951186 0.29864389 420.47135877
+-0.05124858 0.29421622 0.95436387 -43.01006329
+Axis -0.01275615 0.15109534 0.98843689
+Axis point 282.81965590 240.21101021 0.00000000
+Rotation angle (degrees) 170.00569893
+Shift along axis 13.32387113
+> select subtract #18
+Nothing selected
+> hide #!18 models
+> show #!18 models
+> hide #!17 models
+> select add #18
+models selected
+> view matrix models
+> #18,-0.71292,0.17712,-0.6785,584.31,-0.44227,0.63729,0.63107,-109.78,0.54418,0.74999,-0.37601,-58.453
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #18,-0.60845,0.16613,-0.77601,582.51,-0.56737,0.59263,0.57173,-46.453,0.55487,0.78815,-0.26633,-100.21
+> view matrix models
+> #18,-0.53501,-0.18143,-0.82514,668.78,-0.55166,0.81473,0.17855,-9.9926,0.63987,0.55072,-0.53597,9.6575
+> ui mousemode right "translate selected models"
+> view matrix models
+> #18,-0.53501,-0.18143,-0.82514,676.27,-0.55166,0.81473,0.17855,-55.746,0.63987,0.55072,-0.53597,-8.0105
+> view matrix models
+> #18,-0.53501,-0.18143,-0.82514,686.76,-0.55166,0.81473,0.17855,-55.075,0.63987,0.55072,-0.53597,-10.997
+> view matrix models
+> #18,-0.53501,-0.18143,-0.82514,683.39,-0.55166,0.81473,0.17855,-62.825,0.63987,0.55072,-0.53597,-15.419
+> fitmap #18 inMap #8
+Fit map cryosparc_P17_J645_010_volume_map_sharp.mrc in map
+cryosparc_P17_J1163_006_volume_map.mrc using 292439 points
+correlation = 0.8615, correlation about mean = 0.2577, overlap = 9.246e+04
+steps = 124, shift = 4.79, angle = 8.22 degrees
+Position of cryosparc_P17_J645_010_volume_map_sharp.mrc (#18) relative to
+cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
+Matrix rotation and translation
+-0.95287653 -0.30128223 -0.03543080 642.50639609
+.16990142 -0.62678199 0.76044582 202.97462428
+-0.25131620 0.71859123 0.64843413 -52.01912235
+Axis -0.08049372 0.41518546 0.90616874
+Axis point 303.68746244 160.20985177 0.00000000
+Rotation angle (degrees) 164.93072677
+Shift along axis -14.58371648
+> select subtract #18
+Nothing selected
+> hide #!18 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J842_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #19, grid size
+,588,588, pixel 0.95, shown at level 0.15, step 4, values float32
+> volume #19 step 1
+> volume #19 level 0.3083
+> volume #19 level 0.349
+> ui mousemode right "rotate selected models"
+> select add #19
+models selected
+> view matrix models
+> #19,-0.44408,0.45825,0.76993,46.649,-0.84084,-0.50996,-0.18146,698.91,0.30948,-0.72797,0.61178,228.1
+> view matrix models
+> #19,0.74377,0.47854,0.4667,-198.52,-0.1168,0.7805,-0.61415,275.9,-0.65815,0.40228,0.63641,182.36
+> view matrix models
+> #19,0.63923,-0.27239,0.71916,-40.675,0.75039,0.42547,-0.50585,98.912,-0.16819,0.86301,0.47637,-31.378
+> view matrix models
+> #19,0.48406,-0.45879,0.74511,45.429,0.87025,0.16344,-0.46471,124.56,0.091425,0.87338,0.47838,-107
+> view matrix models
+> #19,0.42748,-0.56077,0.70909,99.683,0.84962,-0.018802,-0.52707,198.53,0.30889,0.82776,0.4684,-152.09
+> view matrix models
+> #19,0.34186,-0.69155,0.63631,180.84,0.90812,0.068905,-0.41301,124.28,0.24177,0.71904,0.65156,-158.63
+> view matrix models
+> #19,0.71424,0.27698,0.64276,-188.14,0.046489,0.89756,-0.43844,146.08,-0.69835,0.34303,0.6282,212.11
+> view matrix models
+> #19,0.62219,0.51419,0.59033,-211.39,-0.24699,0.84448,-0.47524,253.15,-0.74288,0.14988,0.65243,269.79
+> ui mousemode right "translate selected models"
+> view matrix models
+> #19,0.62219,0.51419,0.59033,-152.75,-0.24699,0.84448,-0.47524,157.57,-0.74288,0.14988,0.65243,108.45
+> view matrix models
+> #19,0.62219,0.51419,0.59033,-232.8,-0.24699,0.84448,-0.47524,39.083,-0.74288,0.14988,0.65243,122.29
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #19,0.80455,0.20201,0.55847,-189.06,0.21173,0.78102,-0.58752,-37.641,-0.55486,0.59094,0.58559,-30.003
+> view matrix models
+> #19,0.66658,0.035494,0.74459,-161.06,0.34504,0.87073,-0.3504,-170.05,-0.66077,0.49048,0.56817,31.993
+> view matrix models
+> #19,0.69056,-0.011725,0.72318,-148.48,0.35206,0.87887,-0.32193,-182.74,-0.63181,0.47691,0.61104,14.806
+> ui mousemode right "translate selected models"
+> view matrix models
+> #19,0.69056,-0.011725,0.72318,-139.38,0.35206,0.87887,-0.32193,-182.11,-0.63181,0.47691,0.61104,39.587
+> fitmap #19 inMap #8
+Fit map cryosparc_P17_J842_005_volume_map_sharp.mrc in map
+cryosparc_P17_J1163_006_volume_map.mrc using 437476 points
+correlation = 0.926, correlation about mean = 0.3771, overlap = 9.23e+04
+steps = 76, shift = 5.07, angle = 2.91 degrees
+Position of cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) relative to
+cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
+Matrix rotation and translation
+.99898029 -0.04235492 0.01563476 10.76195054
+-0.02350758 -0.78361084 -0.62080710 683.98076137
+.03854581 0.61980652 -0.78380744 301.98502466
+Axis 0.99971420 -0.01846223 0.01518761
+Axis point 0.00000000 289.57241421 269.88486029
+Rotation angle (degrees) 141.64850238
+Shift along axis 2.71749516
+> select subtract #19
+Nothing selected
+> hide #!8 models
+> show #!17 models
+> hide #!19 models
+> show #!19 models
+> hide #!17 models
+> show #!18 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!18 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J845_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J845_005_volume_map_sharp.mrc as #20, grid size
+,588,588, pixel 0.95, shown at level 0.142, step 4, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J846_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J846_005_volume_map_sharp.mrc as #21, grid size
+,588,588, pixel 0.95, shown at level 0.14, step 4, values float32
+> volume #20 step 1
+> volume #20 level 0.1747
+> volume #20 level 0.2443
+> volume #21 step 1
+> volume #21 level 0.2884
+> select add #19
+models selected
+> select subtract #19
+Nothing selected
+> select add #20
+models selected
+> select add #21
+models selected
+> view matrix models
+> #20,1,0,0,0.47841,0,1,0,-12.3,0,0,1,-3.7669,#21,1,0,0,0.47841,0,1,0,-12.3,0,0,1,-3.7669
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #20,0.63928,-0.35722,0.68096,33.855,0.40184,0.91021,0.10024,-135.3,-0.65562,0.20956,0.72543,208.01,#21,0.63928,-0.35722,0.68096,33.855,0.40184,0.91021,0.10024,-135.3,-0.65562,0.20956,0.72543,208.01
+> view matrix models
+> #20,0.44179,-0.40839,0.79877,77.732,0.52263,0.84084,0.14085,-162.96,-0.72916,0.35524,0.58491,225.7,#21,0.44179,-0.40839,0.79877,77.732,0.52263,0.84084,0.14085,-162.96,-0.72916,0.35524,0.58491,225.7
+> view matrix models
+> #20,0.33252,-0.42236,0.84324,103.34,0.57932,0.79701,0.17076,-175.57,-0.74419,0.43173,0.5097,228.18,#21,0.33252,-0.42236,0.84324,103.34,0.57932,0.79701,0.17076,-175.57,-0.74419,0.43173,0.5097,228.18
+> view matrix models
+> #20,0.46255,-0.082779,0.88272,-43.162,0.6141,0.74804,-0.25164,-61.782,-0.63948,0.65847,0.39684,161.31,#21,0.46255,-0.082779,0.88272,-43.162,0.6141,0.74804,-0.25164,-61.782,-0.63948,0.65847,0.39684,161.31
+> ui mousemode right "translate selected models"
+> view matrix models
+> #20,0.46255,-0.082779,0.88272,-108.16,0.6141,0.74804,-0.25164,-245.68,-0.63948,0.65847,0.39684,53.335,#21,0.46255,-0.082779,0.88272,-108.16,0.6141,0.74804,-0.25164,-245.68,-0.63948,0.65847,0.39684,53.335
+> view matrix models
+> #20,0.46255,-0.082779,0.88272,-113.17,0.6141,0.74804,-0.25164,-247,-0.63948,0.65847,0.39684,59.993,#21,0.46255,-0.082779,0.88272,-113.17,0.6141,0.74804,-0.25164,-247,-0.63948,0.65847,0.39684,59.993
+> hide #!19 models
+> show #!8 models
+> fitmap #20 inMap #8
+Fit map cryosparc_P17_J845_005_volume_map_sharp.mrc in map
+cryosparc_P17_J1163_006_volume_map.mrc using 832636 points
+correlation = 0.9229, correlation about mean = 0.5258, overlap = 1.189e+05
+steps = 380, shift = 9.47, angle = 18.4 degrees
+Position of cryosparc_P17_J845_005_volume_map_sharp.mrc (#20) relative to
+cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
+Matrix rotation and translation
+.99901244 -0.04125012 0.01650989 10.10628769
+-0.02203512 -0.78263856 -0.62208628 683.70365274
+.03858241 0.62110813 -0.78277461 301.46889960
+Axis 0.99972305 -0.01774976 0.01545187
+Axis point 0.00000000 289.37571004 269.89498614
+Rotation angle (degrees) 141.55453890
+Shift along axis 2.62616910
+> hide #!21 models
+> show #!21 models
+> fitmap #21 inMap #8
+Fit map cryosparc_P17_J846_005_volume_map_sharp.mrc in map
+cryosparc_P17_J1163_006_volume_map.mrc using 615528 points
+correlation = 0.9307, correlation about mean = 0.4766, overlap = 1.046e+05
+steps = 256, shift = 8.97, angle = 18.4 degrees
+Position of cryosparc_P17_J846_005_volume_map_sharp.mrc (#21) relative to
+cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
+Matrix rotation and translation
+.99901041 -0.04132365 0.01644837 10.15187435
+-0.02212851 -0.78259628 -0.62213616 683.73846275
+.03858136 0.62115652 -0.78273626 301.42350706
+Axis 0.99972248 -0.01779698 0.01543467
+Axis point 0.00000000 289.39631274 269.89032870
+Rotation angle (degrees) 141.55091738
+Shift along axis 2.63294913
+> select subtract #21
+models selected
+> select subtract #20
+Nothing selected
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!19 models
+> hide #!21 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> volume #19 level 0.3
+> volume #20 level 0.3
+> volume #21 level 0.3
+> ui mousemode right zoom
+> lighting soft
+> hide #!20 models
+> hide #!21 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!19 models
+> show #!19 models
+> hide #!20 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!21 models
+> hide #!19 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> hide #!20 models
+> show #!21 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!21 models
+> show #!177 models
+> hide #!19 models
+> show #!19 models
+> fitmap #177 inMap #19
+Fit molecule 6skl (#177) to map cryosparc_P17_J842_005_volume_map_sharp.mrc
+(#19) using 118220 atoms
+average map value = 0.3221, steps = 64
+shifted from previous position = 0.243
+rotated from previous position = 0.297 degrees
+atoms outside contour = 66812, contour level = 0.3
+Position of 6skl (#177) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.52950222 -0.10066174 -0.84231504 552.59666642
+.51811377 0.74784553 -0.41507252 112.80308239
+.67170345 -0.65619683 -0.34383163 339.58429947
+Axis -0.14584759 -0.91577637 0.37427547
+Axis point 163.10260363 0.00000000 350.04343026
+Rotation angle (degrees) 124.24578811
+Shift along axis -56.79921564
+> hide #!19 models
+> select add #177
+atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> select subtract #177
+Nothing selected
+> color #19 #b2b2ff80 models
+> color #19 #b2b2ffb4 models
+> color #19 #b2b2ffbf models
+> color #19 #b2b2ffd8 models
+> color #19 #b2b2ffc6 models
+> color #19 #b2b2ffc7 models
+> set bgColor black
+> set bgColor transparent
+> hide #!177 models
+> show #!177 models
+> color #19 #b2b2ffff models
+> color #19 #b2b2fffb models
+> color #19 #b2b2ffff models
+> hide #!19 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> hide #!177 models
+> show #!19 models
+> show #!1 models
+> hide #!1 models
+> show #!177 models
+> hide #!177 models
+> show #!15 models
+> hide #!15 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!1 models
+> hide #!1 models
+> ui tool show Matchmaker
+> show #!1 models
+> show #!177 models
+> matchmaker #1/I to #177/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 6skl, chain X (#177) with 8xgc, chain I (#1), sequence alignment
+score = 5322.6
+RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
+.839)
+> select #1/8
+atoms, 7098 bonds, 7 pseudobonds, 859 residues, 3 models selected
+> combine #1
+> hide #!22 models
+> delete atoms (#!1 & sel)
+> delete bonds (#!1 & sel)
+> show #!22 models
+> hide #!22 models
+> show #!22 models
+> hide #!22 models
+> select #1/9
+atoms, 4699 bonds, 3 pseudobonds, 573 residues, 2 models selected
+> delete atoms (#!1 & sel)
+> delete bonds (#!1 & sel)
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> hide #!1 models
+> set bgColor white
+> set bgColor #ffffff00
+> hide #!19 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> hide #!177 models
+> show #!177 models
+> combine #177
+[Repeated 2 time(s)]
+> rename #23 6skl-Mcm2
+> hide #!24 models
+> hide #!25 models
+> hide #!177 models
+> hide #!23 models
+> show #!23 models
+> select #23/2
+atoms, 10708 bonds, 8 pseudobonds, 672 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 108697 bonds, 122 pseudobonds, 6649 residues, 4 models selected
+> delete atoms (#!23 & sel)
+> delete bonds (#!23 & sel)
+> select add #23
+atoms, 10708 bonds, 8 pseudobonds, 672 residues, 3 models selected
+> ui tool show "Color Actions"
+> color sel hot pink
+> show #!19 models
+> color #19 #b2b2ffea models
+> color #19 #b2b2ffde models
+> color #19 #b2b2ffff models
+> color #19 #b2b2ffdd models
+> color #19 #b2b2ffd4 models
+> hide #!19 models
+> show #!19 models
+> color #19 #b2b2ffff models
+> select subtract #23
+Nothing selected
+> hide #!19 models
+> show #!19 models
+> color #19 #b2b2ff7f models
+> color #19 #b2b2ffd4 models
+> lighting soft
+> lighting full
+> lighting soft
+> lighting simple
+> lighting full
+> color #19 #b2b2ff82 models
+> color #19 #b2b2ff90 models
+> hide #!19 models
+> show #!19 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> show #!24 models
+> hide #!24 models
+> show #!24 models
+> hide #!24 models
+> show #!24 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!24 models
+> show #!24 models
+> hide #!24 models
+> show #!24 models
+> hide #!24 models
+> hide #!19 models
+> combine #23
+> ui tool show "Show Sequence Viewer"
+> sequence chain #23/2
+Alignment identifier is 23/2
+> select clear
+[Repeated 1 time(s)]
+> select #23/2:173-442
+atoms, 4320 bonds, 270 residues, 1 model selected
+> select #23/2:458-459
+atoms, 47 bonds, 2 residues, 1 model selected
+> select #23/2:458-459
+atoms, 47 bonds, 2 residues, 1 model selected
+> select #23/2:458
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #23/2:173-458
+atoms, 4577 bonds, 286 residues, 1 model selected
+> select #23/2:466-467
+atoms, 21 bonds, 2 residues, 1 model selected
+> select #23/2:173-467
+atoms, 4697 bonds, 295 residues, 1 model selected
+> select #23/2:465-466
+atoms, 28 bonds, 2 residues, 1 model selected
+> select #23/2:465-466
+atoms, 28 bonds, 2 residues, 1 model selected
+> select #23/2:465
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #23/2:173-465
+atoms, 4675 bonds, 293 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 6033 bonds, 8 pseudobonds, 379 residues, 3 models selected
+> delete atoms (#!23 & sel)
+> delete bonds (#!23 & sel)
+> hide #!26 models
+> rename #23 N-Mcm2_6skl
+> show #!26 models
+> hide #!23 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #26/2
+Alignment identifier is 26/2
+> select #26/2:466
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #26/2:466-868
+atoms, 5986 bonds, 1 pseudobond, 376 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 4722 bonds, 7 pseudobonds, 296 residues, 2 models selected
+> delete atoms (#!26 & sel)
+> delete bonds (#!26 & sel)
+> rename #26 C-Mcm2_6skl
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> hide #!26 models
+> show #!24 models
+> lighting simple
+> show #!26 models
+> hide #!24 models
+> show #!24 models
+> hide #!24 models
+> show #!24 models
+> hide #!26 models
+> hide #!24 models
+> show #!24 models
+> select #25/3
+atoms, 9839 bonds, 7 pseudobonds, 618 residues, 3 models selected
+> select add #25
+atoms, 119405 bonds, 130 pseudobonds, 7321 residues, 4 models selected
+> select subtract #25
+Nothing selected
+> hide #!24 models
+> show #!24 models
+> select #24/3
+atoms, 9839 bonds, 7 pseudobonds, 618 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 109566 bonds, 123 pseudobonds, 6703 residues, 4 models selected
+> delete atoms (#!24 & sel)
+> delete bonds (#!24 & sel)
+> rename #24 Mcm3_6skl
+> combine #24
+> ui tool show "Show Sequence Viewer"
+> sequence chain #24/3
+Alignment identifier is 24/3
+> sequence chain #27/3
+Alignment identifier is 27/3
+> hide #!27 models
+> select #24/3:332
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #24/3:18-332
+atoms, 4476 bonds, 1 pseudobond, 282 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 5363 bonds, 6 pseudobonds, 336 residues, 3 models selected
+> delete atoms (#!24 & sel)
+> delete bonds (#!24 & sel)
+> rename #24 N-Mcm3_6skl
+> show #!27 models
+> hide #!24 models
+> select clear
+> select #27/3:337-675
+atoms, 4351 bonds, 1 pseudobond, 275 residues, 2 models selected
+> select clear
+> select #27/3:337-740
+atoms, 5317 bonds, 2 pseudobonds, 334 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 4522 bonds, 5 pseudobonds, 284 residues, 3 models selected
+> delete atoms (#!27 & sel)
+> delete bonds (#!27 & sel)
+> rename #27 C-Mcm3_6skl
+> show #!24 models
+> select add #27
+atoms, 5317 bonds, 2 pseudobonds, 334 residues, 2 models selected
+> select add #24
+atoms, 9793 bonds, 3 pseudobonds, 616 residues, 4 models selected
+> ui tool show "Color Actions"
+> color sel turquoise
+> color sel cyan
+[Repeated 1 time(s)]
+> color sel turquoise
+[Repeated 1 time(s)]
+> color sel pale turquoise
+[Repeated 4 time(s)]
+> color sel turquoise
+[Repeated 1 time(s)]
+> select subtract #27
+atoms, 4476 bonds, 1 pseudobond, 282 residues, 2 models selected
+> select subtract #24
+Nothing selected
+> hide #!24 models
+> hide #!27 models
+> combine #177
+[Repeated 1 time(s)]
+> hide #!28 models
+> hide #!29 models
+> show #!25 models
+> select #25/4
+atoms, 10952 bonds, 11 pseudobonds, 680 residues, 3 models selected
+> select #25/4
+atoms, 10952 bonds, 11 pseudobonds, 680 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 108453 bonds, 119 pseudobonds, 6641 residues, 4 models selected
+> delete atoms (#!25 & sel)
+> delete bonds (#!25 & sel)
+> rename #25 Mcm4_6skl
+> combine #25
+> ui tool show "Show Sequence Viewer"
+> sequence chain #25/4
+Alignment identifier is 25/4
+> sequence chain #30/4
+Alignment identifier is 30/4
+> hide #!30 models
+> select #25/4:469
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #25/4:174-469
+atoms, 4834 bonds, 296 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 6118 bonds, 11 pseudobonds, 384 residues, 3 models selected
+> delete atoms (#!25 & sel)
+> delete bonds (#!25 & sel)
+> rename #25 N-Mcm4_6skl
+> show #!30 models
+> hide #!25 models
+> select clear
+> select #30/4:505-815
+atoms, 4465 bonds, 4 pseudobonds, 280 residues, 2 models selected
+> select #30/4:505-815
+atoms, 4465 bonds, 4 pseudobonds, 280 residues, 2 models selected
+> select #30/4:505-815
+atoms, 4465 bonds, 4 pseudobonds, 280 residues, 2 models selected
+> select clear
+> select #30/4:505-927
+atoms, 6118 bonds, 6 pseudobonds, 383 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 4834 bonds, 5 pseudobonds, 297 residues, 3 models selected
+> delete atoms (#!30 & sel)
+> delete bonds (#!30 & sel)
+> rename #30 C-Mcm4_6skl
+> show #!25 models
+> select add #25
+atoms, 4834 bonds, 296 residues, 1 model selected
+> select add #30
+atoms, 10952 bonds, 6 pseudobonds, 679 residues, 3 models selected
+> ui tool show "Color Actions"
+> color sel forest green
+> color sel sea green
+> color sel turquoise
+> color sel sea green
+> color sel green
+> color sel forest green
+> color sel sea green
+[Repeated 1 time(s)]
+> select subtract #30
+atoms, 4834 bonds, 296 residues, 1 model selected
+> hide #!30 models
+> select subtract #25
+Nothing selected
+> hide #!25 models
+> show #!28 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> select #28/5
+atoms, 9789 bonds, 11 pseudobonds, 614 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 109616 bonds, 119 pseudobonds, 6707 residues, 4 models selected
+> delete atoms (#!28 & sel)
+> delete bonds (#!28 & sel)
+> rename #28 Mcm5_6skl
+> combine #28
+> select add #28
+atoms, 9789 bonds, 11 pseudobonds, 614 residues, 3 models selected
+> select add #31
+atoms, 19578 bonds, 22 pseudobonds, 1228 residues, 6 models selected
+> ui tool show "Color Actions"
+> color sel yellow
+> select subtract #28
+atoms, 9789 bonds, 11 pseudobonds, 614 residues, 3 models selected
+> select subtract #31
+Nothing selected
+> ui tool show "Show Sequence Viewer"
+> sequence chain #28/5
+Alignment identifier is 28/5
+> sequence chain #31/5
+Alignment identifier is 31/5
+> select #28/5:342
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #28/5:20-342
+atoms, 4202 bonds, 4 pseudobonds, 259 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 5587 bonds, 7 pseudobonds, 355 residues, 2 models selected
+> delete atoms (#!28 & sel)
+> delete bonds (#!28 & sel)
+> hide #!31 models
+> rename #28 N-Mcm5_6skl
+> show #!25 models
+> show #!30 models
+> hide #!30 models
+> hide #!25 models
+> show #!31 models
+> hide #!31 models
+> hide #!28 models
+> show #!31 models
+> select #31/5:343
+atoms, 25 bonds, 1 residue, 1 model selected
+> select #31/5:343-694
+atoms, 5540 bonds, 352 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 4249 bonds, 11 pseudobonds, 262 residues, 3 models selected
+> delete atoms (#!31 & sel)
+> delete bonds (#!31 & sel)
+> rename #31 C-Mcm5_6skl
+> show #!28 models
+> hide #!28 models
+> hide #!31 models
+> combine #177
+> hide #!32 models
+> show #!29 models
+> select #29/6
+atoms, 10126 bonds, 9 pseudobonds, 638 residues, 3 models selected
+> select #29/6
+atoms, 10126 bonds, 9 pseudobonds, 638 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 109279 bonds, 121 pseudobonds, 6683 residues, 4 models selected
+> delete atoms (#!29 & sel)
+> delete bonds (#!29 & sel)
+> rename #29 Mcm6_6skl
+> combine #29
+> select add #29
+atoms, 10126 bonds, 9 pseudobonds, 638 residues, 3 models selected
+> select add #33
+atoms, 20252 bonds, 18 pseudobonds, 1276 residues, 6 models selected
+> ui tool show "Color Actions"
+> color sel orange
+> color sel dark orange
+> color sel orange
+> color sel dark orange
+[Repeated 1 time(s)]
+> color sel goldenrod
+> color sel dark orange
+> color sel sandy brown
+> color sel dark orange
+[Repeated 1 time(s)]
+> select subtract #29
+atoms, 10126 bonds, 9 pseudobonds, 638 residues, 3 models selected
+> select subtract #33
+Nothing selected
+> ui tool show "Show Sequence Viewer"
+> sequence chain #29/6
+Alignment identifier is 29/6
+> sequence chain #33/6
+Alignment identifier is 33/6
+> select #29/6:463
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #29/6:459-463
+atoms, 71 bonds, 5 residues, 1 model selected
+> select
+> #29/6:98-102,105-122,134-147,155-161,164-193,277-284,384-386,407-411,500-521,524-533,540-553,580-592,604-609,626-631,640-650,652-658,694-699,702-707,720-735,747-759,766-784,796-814,820-836
+atoms, 4500 bonds, 275 residues, 1 model selected
+> select clear
+[Repeated 1 time(s)]
+> select #29/6:91-463
+atoms, 4908 bonds, 2 pseudobonds, 305 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 5218 bonds, 7 pseudobonds, 333 residues, 3 models selected
+> delete atoms (#!29 & sel)
+> delete bonds (#!29 & sel)
+> rename #29 N-Mcm6_6skl
+> hide #!29 models
+> show #!29 models
+> hide #!33 models
+> show #!33 models
+> hide #!33 models
+> show #!33 models
+> hide #!33 models
+> show #!33 models
+> hide #!33 models
+> show #!33 models
+> hide #!33 models
+> show #!28 models
+> show #!31 models
+> hide #!31 models
+> hide #!29 models
+> hide #!28 models
+> show #!28 models
+> show #!31 models
+> hide #!28 models
+> show #!28 models
+> hide #!31 models
+> show #!31 models
+> hide #!31 models
+> show #!31 models
+> hide #!31 models
+> show #!31 models
+> hide #!28 models
+> show #!28 models
+> hide #!31 models
+> show #!31 models
+> hide #!28 models
+> show #!28 models
+> hide #!31 models
+> show #!31 models
+> hide #!28 models
+> show #!28 models
+> hide #!31 models
+> hide #!28 models
+> show #!28 models
+> hide #!28 models
+> show #!28 models
+> show #!31 models
+> hide #!28 models
+> show #!28 models
+> hide #!28 models
+> hide #!31 models
+> show #!29 models
+> show #!33 models
+> show #!28 models
+> hide #!28 models
+> hide #!33 models
+> show #!33 models
+> hide #!29 models
+> select clear
+[Repeated 2 time(s)]
+> select #33/6:497-838
+atoms, 5218 bonds, 2 pseudobonds, 332 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 4908 bonds, 7 pseudobonds, 306 residues, 3 models selected
+> delete atoms (#!33 & sel)
+> delete bonds (#!33 & sel)
+> rename #33 C-Mcm6_6skl
+> show #!29 models
+> hide #!29 models
+> hide #!33 models
+> show #!32 models
+> select #32/7
+atoms, 10055 bonds, 11 pseudobonds, 636 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 109350 bonds, 119 pseudobonds, 6685 residues, 4 models selected
+> delete atoms (#!32 & sel)
+> delete bonds (#!32 & sel)
+> select add #32
+atoms, 10055 bonds, 11 pseudobonds, 636 residues, 3 models selected
+> rename #32 Mcm7_6skl
+> ui tool show "Color Actions"
+> color sel deep sky blue
+> color sel cornflower blue
+> color sel dodger blue
+> select subtract #32
+Nothing selected
+> combine #32
+> ui tool show "Show Sequence Viewer"
+> sequence chain #32/7
+Alignment identifier is 32/7
+> sequence chain #34/7
+Alignment identifier is 34/7
+> ui tool show "Show Sequence Viewer"
+> sequence chain #32/7
+Destroying pre-existing alignment with identifier 32/7
+Alignment identifier is 32/7
+> sequence chain #34/7
+Destroying pre-existing alignment with identifier 34/7
+Alignment identifier is 34/7
+> select #32/7:385
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #32/7:4-385
+atoms, 4986 bonds, 3 pseudobonds, 317 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 5069 bonds, 8 pseudobonds, 319 residues, 3 models selected
+> delete atoms (#!32 & sel)
+> delete bonds (#!32 & sel)
+> rename #32 N-Mcm7_6skl
+> select clear
+> select #34/7:396-729
+atoms, 5069 bonds, 3 pseudobonds, 318 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 4986 bonds, 8 pseudobonds, 318 residues, 3 models selected
+> delete atoms (#!34 & sel)
+> delete bonds (#!34 & sel)
+> rename #34 C-Mcm7_6skl
+> hide #!34 models
+> hide #!32 models
+> show #!32 models
+> hide #!32 models
+> show #!34 models
+> hide #!34 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> combine #177
+[Repeated 3 time(s)]
+> hide #!36 models
+> hide #!37 models
+> hide #!38 models
+> hide #!35 models
+> show #!23 models
+> show #!24 models
+> show #!25 models
+> show #!26 models
+> show #!27 models
+> show #!28 models
+> show #!29 models
+> show #!30 models
+> show #!31 models
+> show #!32 models
+> show #!33 models
+> show #!34 models
+> hide #!34 models
+> hide #!33 models
+> hide #!32 models
+> hide #!31 models
+> hide #!30 models
+> hide #!29 models
+> hide #!28 models
+> hide #!27 models
+> hide #!26 models
+> hide #!25 models
+> hide #!24 models
+> hide #!23 models
+> show #!35 models
+> select #35/E
+atoms, 9213 bonds, 4 pseudobonds, 564 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 110192 bonds, 126 pseudobonds, 6757 residues, 4 models selected
+> delete atoms (#!35 & sel)
+> delete bonds (#!35 & sel)
+> rename #35 Cdc45_6skl
+> select add #35
+atoms, 9213 bonds, 4 pseudobonds, 564 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel light cyan
+[Repeated 1 time(s)]
+> color sel powder blue
+> color sel light blue
+[Repeated 1 time(s)]
+> color sel light cyan
+> select subtract #35
+Nothing selected
+> lighting soft
+[Repeated 1 time(s)]
+> lighting full
+> hide #!35 models
+> show #!36 models
+> lighting simple
+> select #36/A,B,C,D
+atoms, 13508 bonds, 6 pseudobonds, 810 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 105897 bonds, 124 pseudobonds, 6511 residues, 4 models selected
+> delete atoms (#!36 & sel)
+> delete bonds (#!36 & sel)
+> select add #36
+atoms, 13508 bonds, 6 pseudobonds, 810 residues, 2 models selected
+> rename #36 GINS_6skl
+> ui tool show "Color Actions"
+> color sel silver
+> color sel gray
+> select clear
+> hide #!36 models
+> show #!37 models
+> select #37/F,G,H
+atoms, 20476 bonds, 6 pseudobonds, 1271 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 98929 bonds, 124 pseudobonds, 6050 residues, 4 models selected
+> delete atoms (#!37 & sel)
+> delete bonds (#!37 & sel)
+> select add #37
+atoms, 20476 bonds, 6 pseudobonds, 1271 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel slate blue
+> color sel medium slate blue
+[Repeated 3 time(s)]
+> color sel royal blue
+> color sel dodger blue
+> color sel royal blue
+[Repeated 1 time(s)]
+> color sel dodger blue
+> color sel royal blue
+> select subtract #37
+Nothing selected
+> show #!32 models
+> hide #!32 models
+> hide #!37 models
+> show #!37 models
+> hide #!37 models
+> rename #37 Ctf4_6skl
+> combine #177
+> hide #!39 models
+> show #!38 models
+> select #38/X
+atoms, 11092 bonds, 7 pseudobonds, 665 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 108313 bonds, 123 pseudobonds, 6656 residues, 4 models selected
+> delete atoms (#!38 & sel)
+> delete bonds (#!38 & sel)
+> rename #38 Tof1_6skl
+> select add #38
+atoms, 11092 bonds, 7 pseudobonds, 665 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel slate blue
+> color sel medium slate blue
+> color sel royal blue
+> color sel medium slate blue
+[Repeated 7 time(s)]
+> color sel dark slate blue
+> color sel medium slate blue
+> select subtract #38
+Nothing selected
+> hide #!38 models
+> show #!38 models
+> show #!39 models
+> hide #!38 models
+> select #39/Y
+atoms, 1632 bonds, 94 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 117773 bonds, 130 pseudobonds, 7227 residues, 4 models selected
+> delete atoms (#!39 & sel)
+> delete bonds (#!39 & sel)
+> rename #39 Csm3_6skl
+> select add #39
+atoms, 1632 bonds, 94 residues, 1 model selected
+> hide #!39 models
+> select subtract #39
+Nothing selected
+> show #!39 models
+> show #!38 models
+> show #!37 models
+> show #!36 models
+> show #!35 models
+> show #!34 models
+> show #!33 models
+> show #!32 models
+> show #!31 models
+> show #!30 models
+> show #!29 models
+> show #!28 models
+> show #!27 models
+> show #!26 models
+> show #!25 models
+> show #!24 models
+> show #!23 models
+> select add #39
+atoms, 1632 bonds, 94 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel orchid
+> color sel blue violet
+> color sel deep pink
+> color sel magenta
+> color sel dark magenta
+> color sel purple
+[Repeated 1 time(s)]
+> color sel dark magenta
+> color sel purple
+[Repeated 1 time(s)]
+> color sel medium purple
+> color sel purple
+[Repeated 1 time(s)]
+> select subtract #39
+Nothing selected
+> combine #177
+> hide #!39 models
+> hide #!38 models
+> hide #!37 models
+> hide #!36 models
+> hide #!35 models
+> hide #!34 models
+> show #!35 models
+> hide #!35 models
+> show #!35 models
+> hide #!35 models
+> show #!34 models
+> hide #!33 models
+> hide #!40 models
+> show #!35 models
+> hide #!35 models
+> hide #!34 models
+> hide #!32 models
+> hide #!31 models
+> hide #!30 models
+> hide #!29 models
+> hide #!28 models
+> hide #!27 models
+> hide #!26 models
+> hide #!25 models
+> hide #!24 models
+> hide #!23 models
+> show #!40 models
+> select #40/I,J
+atoms, 2015 bonds, 50 pseudobonds, 59 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 117390 bonds, 80 pseudobonds, 7262 residues, 3 models selected
+> delete atoms (#!40 & sel)
+> delete bonds (#!40 & sel)
+> rename #40 DNA_6skl
+> select #40/I
+atoms, 1279 bonds, 37 residues, 1 model selected
+> color sel black
+> select #40/J
+atoms, 736 bonds, 22 residues, 1 model selected
+> color sel dim gray
+> select clear
+> hide #!40 models
+> show #!19 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!19 models
+> show #!24 models
+> show #!25 models
+> hide #!25 models
+> hide #!24 models
+> hide #!23 models
+> show #!23 models
+> show #!19 models
+> fitmap #23 inMap #19
+Fit molecule N-Mcm2_6skl (#23) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4631 atoms
+average map value = 0.4542, steps = 52
+shifted from previous position = 1.09
+rotated from previous position = 3.28 degrees
+atoms outside contour = 1773, contour level = 0.3
+Position of N-Mcm2_6skl (#23) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.48619287 -0.07981194 -0.87019915 544.75612919
+.53368692 0.76140981 -0.36801274 98.39251819
+.69194998 -0.64333907 -0.32759742 329.31388927
+Axis -0.16188679 -0.91851479 0.36072599
+Axis point 157.28465121 0.00000000 346.27079505
+Rotation angle (degrees) 121.74840423
+Shift along axis -59.77172713
+> fitmap #23 inMap #19
+Fit molecule N-Mcm2_6skl (#23) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4631 atoms
+average map value = 0.4542, steps = 36
+shifted from previous position = 0.0153
+rotated from previous position = 0.0153 degrees
+atoms outside contour = 1772, contour level = 0.3
+Position of N-Mcm2_6skl (#23) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.48612668 -0.08005636 -0.87021368 544.79200838
+.53355946 0.76145094 -0.36811244 98.44034714
+.69209476 -0.64326002 -0.32744679 329.22783276
+Axis -0.16176651 -0.91852227 0.36076090
+Axis point 157.31175798 0.00000000 346.27934228
+Rotation angle (degrees) 121.73971426
+Shift along axis -59.77622153
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!24 models
+> fitmap #24 inMap #19
+Fit molecule N-Mcm3_6skl (#24) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4424 atoms
+average map value = 0.4899, steps = 72
+shifted from previous position = 1.7
+rotated from previous position = 1.03 degrees
+atoms outside contour = 1496, contour level = 0.3
+Position of N-Mcm3_6skl (#24) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.51684057 -0.09904554 -0.85033277 552.53192555
+.53049272 0.74253315 -0.40892786 109.84096466
+.67190275 -0.66244585 -0.33122832 337.40029650
+Axis -0.15211044 -0.91333918 0.37772207
+Axis point 161.67410853 0.00000000 351.20284420
+Rotation angle (degrees) 123.55710836
+Shift along axis -56.92439016
+> hide #!24 models
+> show #!25 models
+> fitmap #25 inMap #19
+Fit molecule N-Mcm4_6skl (#25) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4793 atoms
+average map value = 0.4529, steps = 52
+shifted from previous position = 2.33
+rotated from previous position = 1.94 degrees
+atoms outside contour = 1614, contour level = 0.3
+Position of N-Mcm4_6skl (#25) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.51485483 -0.08657680 -0.85289447 549.29032703
+.51292450 0.76605243 -0.38739145 104.77742894
+.68690099 -0.63692082 -0.34999843 331.94917409
+Axis -0.14931878 -0.92141613 0.35874256
+Axis point 162.77097442 0.00000000 344.51466083
+Rotation angle (degrees) 123.32588851
+Shift along axis -59.47868024
+> hide #!25 models
+> show #!28 models
+> fitmap #28 inMap #19
+Fit molecule N-Mcm5_6skl (#28) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4172 atoms
+average map value = 0.5001, steps = 48
+shifted from previous position = 0.477
+rotated from previous position = 0.518 degrees
+atoms outside contour = 1491, contour level = 0.3
+Position of N-Mcm5_6skl (#28) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.52208241 -0.10009271 -0.84700143 552.10007852
+.52281543 0.74707399 -0.41054169 110.98680483
+.67386497 -0.65716201 -0.33770418 337.87117097
+Axis -0.14839770 -0.91514390 0.37481963
+Axis point 162.27606171 0.00000000 350.25308806
+Rotation angle (degrees) 123.80418376
+Shift along axis -56.85853328
+> hide #!28 models
+> show #!29 models
+> fitmap #29 inMap #19
+Fit molecule N-Mcm6_6skl (#29) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4862 atoms
+average map value = 0.4386, steps = 64
+shifted from previous position = 1.82
+rotated from previous position = 1.81 degrees
+atoms outside contour = 1794, contour level = 0.3
+Position of N-Mcm6_6skl (#29) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.50972104 -0.08434926 -0.85619488 547.63107126
+.52443527 0.75845239 -0.38693363 104.75971281
+.68202061 -0.64624700 -0.34236341 333.92722557
+Axis -0.15485966 -0.91860876 0.36356077
+Axis point 160.21705818 0.00000000 346.31455571
+Rotation angle (degrees) 123.14885220
+Shift along axis -59.63631555
+> hide #!29 models
+> show #!32 models
+> fitmap #32 inMap #19
+Fit molecule N-Mcm7_6skl (#32) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 4942 atoms
+average map value = 0.4432, steps = 72
+shifted from previous position = 2.55
+rotated from previous position = 2 degrees
+atoms outside contour = 1716, contour level = 0.3
+Position of N-Mcm7_6skl (#32) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.50209844 -0.09646270 -0.85941382 551.56164113
+.52217420 0.75834411 -0.39019012 105.12547600
+.68937019 -0.64467757 -0.33039306 330.21496061
+Axis -0.15084576 -0.91803150 0.36669294
+Axis point 162.01873803 0.00000000 348.31963616
+Rotation angle (degrees) 122.48465413
+Shift along axis -58.62173799
+> hide #!32 models
+> show #!26 models
+> hide #!26 models
+> show #!27 models
+> fitmap #27 inMap #19
+Fit molecule C-Mcm3_6skl (#27) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5283 atoms
+average map value = 0.2453, steps = 68
+shifted from previous position = 2.23
+rotated from previous position = 2.57 degrees
+atoms outside contour = 3746, contour level = 0.3
+Position of C-Mcm3_6skl (#27) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.49125191 -0.10951013 -0.86410596 552.71575277
+.52980778 0.74986873 -0.39623302 105.24621685
+.69135757 -0.65246028 -0.31035512 328.13372850
+Axis -0.15062172 -0.91437023 0.37581934
+Axis point 161.23471230 0.00000000 351.59387631
+Rotation angle (degrees) 121.72677225
+Shift along axis -56.16600219
+> hide #!27 models
+> show #!26 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> fitmap #26 inMap #19
+Fit molecule C-Mcm2_6skl (#26) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5941 atoms
+average map value = 0.2499, steps = 120
+shifted from previous position = 7.11
+rotated from previous position = 16.9 degrees
+atoms outside contour = 4089, contour level = 0.3
+Position of C-Mcm2_6skl (#26) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.72499338 -0.17926092 -0.66501889 564.61757623
+.30570305 0.78146839 -0.54392354 172.58562424
+.61719547 -0.59763926 -0.51175880 374.68531048
+Axis -0.03915385 -0.93461689 0.35349433
+Axis point 195.27960459 0.00000000 339.48855257
+Rotation angle (degrees) 136.68906839
+Shift along axis -50.95925582
+> hide #!26 models
+> show #!27 models
+> hide #!27 models
+> show #!30 models
+> hide #!30 models
+> show #!31 models
+> fitmap #31 inMap #19
+Fit molecule C-Mcm5_6skl (#31) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5504 atoms
+average map value = 0.2192, steps = 72
+shifted from previous position = 1.38
+rotated from previous position = 0.644 degrees
+atoms outside contour = 4241, contour level = 0.3
+Position of C-Mcm5_6skl (#31) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.52798995 -0.11167009 -0.84187672 553.62723896
+.51297984 0.74809912 -0.42095058 113.66344352
+.67681482 -0.65412346 -0.33770431 336.54923223
+Axis -0.14058346 -0.91564213 0.37661090
+Axis point 164.28052383 0.00000000 350.23415639
+Rotation angle (degrees) 123.97268209
+Shift along axis -55.15775830
+> hide #!31 models
+> show #!32 models
+> hide #!32 models
+> show #!33 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> fitmap #33 inMap #19
+Fit molecule C-Mcm6_6skl (#33) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5182 atoms
+average map value = 0.2506, steps = 100
+shifted from previous position = 2.49
+rotated from previous position = 3.08 degrees
+atoms outside contour = 3615, contour level = 0.3
+Position of C-Mcm6_6skl (#33) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.56822296 -0.11833571 -0.81432140 555.66185955
+.48213507 0.75407081 -0.44600784 124.85237619
+.66683465 -0.64604479 -0.37142655 342.86696321
+Axis -0.12419139 -0.91956426 0.37279763
+Axis point 169.39701035 0.00000000 347.59627562
+Rotation angle (degrees) 126.35519939
+Shift along axis -55.99821082
+> hide #!33 models
+> show #!34 models
+> fitmap #34 inMap #19
+Fit molecule C-Mcm7_6skl (#34) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5038 atoms
+average map value = 0.2488, steps = 84
+shifted from previous position = 3.58
+rotated from previous position = 6.44 degrees
+atoms outside contour = 3687, contour level = 0.3
+Position of C-Mcm7_6skl (#34) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.60810284 -0.04397762 -0.79263921 541.80870758
+.49024443 0.76452307 -0.41852703 112.51289532
+.62439678 -0.64309443 -0.44334887 361.42999934
+Axis -0.14668479 -0.92559125 0.34894756
+Axis point 166.00281620 0.00000000 336.12434083
+Rotation angle (degrees) 130.05063287
+Shift along axis -57.49592849
+> hide #!34 models
+> show #!26 models
+> fitmap #26 inMap #19
+Fit molecule C-Mcm2_6skl (#26) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5941 atoms
+average map value = 0.2499, steps = 40
+shifted from previous position = 0.00827
+rotated from previous position = 0.0158 degrees
+atoms outside contour = 4089, contour level = 0.3
+Position of C-Mcm2_6skl (#26) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.72508101 -0.17912737 -0.66495934 564.59530186
+.30560205 0.78160601 -0.54378253 172.54320727
+.61714254 -0.59749932 -0.51198599 374.71726789
+Axis -0.03915999 -0.93466297 0.35337179
+Axis point 195.28291115 0.00000000 339.45035239
+Rotation angle (degrees) 136.69646920
+Shift along axis -50.96478166
+> hide #!26 models
+> show #!27 models
+> fitmap #27 inMap #19
+Fit molecule C-Mcm3_6skl (#27) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5283 atoms
+average map value = 0.2453, steps = 48
+shifted from previous position = 0.00561
+rotated from previous position = 0.0144 degrees
+atoms outside contour = 3745, contour level = 0.3
+Position of C-Mcm3_6skl (#27) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.49119447 -0.10962931 -0.86412349 552.72708725
+.52963562 0.75000136 -0.39621215 105.24134461
+.69153026 -0.65228780 -0.31033293 328.08057761
+Axis -0.15052098 -0.91441153 0.37575921
+Axis point 161.25504150 0.00000000 351.58454506
+Rotation angle (degrees) 121.71962364
+Shift along axis -56.15162171
+> fitmap #27 inMap #19
+Fit molecule C-Mcm3_6skl (#27) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5283 atoms
+average map value = 0.2453, steps = 44
+shifted from previous position = 0.00644
+rotated from previous position = 0.00323 degrees
+atoms outside contour = 3747, contour level = 0.3
+Position of C-Mcm3_6skl (#27) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.49121423 -0.10960226 -0.86411569 552.72290598
+.52966978 0.74997300 -0.39622018 105.24674287
+.69149006 -0.65232495 -0.31034441 328.08956470
+Axis -0.15054136 -0.91440312 0.37577152
+Axis point 161.25087455 0.00000000 351.58379235
+Rotation angle (degrees) 121.72163061
+Shift along axis -56.15889268
+> hide #!27 models
+> show #!33 models
+> hide #!33 models
+> show #!34 models
+> fitmap #34 inMap #19
+Fit molecule C-Mcm7_6skl (#34) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 5038 atoms
+average map value = 0.2488, steps = 40
+shifted from previous position = 0.021
+rotated from previous position = 0.0237 degrees
+atoms outside contour = 3683, contour level = 0.3
+Position of C-Mcm7_6skl (#34) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.60807905 -0.04366734 -0.79267461 541.74998075
+.49057375 0.76436052 -0.41843804 112.46427092
+.62416126 -0.64330876 -0.44336957 361.50164606
+Axis -0.14689577 -0.92554158 0.34899056
+Axis point 165.95199356 0.00000000 336.12532515
+Rotation angle (degrees) 130.05660056
+Shift along axis -57.51048000
+> hide #!34 models
+> show #!35 models
+> fitmap #35 inMap #19
+Fit molecule Cdc45_6skl (#35) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 9129 atoms
+average map value = 0.4936, steps = 32
+shifted from previous position = 0.989
+rotated from previous position = 0.293 degrees
+atoms outside contour = 3011, contour level = 0.3
+Position of Cdc45_6skl (#35) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.53238330 -0.10222439 -0.84030840 552.34452064
+.51398389 0.74970935 -0.41684104 113.43549525
+.67259838 -0.65382418 -0.34659105 340.11300103
+Axis -0.14356656 -0.91653277 0.37330461
+Axis point 163.36596759 0.00000000 349.77928908
+Rotation angle (degrees) 124.37677529
+Shift along axis -56.29979678
+> hide #!35 models
+> show #!36 models
+> fitmap #36 inMap #19
+Fit molecule GINS_6skl (#36) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 13385 atoms
+average map value = 0.5009, steps = 64
+shifted from previous position = 1.25
+rotated from previous position = 0.693 degrees
+atoms outside contour = 4520, contour level = 0.3
+Position of GINS_6skl (#36) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.53440728 -0.10575367 -0.83858514 554.21323619
+.51997798 0.74104668 -0.42482082 114.22988038
+.66635709 -0.66307314 -0.34103116 341.67599231
+Axis -0.14464380 -0.91365555 0.37988381
+Axis point 163.82286606 0.00000000 351.69409164
+Rotation angle (degrees) 124.55491640
+Shift along axis -54.73309110
+> hide #!36 models
+> show #!37 models
+> fitmap #37 inMap #19
+Fit molecule Ctf4_6skl (#37) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 20221 atoms
+average map value = 0.3967, steps = 68
+shifted from previous position = 1.75
+rotated from previous position = 0.685 degrees
+atoms outside contour = 7725, contour level = 0.3
+Position of Ctf4_6skl (#37) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.53679956 -0.10566869 -0.83706653 554.09013415
+.51701361 0.74282869 -0.42532631 116.11912844
+.66674070 -0.66108976 -0.34411796 343.05037030
+Axis -0.14335492 -0.91438332 0.37861921
+Axis point 163.58631600 0.00000000 352.06583111
+Rotation angle (degrees) 124.68361653
+Shift along axis -55.72348034
+> hide #!37 models
+> show #!38 models
+> fitmap #38 inMap #19
+Fit molecule Tof1_6skl (#38) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 10990 atoms
+average map value = 0.3486, steps = 52
+shifted from previous position = 2.71
+rotated from previous position = 2.1 degrees
+atoms outside contour = 4840, contour level = 0.3
+Position of Tof1_6skl (#38) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.50884095 -0.07790103 -0.85732860 546.87430545
+.52700003 0.75928729 -0.38177714 104.30156172
+.68069954 -0.64607604 -0.34530262 334.50800166
+Axis -0.15791244 -0.91893600 0.36141430
+Axis point 159.52485154 0.00000000 345.83620169
+Rotation angle (degrees) 123.19075103
+Shift along axis -61.30873983
+> hide #!38 models
+> show #!39 models
+> fitmap #39 inMap #19
+Fit molecule Csm3_6skl (#39) to map
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) using 1616 atoms
+average map value = 0.3779, steps = 60
+shifted from previous position = 2.5
+rotated from previous position = 1.9 degrees
+atoms outside contour = 645, contour level = 0.3
+Position of Csm3_6skl (#39) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.51530602 -0.07349129 -0.85384937 547.02376900
+.53880358 0.74699785 -0.38946748 106.53379719
+.66644611 -0.66075203 -0.34533512 340.04339220
+Axis -0.16330007 -0.91514372 0.36857164
+Axis point 158.27460801 0.00000000 348.00938205
+Rotation angle (degrees) 123.83627701
+Shift along axis -61.49240111
+> hide #!39 models
+> show #!40 models
+> fitmap #40 inMap #19
+Fit molecule DNA_6skl (#40) to map cryosparc_P17_J842_005_volume_map_sharp.mrc
+(#19) using 1878 atoms
+average map value = 0.3403, steps = 80
+shifted from previous position = 1.35
+rotated from previous position = 3.78 degrees
+atoms outside contour = 831, contour level = 0.3
+Position of DNA_6skl (#40) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc (#19) coordinates:
+Matrix rotation and translation
+-0.47993510 -0.10126507 -0.87144001 550.20291579
+.51412450 0.77241029 -0.37290528 101.33591686
+.71087151 -0.62699899 -0.31864396 321.37532285
+Axis -0.14801492 -0.92172967 0.35847734
+Axis point 161.49135847 0.00000000 346.98780116
+Rotation angle (degrees) 120.86949809
+Shift along axis -59.63678931
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> combine #23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40
+Remapping chain ID '2' in C-Mcm2_6skl #26 to '5'
+Remapping chain ID '3' in C-Mcm3_6skl #27 to '6'
+Remapping chain ID '5' in N-Mcm5_6skl #28 to '7'
+Remapping chain ID '6' in N-Mcm6_6skl #29 to '8'
+Remapping chain ID '4' in C-Mcm4_6skl #30 to '9'
+Remapping chain ID '5' in C-Mcm5_6skl #31 to '0'
+Remapping chain ID '7' in N-Mcm7_6skl #32 to 'AA'
+Remapping chain ID '6' in C-Mcm6_6skl #33 to 'AB'
+Remapping chain ID '7' in C-Mcm7_6skl #34 to 'AC'
+> hide #!19 models
+> select add #41
+atoms, 119265 bonds, 97 pseudobonds, 7310 residues, 3 models selected
+> cartoon style (#!41 & sel) xsection oval modeHelix default
+> cartoon style (#!41 & sel) xsection rectangle modeHelix default
+> cartoon style (#!41 & sel & coil) xsection oval
+> cartoon style (#!41 & sel) xsection barbell modeHelix default
+> cartoon style (#!41 & sel) xsection oval modeHelix default
+> cartoon hide (#!41 & sel)
+> show (#!41 & sel) target ab
+> ui tool show "Color Zone"
+> select subtract #41
+Nothing selected
+> hide #!41 models
+> show #!19 models
+> color #19 #b2b2ffff models
+> volume copy #19
+Opened cryosparc_P17_J842_005_volume_map_sharp.mrc copy as #42, grid size
+,588,588, pixel 0.95, shown at step 1, values float32
+> hide #!42 models
+> show #!42 models
+> show #!41 models
+> hide #!41 models
+> ui tool show "Hide Dust"
+> surface dust #42 size 5.7
+> surface dust #42 size 5.67
+> surface dust #42 size 6.93
+> surface dust #42 size 7.1
+> surface dust #42 size 5.86
+> surface dust #42 size 5.91
+> surface dust #42 size 6.71
+> show #!41 models
+> color zone #42 near #41 distance 5.7
+> hide #!41 models
+> lighting soft
+> lighting simple
+> graphics silhouettes true
+> color zone #42 near #41 distance 5.8
+> color zone #42 near #41 distance 5.9
+> show #!41 models
+> color zone #42 near #41 distance 5.9
+> color zone #42 near #41 distance 6.2
+> color zone #42 near #41 distance 7.58
+> color zone #42 near #41 distance 6.79
+> color zone #42 near #41 distance 10.77
+> color zone #42 near #41 distance 11.05
+> color zone #42 near #41 distance 8.88
+> color zone #42 near #41 distance 10.95
+> color zone #42 near #41 distance 9.58
+> hide #!42 models
+> show #!42 models
+> color zone #42 near #41 distance 9.68
+> color zone #42 near #41 distance 9.6
+> color zone #42 near #41 distance 9
+> color zone #42 near #41 distance 9.9
+> color zone #42 near #41 distance 9.99
+> color zone #42 near #41 distance 10.42
+> color zone #42 near #41 distance 11.42
+> hide #!42 models
+> show #!42 models
+> lighting soft
+> hide #!41 models
+> hide #!42 models
+> show #!42 models
+> lighting simple
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+[Repeated 1 time(s)]
+\u2014\u2014\u2014 End of log from Wed Sep 4 05:32:36 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> show #!3 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> lighting full
+> lighting soft
+> lighting simple
+> show #2 models
+> hide #2 models
+> show #2 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!22 models
+> hide #!22 models
+> show #!1 models
+> ui tool show Matchmaker
+> matchmaker #1/I to #38/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker Tof1_6skl, chain X (#38) with 8xgc, chain I (#1), sequence
+alignment score = 5308.2
+RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
+.839)
+> hide #!3 models
+> show #!3 models
+> combine #1
+> hide #!1 models
+> show #!22 models
+> hide #!22 models
+> rename #22 8xgc_with_polE
+> hide #!43 models
+> show #!43 models
+> hide #!43 models
+> show #!43 models
+> select #43/L,M,P,Q,N,R,O,S
+atoms, 9480 bonds, 10 pseudobonds, 1379 residues, 2 models selected
+> hide (#!43 & sel) target a
+> cartoon hide (#!43 & sel)
+> hide #2 models
+> show #2 models
+> hide #2 models
+> cartoon (#!43 & sel)
+> delete atoms (#!43 & sel)
+> delete bonds (#!43 & sel)
+> hide #!43 models
+> show #!43 models
+> select #43/2,I
+atoms, 12460 bonds, 7 pseudobonds, 1525 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 50669 bonds, 146 pseudobonds, 6085 residues, 4 models selected
+> select #43/2,I,X,Y
+atoms, 14513 bonds, 93 pseudobonds, 1615 residues, 4 models selected
+> select ~sel & ##selected
+atoms, 48616 bonds, 60 pseudobonds, 5995 residues, 3 models selected
+> delete atoms (#!43 & sel)
+> delete bonds (#!43 & sel)
+> hide #!43 models
+> show #!43 models
+> rename #43 Tof1_Mcm2_DNA_8xgc
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> hide #!43 models
+> show #!43 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> ui tool show "Fit in Map"
+> hide #!3 models
+> show #!3 models
+> hide #!8 models
+> show #!8 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> show #!9 models
+> hide #!9 models
+> fitmap #3 inMap #8
+Fit map cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc in map
+cryosparc_P17_J1163_006_volume_map.mrc using 193604 points
+correlation = 0.9192, correlation about mean = 0.0445, overlap = 1.418e+04
+steps = 72, shift = 2.72, angle = 2.42 degrees
+Position of cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) relative
+to cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
+Matrix rotation and translation
+.59052855 0.53373057 -0.60531621 170.37442141
+-0.50876033 -0.33602858 -0.79262080 554.64399601
+-0.62644949 0.77602608 0.07310647 351.56427577
+Axis 0.83279921 0.01121972 -0.55346146
+Axis point 0.00000000 138.28597245 467.32476580
+Rotation angle (degrees) 109.64532984
+Shift along axis -46.46664408
+> hide #!8 models
+> show #!232 models
+> hide #!232 models
+> show #!234 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> hide #!234 models
+> show #!234 models
+> hide #!3 models
+> show #!3 models
+> fitmap #234 inMap #3
+Fit molecule copy of 1id3 (#234) to map
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) using 6114 atoms
+average map value = 0.2545, steps = 96
+shifted from previous position = 4.78
+rotated from previous position = 8.84 degrees
+atoms outside contour = 2956, contour level = 0.25
+Position of copy of 1id3 (#234) relative to
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc (#3) coordinates:
+Matrix rotation and translation
+-0.05320350 -0.99827136 0.02497348 191.32301696
+-0.66299192 0.05401395 0.74667544 251.48569117
+-0.74673362 0.02316853 -0.66471958 182.33677195
+Axis -0.65199157 0.69542739 0.30213861
+Axis point 246.33178982 0.00000000 -20.06616176
+Rotation angle (degrees) 146.30004573
+Shift along axis 105.24002362
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> hide #!234 models
+> show #!177 models
+> hide #!177 models
+> show #!232 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> select #43/x
+atoms, 1159 bonds, 51 residues, 1 model selected
+> color sel black
+> select #43/y
+atoms, 894 bonds, 39 residues, 1 model selected
+> color sel gray
+> select clear
+> select #232/J
+atoms, 3354 bonds, 6 pseudobonds, 160 residues, 2 models selected
+> color (#!232 & sel) black
+> select #232/I
+atoms, 3354 bonds, 3 pseudobonds, 162 residues, 2 models selected
+> color (#!232 & sel) gray
+> select clear
+> select #232/A#232/E#234/A#234/E
+atoms, 3252 bonds, 410 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel khaki
+[Repeated 4 time(s)]
+> color sel peach puff
+> color sel moccasin
+[Repeated 1 time(s)]
+> color sel khaki
+[Repeated 4 time(s)]
+> select #232/B#232/F#234/B#234/F
+atoms, 2652 bonds, 346 residues, 2 models selected
+> color sel khaki
+[Repeated 1 time(s)]
+> select #232/C#232/G#234/C#234/G
+atoms, 3400 bonds, 4 pseudobonds, 462 residues, 4 models selected
+> color sel plum
+[Repeated 2 time(s)]
+> select #232/D#232/H#234/D#234/H
+atoms, 2988 bonds, 2 pseudobonds, 406 residues, 4 models selected
+> color sel plum
+> select clear
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> volume copy #3
+Opened cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy as #44, grid
+size 440,440,440, pixel 0.95, shown at step 1, values float32
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!43 models
+> hide #!42 models
+> hide #!44 models
+> show #!44 models
+> hide #!232 models
+> show #!232 models
+> ui tool show "Color Zone"
+> hide #!44 models
+> show #!44 models
+> color zone #44 near #232 distance 5.7
+> hide #!232 models
+> lighting soft
+> show #!42 models
+> lighting soft
+> lighting full
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!43 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> select #43/2
+atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
+> color sel hot pink
+> select clear
+> ui tool show "Show Sequence Viewer"
+> sequence chain #43/I
+Alignment identifier is 43/I
+> select #43/2
+atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
+> cartoon hide (#!43 & sel)
+> lighting simple
+> lighting soft
+> show #!8 models
+> color #8 #d6d6d6ff models
+> color #8 #ebebebff models
+> color #8 #ebebeb80 models
+> color #8 silver models
+[Repeated 1 time(s)]
+> color #8 #c0c0c080 models
+> color #8 #c0c0c08b models
+> color #8 #c0c0c09e models
+> color #8 #c0c0c0f5 models
+> color #8 #c0c0c0f1 models
+> color #8 #c0c0c0ad models
+> color #8 #c0c0c0a1 models
+> color #8 #c0c0c0ab models
+> color #8 #c0c0c0ad models
+> color #8 #c0c0c0b4 models
+> color #8 #c0c0c0b6 models
+> color #8 #c0c0c0b9 models
+> color #8 #c0c0c0bd models
+> color #8 #c0c0c0c1 models
+> color #8 #c0c0c0bf models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> select #43/I:641
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #43/I:641-642
+atoms, 18 bonds, 2 residues, 1 model selected
+> select #43/I:649
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #43/I:649-650
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #43/I:630
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #43/I:630-631
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #43/I:618
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #43/I:618-619
+atoms, 21 bonds, 2 residues, 1 model selected
+> select #43/I:621
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:621-622
+atoms, 17 bonds, 2 residues, 1 model selected
+> select #43/I:616
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:616
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I
+atoms, 6171 bonds, 2 pseudobonds, 745 residues, 2 models selected
+> color sel slate blue
+[Repeated 1 time(s)]
+> color sel medium slate blue
+> color sel slate blue
+[Repeated 6 time(s)]
+> color sel medium slate blue
+> color sel medium orchid
+> color sel dark orchid
+> color sel magenta
+> color sel dark slate blue
+> color sel slate blue
+> color sel violet
+> color sel slate blue
+> color sel medium slate blue
+[Repeated 1 time(s)]
+> select clear
+> select #43/I:613
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #43/I:613-657
+atoms, 362 bonds, 45 residues, 1 model selected
+> color sel light coral
+> show #!8 models
+> hide #!8 models
+> select clear
+> select #43/I:613-657
+atoms, 362 bonds, 45 residues, 1 model selected
+> select #43/I:616
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:616
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:618
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #43/I:618-619
+atoms, 21 bonds, 2 residues, 1 model selected
+> select #43/I:616
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:616
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:616,618-619
+atoms, 29 bonds, 3 residues, 1 model selected
+> select #43/I:616,618-619,621-622
+atoms, 46 bonds, 5 residues, 1 model selected
+> show sel target ab
+> style sel ball
+Changed 49 atom styles
+> color sel dodger blue
+> color sel royal blue
+> color sel deep sky blue
+> style sel ball
+Changed 49 atom styles
+> style sel sphere
+Changed 49 atom styles
+> style sel stick
+Changed 49 atom styles
+> style sel ball
+Changed 49 atom styles
+> select clear
+> select #43/I:616,618-619,621-622,629
+atoms, 53 bonds, 6 residues, 1 model selected
+> select #43/I:616,618-619,621-622,629
+atoms, 53 bonds, 6 residues, 1 model selected
+> select
+> #43/I:12-31,51-65,72-80,82-109,117-136,146-170,173-188,195-215,244-271,278-295,298-303,330-353,379-395,407-412,430-461,468-493,497-523,526-550,556-565,568-576,584-606,626-638,640-653,658-680,686-702,712-724,733-756,758-763,773-780
+atoms, 4319 bonds, 523 residues, 1 model selected
+> select clear
+> select
+> #43/I:12-31,51-65,72-80,82-109,117-136,146-170,173-188,195-215,244-271,278-295,298-303,330-353,379-395,407-412,430-461,468-493,497-523,526-550,556-565,568-576,584-606,626-638,640-653,658-680,686-702,712-724,733-756,758-763,773-780
+atoms, 4319 bonds, 523 residues, 1 model selected
+> select clear
+> select #43/I:629
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #43/I:629
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #43/I:629,635-637
+atoms, 33 bonds, 4 residues, 1 model selected
+> select #43/I:629,635-637,640
+atoms, 40 bonds, 5 residues, 1 model selected
+> select #43/I:629,635-637,640,642-643
+atoms, 56 bonds, 7 residues, 1 model selected
+> select #43/I:629,635-637,640,642-643,646
+atoms, 63 bonds, 8 residues, 1 model selected
+> show sel target ab
+> color sel crimson
+> style sel ball
+Changed 68 atom styles
+> select clear
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> color #8 #00fdffff models
+> color #8 #73fdffff models
+> color #8 #009193ff models
+> color #8 #00fdffff models
+> color #8 #76d6ffff models
+> color #8 #00fdffff models
+> color #8 #76d6ffff models
+> color #8 #76d6ffd2 models
+> color #8 #76d6ff85 models
+> color #8 #76d6ff86 models
+> color #8 #76d6ffa6 models
+> color #8 #76d6ff80 models
+> lighting full
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> lighting soft
+> lighting full
+> lighting soft
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side.png
+> supersample 6 width 2000 transparentBackground true
+> lighting full
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side2.png
+> supersample 6 width 2000 transparentBackground true
+> hide #!43 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side2.png
+> supersample 6 width 2000 transparentBackground true
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting soft
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side.png
+> supersample 6 width 2000 transparentBackground true
+> hide #!42 models
+> hide #!44 models
+> show #!8 models
+> color #8 #76d6ffff models
+> lighting soft
+> lighting full
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side_single_map.png
+> supersample 6 width 2000 transparentBackground true
+> ui tool show "Hide Dust"
+> surface dust #8 size 5.7
+> surface dust #8 size 5.94
+> surface dust #8 size 8.07
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_side_single_map.png
+> supersample 6 width 2000 transparentBackground true
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc
+Opened cryosparc_P17_J544_007_volume_map_EMReady_zflip.mrc as #45, grid size
+,588,588, pixel 0.95, shown at level 0.957, step 4, values float32
+> hide #!8 models
+> volume #45 step 1
+> show #!8 models
+> lighting simple
+> select add #8
+models selected
+> view sel
+> select subtract #8
+Nothing selected
+> hide #!8 models
+> show #!42 models
+> show #!44 models
+> show #!43 models
+> lighting soft
+> lighting full
+> lighting soft
+> lighting full
+> hide #!44 models
+> hide #!43 models
+> hide #!42 models
+> show #!45 models
+> hide #!45 models
+> show #!8 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_bottom-
+> up_single_map.png supersample 6 width 2000 transparentBackground true
+> hide #!8 models
+> show #!42 models
+> show #!44 models
+> show #!45 models
+> hide #!45 models
+> show #!43 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_compos_bottom-
+> up_composite_map.png supersample 6 width 2000 transparentBackground true
+> hide #!44 models
+> hide #!43 models
+> hide #!42 models
+> show #!44 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> select add #232
+atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
+> ui mousemode right "rotate selected models"
+> select subtract #232
+Nothing selected
+> select add #232
+atoms, 12854 bonds, 220 pseudobonds, 1134 residues, 3 models selected
+> view matrix models
+> #232,-0.029351,-0.99871,0.041463,192.22,-0.84724,0.046867,0.52914,242.8,-0.5304,-0.019599,-0.84752,167.58
+> view matrix models
+> #232,-0.020898,-0.996,0.086876,194.54,-0.84044,0.064565,0.53805,243.54,-0.54151,-0.06177,-0.83842,167.34
+> view matrix models
+> #232,-0.042506,-0.99356,0.10504,195.69,-0.86935,0.088592,0.48619,241.57,-0.49236,-0.070649,-0.86752,165.27
+> view matrix models
+> #232,-0.053907,-0.99204,0.11378,196.27,-0.88276,0.1006,0.45894,240.51,-0.46673,-0.0757,-0.88115,164.26
+> ui mousemode right "translate selected models"
+> view matrix models
+> #232,-0.053907,-0.99204,0.11378,197.1,-0.88276,0.1006,0.45894,241.87,-0.46673,-0.0757,-0.88115,162.33
+> view matrix models
+> #232,-0.053907,-0.99204,0.11378,197.14,-0.88276,0.1006,0.45894,241.9,-0.46673,-0.0757,-0.88115,162.25
+> select subtract #232
+Nothing selected
+> hide #!44 models
+> show #!44 models
+> fitmap #232 inMap #44
+Fit molecule 1id3 (#232) to map
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy (#44) using 12124
+atoms
+average map value = 0.2847, steps = 68
+shifted from previous position = 3.51
+rotated from previous position = 4.37 degrees
+atoms outside contour = 5383, contour level = 0.25
+Position of 1id3 (#232) relative to
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy (#44) coordinates:
+Matrix rotation and translation
+-0.03410625 -0.99613821 0.08090390 194.35377785
+-0.72343655 0.08045913 0.68568644 250.18361614
+-0.68954791 -0.03514264 -0.72338695 177.33095720
+Axis -0.66146232 0.70699818 0.25024222
+Axis point 246.51764404 0.00000000 -9.19791182
+Rotation angle (degrees) 146.98385179
+Shift along axis 92.69735224
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!177 models
+> hide #!177 models
+> show #!232 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+\u2014\u2014\u2014 End of log from Wed Sep 4 08:32:44 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1328_map_sharp_zflip.mrc
+Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
+pixel 0.95, shown at level 0.0365, step 2, values float32
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #46 step 1
+> volume #46 level 0.1209
+> volume #46 level 0.27
+> ui tool show "Fit in Map"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+[Repeated 1 time(s)]
+> fitmap #46 inMap #44
+Fit map cryosparc_P17_J1328_map_sharp_zflip.mrc in map
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy using 183011 points
+correlation = 0.9983, correlation about mean = 0.9843, overlap = 3.392e+04
+steps = 136, shift = 8.18, angle = 15.4 degrees
+Position of cryosparc_P17_J1328_map_sharp_zflip.mrc (#46) relative to
+cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy (#44) coordinates:
+Matrix rotation and translation
+.99999993 0.00020825 0.00029549 -0.11547030
+-0.00020819 0.99999995 -0.00022028 0.08133560
+-0.00029553 0.00022022 0.99999993 0.01845130
+Axis 0.52030825 0.69808953 -0.49188447
+Axis point 41.74969574 0.00000000 368.99527237
+Rotation angle (degrees) 0.02425404
+Shift along axis -0.01237652
+> ui tool show "Hide Dust"
+> surface dust #46 size 5.7
+> surface dust #46 size 5.88
+> surface dust #46 size 7.58
+> surface undust #46
+> surface dust #46 size 7.58
+> show #!234 models
+> hide #!234 models
+> hide #!232 models
+> show #!42 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J1293_003_volume_map.mrc
+Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
+pixel 0.95, shown at level 0.131, step 4, values float32
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #47 step 1
+> volume #47 level 0.2274
+> select add #47
+models selected
+> lighting simple
+> ui mousemode right "translate selected models"
+> view matrix models #47,1,0,0,34.934,0,1,0,115.11,0,0,1,-196.72
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #47,0.80862,0.53112,-0.25306,75.22,-0.548,0.52343,-0.65247,630.75,-0.21408,0.66628,0.71431,-166.12
+> view matrix models
+> #47,-0.052033,0.59696,-0.80058,521.42,-0.88318,-0.4017,-0.24213,761.94,-0.46614,0.69446,0.54813,-35.04
+> view matrix models
+> #47,-0.56463,0.51635,-0.64387,621.88,-0.70577,-0.70651,0.052329,660.64,-0.42788,0.48397,0.76334,-85.832
+> view matrix models
+> #47,-0.64839,0.75691,-0.081716,371.53,-0.75724,-0.63011,0.17189,611.51,0.078617,0.17333,0.98172,-248.96
+> view matrix models
+> #47,-0.77683,0.61612,-0.13012,457.28,-0.62893,-0.76938,0.11179,628.86,-0.031234,0.16868,0.98518,-218.23
+> view matrix models
+> #47,0.12044,0.50172,0.8566,-162.62,-0.47586,-0.72811,0.49337,425.68,0.87123,-0.46705,0.15105,-7.2804
+> view matrix models
+> #47,0.92809,0.13752,0.34603,-111.13,-0.079004,-0.83541,0.54392,316.34,0.36388,-0.53214,-0.76447,512.58
+> view matrix models
+> #47,0.95173,-0.049595,-0.3029,179.09,0.060764,-0.93688,0.34433,377.51,-0.30086,-0.34611,-0.88865,710
+> view matrix models
+> #47,0.74227,-0.056059,-0.66775,384.14,0.082804,-0.98118,0.17442,448.01,-0.66497,-0.18476,-0.72366,713.19
+> view matrix models
+> #47,0.70283,0.024432,-0.71094,395.12,0.12328,-0.98847,0.0879,472.34,-0.7006,-0.14942,-0.69774,705.44
+> view matrix models
+> #47,0.054631,-0.15566,-0.9863,726.27,-0.030531,-0.98757,0.15417,489.48,-0.99804,0.02169,-0.058704,500.1
+> view matrix models
+> #47,0.60463,-0.27385,-0.74795,501.6,0.099908,-0.90554,0.41232,332.8,-0.79021,-0.32403,-0.52016,698.05
+> view matrix models
+> #47,0.52044,-0.22451,-0.82386,544.88,0.38474,-0.79968,0.46097,210.17,-0.76231,-0.55688,-0.32981,664.82
+> ui mousemode right "translate selected models"
+> color #47.1 light gray
+> view matrix models
+> #47,0.52044,-0.22451,-0.82386,558.57,0.38474,-0.79968,0.46097,110.43,-0.76231,-0.55688,-0.32981,702.7
+> view matrix models
+> #47,0.52044,-0.22451,-0.82386,437.12,0.38474,-0.79968,0.46097,87.569,-0.76231,-0.55688,-0.32981,677.12
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #47,0.56523,-0.45015,-0.69129,420.43,0.27696,-0.6858,0.67303,9.7394,-0.77705,-0.57187,-0.26296,658.06
+> ui mousemode right "translate selected models"
+> view matrix models
+> #47,0.56523,-0.45015,-0.69129,423.1,0.27696,-0.6858,0.67303,13.1,-0.77705,-0.57187,-0.26296,647.01
+> hide #!8 models
+> show #!8 models
+> fitmap #47 inMap #8
+Fit map cryosparc_P17_J1293_003_volume_map.mrc in map
+cryosparc_P17_J1163_006_volume_map.mrc using 254592 points
+correlation = 0.9671, correlation about mean = 0.6025, overlap = 1.762e+04
+steps = 160, shift = 4.19, angle = 15.7 degrees
+Position of cryosparc_P17_J1293_003_volume_map.mrc (#47) relative to
+cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
+Matrix rotation and translation
+.99987281 0.00432290 0.01535233 -6.92417661
+-0.00420416 0.99996106 -0.00775858 5.37169883
+-0.01538527 0.00769307 0.99985205 1.46498711
+Axis 0.43594765 0.86722038 -0.24057941
+Axis point 110.65380262 0.00000000 488.49257940
+Rotation angle (degrees) 1.01544392
+Shift along axis 1.28742242
+> select subtract #47
+Nothing selected
+> hide #!46 models
+> show #!18 models
+> hide #!18 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> color #16 #009193ff models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!8 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> hide #!8 models
+> show #!8 models
+> fitmap #47 inMap #8
+Fit map cryosparc_P17_J1293_003_volume_map.mrc in map
+cryosparc_P17_J1163_006_volume_map.mrc using 254592 points
+correlation = 0.9671, correlation about mean = 0.6024, overlap = 1.762e+04
+steps = 48, shift = 0.0108, angle = 0.0117 degrees
+Position of cryosparc_P17_J1293_003_volume_map.mrc (#47) relative to
+cryosparc_P17_J1163_006_volume_map.mrc (#8) coordinates:
+Matrix rotation and translation
+.99987335 0.00426622 0.01533290 -6.90697298
+-0.00414464 0.99995979 -0.00795249 5.42282003
+-0.01536621 0.00788795 0.99985082 1.41490067
+Axis 0.44553022 0.86344648 -0.23656498
+Axis point 106.89545515 -0.00000000 488.26292061
+Rotation angle (degrees) 1.01860486
+Shift along axis 1.27033373
+> hide #!8 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!42 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!46 models
+> show #!46 models
+> fitmap #44 inMap #46
+Fit map cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy in map
+cryosparc_P17_J1328_map_sharp_zflip.mrc using 193604 points
+correlation = 0.9979, correlation about mean = 0.9843, overlap = 3.462e+04
+steps = 40, shift = 0.00361, angle = 0.00695 degrees
+Position of cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy (#44)
+relative to cryosparc_P17_J1328_map_sharp_zflip.mrc (#46) coordinates:
+Matrix rotation and translation
+.99999996 -0.00014217 -0.00023873 0.08639737
+.00014220 0.99999998 0.00013580 -0.05048921
+.00023872 -0.00013583 0.99999996 -0.02306461
+Axis -0.43914796 -0.77188188 0.45972540
+Axis point 78.23841730 0.00000000 344.27567005
+Rotation angle (degrees) 0.01772022
+Shift along axis -0.00957291
+> fitmap #44 inMap #46
+Fit map cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy in map
+cryosparc_P17_J1328_map_sharp_zflip.mrc using 193604 points
+correlation = 0.9979, correlation about mean = 0.9843, overlap = 3.462e+04
+steps = 40, shift = 0.000257, angle = 0.000437 degrees
+Position of cryosparc_P17_J1206_003_volume_map_sharp_zflip.mrc copy (#44)
+relative to cryosparc_P17_J1328_map_sharp_zflip.mrc (#46) coordinates:
+Matrix rotation and translation
+.99999996 -0.00014232 -0.00024540 0.08755876
+.00014235 0.99999998 0.00013952 -0.05131539
+.00024538 -0.00013955 0.99999996 -0.02371294
+Axis -0.44137314 -0.77620112 0.45022392
+Axis point 79.27979005 0.00000000 339.72277629
+Rotation angle (degrees) 0.01811329
+Shift along axis -0.00949115
+> hide #!44 models
+> show #!44 models
+> hide #!46 models
+> show #!46 models
+> hide #!44 models
+> show #!232 models
+> show #!234 models
+> hide #!232 models
+> fitmap #234 inMap #46
+Fit molecule copy of 1id3 (#234) to map
+cryosparc_P17_J1328_map_sharp_zflip.mrc (#46) using 6114 atoms
+average map value = 0.2627, steps = 48
+shifted from previous position = 0.184
+rotated from previous position = 0.919 degrees
+atoms outside contour = 3238, contour level = 0.27
+Position of copy of 1id3 (#234) relative to
+cryosparc_P17_J1328_map_sharp_zflip.mrc (#46) coordinates:
+Matrix rotation and translation
+-0.04201562 -0.99848675 0.03548092 191.85732882
+-0.66725181 0.05447399 0.74283754 251.20982793
+-0.74364623 0.00753607 -0.66853085 181.90203052
+Axis -0.65572927 0.69481226 0.29538966
+Axis point 247.93591832 0.00000000 -19.62380013
+Rotation angle (degrees) 145.89753760
+Shift along axis 102.46918037
+> hide #!46 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> show #!232 models
+> hide #!234 models
+> show #!234 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> ui tool show Matchmaker
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> matchmaker #232/A to #234/A pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker copy of 1id3, chain A (#234) with 1id3, chain A (#232), sequence
+alignment score = 617.3
+RMSD between 97 pruned atom pairs is 0.000 angstroms; (across all 97 pairs:
+.000)
+> hide #!234 models
+> show #!234 models
+> hide #!46 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!234 models
+> ui mousemode right zoom
+> select #232/C#232/G#234/C#234/G
+atoms, 3400 bonds, 4 pseudobonds, 462 residues, 4 models selected
+> ui tool show "Color Actions"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> color sel light goldenrod yellow
+> color sel light yellow
+[Repeated 15 time(s)]
+> color sel light goldenrod yellow
+[Repeated 1 time(s)]
+> color sel yellow
+[Repeated 10 time(s)]
+> color sel yellow green
+[Repeated 16 time(s)]
+> color sel lime
+> color sel yellow green
+[Repeated 7 time(s)]
+> select #232/D#232/H#234/D#234/H
+atoms, 2988 bonds, 2 pseudobonds, 406 residues, 4 models selected
+> select #232/D#232/H#234/D#234/H
+atoms, 2988 bonds, 2 pseudobonds, 406 residues, 4 models selected
+> color sel red
+> color sel dark red
+> color sel crimson
+> color sel orange red
+> color sel red
+[Repeated 1 time(s)]
+> color sel crimson
+[Repeated 1 time(s)]
+> color sel fire brick
+[Repeated 4 time(s)]
+> select #232/C#232/G#234/C#234/G
+atoms, 3400 bonds, 4 pseudobonds, 462 residues, 4 models selected
+> color sel gold
+[Repeated 3 time(s)]
+> color sel dark orange
+> color sel gold
+[Repeated 4 time(s)]
+> select #232/A#232/E#234/A#234/E
+atoms, 3252 bonds, 410 residues, 2 models selected
+> color sel dodger blue
+> color sel dark blue
+> color sel medium blue
+> color sel blue
+[Repeated 1 time(s)]
+> color sel deep sky blue
+[Repeated 1 time(s)]
+> color sel cyan
+> color sel deep sky blue
+> color sel light sky blue
+[Repeated 2 time(s)]
+> color sel sky blue
+[Repeated 1 time(s)]
+> color sel light steel blue
+[Repeated 4 time(s)]
+> color sel powder blue
+> color sel light steel blue
+[Repeated 11 time(s)]
+> color sel slate gray
+> color sel light slate gray
+> color sel cadet blue
+> color sel steel blue
+[Repeated 5 time(s)]
+> color sel blue
+[Repeated 3 time(s)]
+> color sel medium blue
+> color sel blue
+[Repeated 3 time(s)]
+> color sel dodger blue
+> color sel steel blue
+[Repeated 4 time(s)]
+> select #232/B#232/F#234/B#234/F
+atoms, 2652 bonds, 346 residues, 2 models selected
+> color sel medium aquamarine
+> color sel dark cyan
+> color sel medium aquamarine
+[Repeated 1 time(s)]
+> color sel dark cyan
+> color sel turquoise
+> color sel medium sea green
+[Repeated 2 time(s)]
+> color sel sea green
+[Repeated 1 time(s)]
+> color sel medium sea green
+[Repeated 1 time(s)]
+> color sel forest green
+> color sel medium sea green
+[Repeated 1 time(s)]
+> color sel forest green
+> color sel medium sea green
+[Repeated 3 time(s)]
+> select clear
+> show #!235 models
+> hide #!235 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!46 models
+> show #!46 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!46 models
+> color #47 #d3d3d381 models
+> color #47 #d6d6d6ff models
+> color #47 silver models
+> color #47 #c0c0c082 models
+> color #47 #c0c0c0c8 models
+> color #47 #c0c0c0c5 models
+> color #47 #c0c0c0c1 models
+> color #47 #c0c0c0be models
+> color #47 #c0c0c0c2 models
+> color #47 #c0c0c0c1 models
+> color #47 #c0c0c0be models
+> color #47 #c0c0c0c0 models
+> color #47 #c0c0c0bf models
+> hide #!232 models
+> show #!232 models
+> hide #!47 models
+> hide #!42 models
+> show #!42 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> show #!47 models
+> hide #!46 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> hide #!47 models
+> show #!47 models
+> hide #!46 models
+> hide #!47 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!232 models
+> show #!232 models
+> hide #!42 models
+> show #!42 models
+> show #!41 models
+> hide #!41 models
+> show #!41 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> hide #!41 models
+> show #!41 models
+> hide #!41 models
+> show #!41 models
+> hide #!41 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> show #!41 models
+> hide #!41 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> show #!19 models
+> hide #!19 models
+> hide #!1 models
+> show #!1 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> hide #!177 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!22 models
+> hide #!22 models
+> show #!177 models
+> hide #!177 models
+> show #!177 models
+> show #!232 models
+> hide #!232 models
+> hide #!177 models
+> show #!41 models
+> hide #!41 models
+> show #!41 models
+> hide #!41 models
+> show #!38 models
+> hide #!38 models
+> show #!38 models
+> hide #!38 models
+> show #!38 models
+> hide #!38 models
+> matchmaker #1/I to #38/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker Tof1_6skl, chain X (#38) with 8xgc, chain I (#1), sequence
+alignment score = 5308.2
+RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
+.839)
+> matchmaker #1/I to #38/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker Tof1_6skl, chain X (#38) with 8xgc, chain I (#1), sequence
+alignment score = 5308.2
+RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
+.839)
+> matchmaker #1/I to #38/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker Tof1_6skl, chain X (#38) with 8xgc, chain I (#1), sequence
+alignment score = 5308.2
+RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
+.839)
+> matchmaker #1/I to #38/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker Tof1_6skl, chain X (#38) with 8xgc, chain I (#1), sequence
+alignment score = 5308.2
+RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
+.839)
+> show #!38 models
+> hide #!1 models
+> show #!1 models
+> hide #!38 models
+> show #!40 models
+> hide #!40 models
+> combine #1
+> hide #!48 models
+> show #!48 models
+> hide #!1 models
+> hide #!48 models
+> show #!48 models
+> select #48/X,Y
+atoms, 2053 bonds, 86 pseudobonds, 90 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 70556 bonds, 77 pseudobonds, 8899 residues, 3 models selected
+> delete atoms (#!48 & sel)
+> delete bonds (#!48 & sel)
+> hide #!48 models
+> show #!48 models
+> rename #48 DNA_8xgc
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> hide #!40 models
+> show #!40 models
+> select #48/X
+atoms, 1159 bonds, 51 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel black
+> select #48/Y
+atoms, 894 bonds, 39 residues, 1 model selected
+> color sel gray
+> color sel dark gray
+> color sel dim gray
+> select clear
+> hide #!48 models
+> show #!48 models
+> hide #!48 models
+> show #!48 models
+> hide #!48 models
+> show #!48 models
+> hide #!40 models
+> show #!40 models
+> hide #!48 models
+> show #!48 models
+> hide #!48 models
+> show #!48 models
+> hide #!40 models
+> show #!40 models
+> hide #!48 models
+> hide #!40 models
+> show #!8 models
+> hide #!8 models
+> show #!19 models
+> hide #!19 models
+> show #!42 models
+> show #!48 models
+> fitmap #48 inMap #42
+Fit molecule DNA_8xgc (#48) to map cryosparc_P17_J842_005_volume_map_sharp.mrc
+copy (#42) using 1837 atoms
+average map value = 0.2869, steps = 136
+shifted from previous position = 2.41
+rotated from previous position = 2.94 degrees
+atoms outside contour = 1074, contour level = 0.3
+Position of DNA_8xgc (#48) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc copy (#42) coordinates:
+Matrix rotation and translation
+.97626723 0.21196039 0.04444217 20.25889577
+.20777495 -0.97457455 0.08386920 422.39463428
+.06108915 -0.07264478 -0.99548524 498.45034022
+Axis -0.99403982 -0.10572708 -0.02658227
+Axis point 0.00000000 219.96323566 240.74169709
+Rotation angle (degrees) 175.48464775
+Shift along axis -78.04663897
+> hide #!48 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+> show #!234 models
+> hide #!234 models
+> show #!232 models
+> lighting soft
+> lighting full
+> lighting simple
+> lighting full
+> lighting soft
+[Repeated 3 time(s)]
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting full
+> lighting simple
+> lighting soft
+> lighting full
+> lighting soft
+> show #!234 models
+> hide #!232 models
+> hide #!42 models
+> show #!41 models
+> select #41/G
+atoms, 6778 bonds, 2 pseudobonds, 422 residues, 2 models selected
+> select #41/H,G,F
+atoms, 20476 bonds, 6 pseudobonds, 1271 residues, 2 models selected
+> select
+> #1/F#1/G#1/H#22/F#22/G#22/H#37/F#37/G#37/H#41/F#41/G#41/H#177/F#177/G#177/H
+atoms, 82328 bonds, 30 pseudobonds, 6355 residues, 10 models selected
+> color sel royal blue
+[Repeated 2 time(s)]
+> color sel slate gray
+> color sel royal blue
+> color sel deep sky blue
+> color sel royal blue
+> color sel light sky blue
+> color sel light blue
+> color sel powder blue
+> color sel deep sky blue
+[Repeated 2 time(s)]
+> color sel cyan
+> color sel deep sky blue
+[Repeated 2 time(s)]
+> color sel dark turquoise
+> color sel deep sky blue
+> color sel steel blue
+> color sel royal blue
+> color sel dodger blue
+> color sel deep sky blue
+[Repeated 8 time(s)]
+> select #1/I#22/I#38/X#41/X#43/I#177/X
+atoms, 51789 bonds, 27 pseudobonds, 4230 residues, 12 models selected
+> color sel medium slate blue
+[Repeated 1 time(s)]
+> color sel slate blue
+> color sel medium slate blue
+> color sel medium orchid
+> color sel dark slate blue
+> color sel medium slate blue
+> color sel slate blue
+> color sel medium slate blue
+> color sel indigo
+> color sel medium purple
+[Repeated 4 time(s)]
+> color sel medium slate blue
+> color sel medium purple
+> color sel medium slate blue
+[Repeated 1 time(s)]
+> color sel slate blue
+> color sel medium slate blue
+[Repeated 5 time(s)]
+> select clear
+> combine #1
+> hide #!49 models
+> show #!49 models
+> select #49/2
+atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 66320 bonds, 158 pseudobonds, 8209 residues, 4 models selected
+> delete atoms (#!49 & sel)
+> delete bonds (#!49 & sel)
+> rename #49 N-term-Mcm2_8xgc
+> select add #49
+atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
+> color sel hot pink
+> select clear
+> matchmaker #49/2 to #23/2 pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker N-Mcm2_6skl, chain 2 (#23) with N-term-Mcm2_8xgc, chain 2 (#49),
+sequence alignment score = 3482.9
+RMSD between 276 pruned atom pairs is 0.698 angstroms; (across all 293 pairs:
+.967)
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> ui tool show "Show Sequence Viewer"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> sequence chain #49/2
+Alignment identifier is 49/2
+> select #49/2:126
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #49/2:126-152
+atoms, 215 bonds, 27 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 6074 bonds, 5 pseudobonds, 753 residues, 3 models selected
+> delete atoms (#!49 & sel)
+> delete bonds (#!49 & sel)
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison.cxs
+\u2014\u2014\u2014 End of log from Fri Sep 6 16:21:36 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> show #!48 models
+> hide #!48 models
+> hide #!49 models
+> show #!49 models
+> rename #49 N-patch-Mcm2_8xgc
+> show #!43 models
+> hide #!43 models
+> show #!43 models
+> ui tool show Matchmaker
+> matchmaker #43/I to #38/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker Tof1_6skl, chain X (#38) with Tof1_Mcm2_DNA_8xgc, chain I (#43),
+sequence alignment score = 5320.2
+RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
+.839)
+> matchmaker #43/I to #38/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker Tof1_6skl, chain X (#38) with Tof1_Mcm2_DNA_8xgc, chain I (#43),
+sequence alignment score = 5320.2
+RMSD between 645 pruned atom pairs is 0.608 angstroms; (across all 665 pairs:
+.839)
+> hide #!49 models
+> hide #!43 models
+> hide #!41 models
+> show #!178 models
+> hide #!178 models
+> open /Users/cvetkom/Documents/cryoSPARC/J842_005_volume_map_EMReady.mrc
+Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
+.95, shown at level 0.116, step 4, values float32
+> volume #50 level 3.037
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #50 step 1
+> volume #50 level 2.102
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> show #!9 models
+> hide #!9 models
+> show #!47 models
+> hide #!50 models
+> show #!50 models
+> show #!42 models
+> select add #50
+models selected
+> lighting simple
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> view matrix models #50,1,0,0,-65.632,0,1,0,-229.59,0,0,1,71.364
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #50,0.4343,-0.44532,0.78299,-22.581,0.48395,0.84849,0.21414,-387.73,-0.75972,0.28593,0.58401,330.58
+> ui mousemode right "move picked models"
+> view matrix models
+> #50,0.4343,-0.44532,0.78299,26.602,0.48395,0.84849,0.21414,-312.09,-0.75972,0.28593,0.58401,140.59
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #50,0.61953,-0.0088021,0.78493,-144.45,0.53432,0.73727,-0.41346,-106.79,-0.57506,0.67555,0.46146,19.955
+> ui mousemode right "translate selected models"
+> view matrix models
+> #50,0.61953,-0.0088021,0.78493,-121.97,0.53432,0.73727,-0.41346,-120.25,-0.57506,0.67555,0.46146,29.342
+> view matrix models
+> #50,0.61953,-0.0088021,0.78493,-138.14,0.53432,0.73727,-0.41346,-168.26,-0.57506,0.67555,0.46146,-2.6429
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #50,0.59893,-0.097848,0.7948,-111.13,0.56367,0.7565,-0.33163,-206.33,-0.56881,0.64663,0.50825,-10.607
+> ui mousemode right zoom
+> ui tool show "Fit in Map"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+[Repeated 1 time(s)]
+> select add #47
+models selected
+> select subtract #47
+models selected
+> hide #!47 models
+> show #!47 models
+> select subtract #50
+Nothing selected
+> select add #50
+models selected
+> select subtract #50
+Nothing selected
+> hide #!50 models
+> show #!50 models
+> hide #!42 models
+> show #!42 models
+> fitmap #50 inMap #42
+Fit map J842_005_volume_map_EMReady.mrc in map
+cryosparc_P17_J842_005_volume_map_sharp.mrc copy using 773474 points
+correlation = 0.9586, correlation about mean = 0.8187, overlap = 1.895e+06
+steps = 176, shift = 18.3, angle = 13 degrees
+Position of J842_005_volume_map_EMReady.mrc (#50) relative to
+cryosparc_P17_J842_005_volume_map_sharp.mrc copy (#42) coordinates:
+Matrix rotation and translation
+.00000000 0.00008926 0.00001426 -0.02716721
+-0.00008926 1.00000000 0.00004509 0.03060850
+-0.00001425 -0.00004509 1.00000000 0.00885891
+Axis -0.44634943 0.14111659 -0.88366187
+Axis point 329.25912566 261.27343201 0.00000000
+Rotation angle (degrees) 0.00578781
+Shift along axis 0.00861716
+> hide #!42 models
+> show #!46 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> volume #47 level 0.3135
+> volume #47 level 0.3842
+> hide #!46 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> volume #47 level 0.3043
+> volume #47 level 0.2735
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!46 models
+> ui mousemode right "map eraser"
+> hide #!47 models
+> show #!47 models
+> hide #!50 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_2.cxs
+> volume erase #47 center 193.29,217.64,214.85 radius 57.536
+Opened cryosparc_P17_J1293_003_volume_map.mrc copy as #52, grid size
+,588,588, pixel 0.95, shown at step 1, values float32
+> hide #!52 models
+> show #!52 models
+> hide #!52 models
+> show #!52 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!46 models
+> show #!42 models
+> hide #!42 models
+> show #!50 models
+> hide #!52 models
+> show #!52 models
+> close #52
+> show #!49 models
+> hide #!49 models
+> show #!49 models
+> hide #!49 models
+> show #!47 models
+> hide #!46 models
+> hide #!50 models
+> volume erase #47 center 179.18,226.56,216.65 radius 57.536
+Opened cryosparc_P17_J1293_003_volume_map.mrc copy as #52, grid size
+,588,588, pixel 0.95, shown at step 1, values float32
+> hide #51 models
+> show #!46 models
+> volume add #46,52
+Opened volume sum as #53, grid size 1018,965,865, pixel 0.95, shown at step 1,
+values float32
+> volume #53 level 0.3701
+> volume #53 level 0.4202
+> volume #53 level 0.4569
+> volume #53 level 0.5103
+> select add #53
+models selected
+> close #53
+> show #51 models
+> hide #51 models
+> show #!50 models
+> show #!48 models
+> hide #!48 models
+> hide #!234 models
+> show #!47 models
+> volume add #47,50
+Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at step 1,
+values float32
+> volume #53 level 0.3458
+> volume #53 level 0.4721
+> volume #53 level 0.3819
+> volume #53 level 0.2374
+> volume #53 level 0.2555
+[Repeated 1 time(s)]
+> show #!47 models
+> hide #!47 models
+> show #!46 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> show #!232 models
+> hide #!234 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+> close #45,236
+> show #!235 models
+> close #235
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!178 models
+> hide #!178 models
+> close #178-179
+> show #!52 models
+> hide #!52 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> hide #!46 models
+> show #!46 models
+> show #!47 models
+> hide #!47 models
+> hide #!46 models
+> show #!46 models
+> show #!44 models
+> hide #!44 models
+> show #!44 models
+> hide #!44 models
+> close #44
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!42 models
+> hide #!42 models
+> show #!21 models
+> hide #!21 models
+> show #!20 models
+> hide #!20 models
+> close #16-21
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> close #15
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> hide #!14 models
+> show #!13 models
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> hide #!13 models
+> show #!13 models
+> hide #!14 models
+> show #!12 models
+> hide #!12 models
+> close #12
+> show #!14 models
+> hide #!14 models
+> hide #!46 models
+> hide #!53 models
+> hide #!232 models
+> show #!234 models
+> hide #!234 models
+> show #!232 models
+> color #13 #b2ffff7e models
+> color #13 #b2ffffb3 models
+> color #13 #b2ffffc2 models
+> close #23-40
+> show #!22 models
+> close #22
+> show #!1 models
+> hide #!1 models
+> show #2 models
+> select add #2
+atoms, 25142 bonds, 1555 residues, 1 model selected
+> close #2
+> show #!11 models
+> hide #!11 models
+> close #11
+> show #!10 models
+> close #10
+> show #!9 models
+> hide #!9 models
+> close #9
+> show #!8 models
+> show #!7 models
+> hide #!8 models
+> close #7
+> show #!6 models
+> close #6
+> show #!5 models
+> close #5
+> show #!4 models
+> close #4
+> show #!8 models
+> hide #!8 models
+> show #!3 models
+> close #3
+> show #!1 models
+> hide #!1 models
+> show #!8 models
+> hide #!8 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!234 models
+> show #!234 models
+> hide #!232 models
+> rename #234 histones
+> show #!233 models
+> hide #!234 models
+> show #!46 models
+> hide #!233 models
+> show #!233 models
+> hide #!13 models
+> hide #!233 models
+> show #!233 models
+> hide #!46 models
+> show #!46 models
+> hide #!233 models
+> show #!233 models
+> hide #!46 models
+> color #233 #b2b2b27c models
+> show #!232 models
+> color #233 #b2b2b27d models
+> show #!41 models
+> hide #!41 models
+> show #!14 models
+> hide #!233 models
+> hide #!14 models
+> show #!13 models
+> close #14
+> show #!8 models
+> hide #!13 models
+> hide #!8 models
+> rename #1 Zhai
+> show #!8 models
+> rename #8 consensus_extended.mrc
+> show #!13 models
+> hide #!8 models
+> rename #13 "deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z
+> flip"
+> show #!41 models
+> hide #!13 models
+> hide #!41 models
+> show #!41 models
+> rename #41 fitted_replisome
+> show #!42 models
+> hide #!41 models
+> rename #42 "sharpened_replisome.mrc copy"
+> show #!43 models
+> hide #!42 models
+> hide #!232 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> show #!233 models
+> hide #!46 models
+> show #!13 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!232 models
+> show #!232 models
+> hide #!233 models
+> hide #!232 models
+> show #!232 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> hide #!233 models
+> show #!233 models
+> show #!41 models
+> hide #!41 models
+> show #!47 models
+> hide #!47 models
+> show #!47 models
+> hide #!47 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> hide #!46 models
+> show #!46 models
+> rename #233 hetero_ref_good_nucleosome.mrc
+> hide #!232 models
+> show #!232 models
+> rename #232 full_nucleosome
+> show #!177 models
+> hide #!232 models
+> hide #!233 models
+> rename #177 Baretic
+> show #!53 models
+> hide #!177 models
+> show #!52 models
+> hide #!53 models
+> hide #!52 models
+> show #!52 models
+> hide #!52 models
+> show #!52 models
+> hide #!46 models
+> hide #!43 models
+> hide #!13 models
+> rename #52 bad_nucleosome
+> show #!50 models
+> volume add #47,50
+Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at step 1,
+values float32
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+> hide #!53 models
+> hide #!52 models
+> close #51
+> show #!50 models
+> hide #!2 models
+> show #!49 models
+> hide #!50 models
+> ui mousemode right zoom
+> close #3
+> show #!41 models
+> combine #41 #49
+Remapping chain ID '2' in N-patch-Mcm2_8xgc #49 to 'AD'
+> close #41
+> close #49
+> hide #!3 models
+> show #!3 models
+> rename #3 full_replisome
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> close #4
+> show #!233 models
+> select ~sel & ##selected
+Nothing selected
+> select ~sel & ##selected
+Nothing selected
+> select ~sel & ##selected
+Nothing selected
+> select ~sel & ##selected
+Nothing selected
+> select ~sel & ##selected
+Nothing selected
+> color #233 #b2b2b2ff models
+> hide #!2 models
+> hide #!3 models
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> hide #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!8 models
+> hide #!8 models
+> show #!13 models
+> hide #!233 models
+> show #!2 models
+> show #!232 models
+> combine #232
+> rename #4 trimmed_nucleosome
+> hide #!2 models
+> select #13
+models selected
+> view sel
+> select #232/I:21
+atoms, 21 bonds, 1 residue, 1 model selected
+> ui tool show "Show Sequence Viewer"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> sequence chain #232/I
+Alignment identifier is 232/I
+> sequence chain #232/J
+Alignment identifier is 232/J
+> select #232/I:21
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #232/I:1-21
+atoms, 472 bonds, 21 residues, 1 model selected
+> hide #!4 models
+> show #!4 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> delete atoms sel
+> delete bonds sel
+> select #232/J:292
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #232/J:255-292
+atoms, 882 bonds, 38 residues, 1 model selected
+> hide #!232 models
+> hide #!4 models
+> show #!4 models
+> rename #4 full_nucleosome
+> rename #232 trimmed_nucleosome
+> show #!232 models
+> hide #!4 models
+> combine #232/I,J
+> hide sel atoms
+> hide sel cartoons
+[Repeated 1 time(s)]
+> show #232/I,J
+> undo
+> select ~sel & ##selected
+atoms, 11499 bonds, 188 pseudobonds, 1075 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 882 bonds, 38 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 11499 bonds, 188 pseudobonds, 1075 residues, 3 models selected
+> select #232/I,J
+atoms, 6235 bonds, 185 pseudobonds, 301 residues, 3 models selected
+> hide sel cartoons
+> show sel atoms
+> hide sel atoms
+> show sel cartoons
+> show sel atoms
+> style sel ball
+Changed 5588 atom styles
+> select #232/J:162
+atoms, 20 bonds, 1 residue, 1 model selected
+> select #232/J:162
+atoms, 20 bonds, 1 residue, 1 model selected
+> select #232/J:147-162
+atoms, 355 bonds, 16 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> close #5
+> show #!4 models
+> hide #!4 models
+> undo
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> undo
+[Repeated 5 time(s)]
+> close #232
+> show #!4 models
+> combine #4
+> rename #5 trimmedfull_nucleosome
+> rename #5 trimmed_nucleosome
+> show #!13 models
+> select #4/I,J
+atoms, 6708 bonds, 217 pseudobonds, 322 residues, 3 models selected
+> show sel atoms
+> style sel ball
+Changed 6010 atom styles
+> select clear
+> select #4/I:20@O4
+atom, 1 residue, 1 model selected
+> select clear
+> select #4/I:20@C7
+atom, 1 residue, 1 model selected
+> select add #4/J:274@O2
+atoms, 2 residues, 1 model selected
+> ui tool show "Show Sequence Viewer"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> sequence chain #5/I
+Alignment identifier is 5/I
+> sequence chain #5/J
+Alignment identifier is 5/J
+> hide #!4 models
+> select #5/I,J
+atoms, 6708 bonds, 217 pseudobonds, 322 residues, 3 models selected
+> show sel atoms
+> style sel ball
+Changed 6010 atom styles
+> select #5/I:20@C7
+atom, 1 residue, 1 model selected
+> select add #5/J:274@C7
+atoms, 2 residues, 1 model selected
+> select #5/J:274
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #5/J:274-292
+atoms, 441 bonds, 19 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select #5/I:21
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #5/I:1-21
+atoms, 472 bonds, 21 residues, 1 model selected
+> select #5/I:20
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #5/I:1-20
+atoms, 450 bonds, 20 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> show #!1 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> color #2 white models
+> color #2 #ffffff83 models
+> color #2 #ffffff82 models
+> show #!48 models
+> hide #!1 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> select add #48
+atoms, 2053 bonds, 86 pseudobonds, 90 residues, 2 models selected
+> show sel atoms
+> style sel ball
+Changed 1837 atom styles
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!2 models
+> select #48/X:25
+atoms, 23 bonds, 1 residue, 1 model selected
+> select add #5/I:93
+atoms, 44 bonds, 2 residues, 2 models selected
+> select add #48/X:14
+atoms, 65 bonds, 3 residues, 2 models selected
+> select add #48/Y:37
+atoms, 86 bonds, 4 residues, 2 models selected
+> select add #48/Y:48
+atoms, 109 bonds, 5 residues, 2 models selected
+> combine #48
+> rename #6 Zhai_DNA_trimmed
+> ui tool show "Show Sequence Viewer"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> sequence chain #6/X
+Alignment identifier is 6/X
+> sequence chain #6/Y
+Alignment identifier is 6/Y
+> rename #6 Zhai_DNA
+> rename #48 Zhai_DNA_trimmed
+> ui tool show "Show Sequence Viewer"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> sequence chain #48/X
+Alignment identifier is 48/X
+> sequence chain #48/Y
+Alignment identifier is 48/Y
+> select #48/X:14
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #48/X:14-25
+atoms, 273 bonds, 12 residues, 1 model selected
+> select #48/X:13
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #48/X:9-13
+atoms, 115 bonds, 5 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select #48/X:26
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #48/X:26-59
+atoms, 769 bonds, 34 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select #48/Y:32
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #48/Y:15-32
+atoms, 410 bonds, 18 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select #48/Y:49
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #48/Y:49-53
+atoms, 113 bonds, 5 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> hide #!6 models
+> ui tool show "Fit in Map"
+> show #!2 models
+> ui tool show "Fit in Map"
+> fitmap #48 inMap #2
+Fit molecule Zhai_DNA_trimmed (#48) to map volume sum (#2) using 574 atoms
+average map value = 4.031, steps = 592
+shifted from previous position = 14.2
+rotated from previous position = 167 degrees
+atoms outside contour = 5, contour level = 0.27354
+Position of Zhai_DNA_trimmed (#48) relative to volume sum (#2) coordinates:
+Matrix rotation and translation
+-0.91975243 -0.27575503 0.27931101 510.33728112
+-0.23429189 -0.18521113 -0.95436061 602.17741898
+.31490125 -0.94321578 0.10574123 368.51075021
+Axis 0.19984288 -0.63818439 0.74349412
+Axis point 200.04559281 464.04730525 0.00000000
+Rotation angle (degrees) 178.40215888
+Shift along axis -8.32738387
+> volume #52 level 0.3197
+> volume #2 level 0.9596
+> volume #2 level 1.05
+> hide #!2 models
+> ui tool show Matchmaker
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> matchmaker #48/X to #1/6 pairing ss
+Match chain (Zhai_DNA_trimmed (#48) chain X) not compatible with BLOSUM-62
+similarity matrix
+> close #48
+> show #!6 models
+> combine #6
+> hide #!3 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> select add #3
+atoms, 119480 bonds, 97 pseudobonds, 7337 residues, 3 models selected
+> select add #5
+atoms, 131441 bonds, 284 pseudobonds, 8432 residues, 6 models selected
+> ui tool show "Color Zone"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> color zone #2 near #3 distance 2.68
+> select clear
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> select add #5
+atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 3 models selected
+> select add #2
+atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 5 models selected
+> color zone #2 near sel distance 2.68
+[Repeated 1 time(s)]
+> hide #!3 models
+> hide #!5 models
+> show #!5 models
+> hide #!2 models
+> show #!2 models
+> show #!3 models
+> hide #!52 models
+> hide #!13 models
+> select subtract #5
+models selected
+> select add #5
+atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 5 models selected
+> select subtract #2
+atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 3 models selected
+> select add #2
+atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 5 models selected
+> select subtract #2
+atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 3 models selected
+> select add #2
+atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 5 models selected
+> select subtract #2
+atoms, 11961 bonds, 187 pseudobonds, 1095 residues, 3 models selected
+> select add #3
+atoms, 131441 bonds, 284 pseudobonds, 8432 residues, 6 models selected
+> color zone #2 near sel distance 2.68
+> hide #!5 models
+> hide #!3 models
+> volume #233 level 2.785
+> volume #2 level 1.357
+> volume #2 level 0.8512
+> volume #2 level 0.4721
+> volume #2 level 0.3096
+> color zone #2 near sel distance 5
+> color zone #2 near sel distance 3
+> color zone #2 near sel distance 3.5
+> color zone #2 near sel distance 4
+[Repeated 1 time(s)]
+> volume splitbyzone #2
+Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 1 as #9.2, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 2 as #9.3, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 3 as #9.4, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 4 as #9.5, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 5 as #9.6, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 6 as #9.7, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 7 as #9.8, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 8 as #9.9, grid size 636,840,859, pixel 0.95, shown at level
+.31, step 1, values float32
+Opened volume sum 9 as #9.10, grid size 636,840,859, pixel 0.95, shown at
+level 0.31, step 1, values float32
+Opened volume sum 10 as #9.11, grid size 636,840,859, pixel 0.95, shown at
+level 0.31, step 1, values float32
+Opened volume sum 11 as #9.12, grid size 636,840,859, pixel 0.95, shown at
+level 0.31, step 1, values float32
+Opened volume sum 12 as #9.13, grid size 636,840,859, pixel 0.95, shown at
+level 0.31, step 1, values float32
+Opened volume sum 13 as #9.14, grid size 636,840,859, pixel 0.95, shown at
+level 0.31, step 1, values float32
+Opened volume sum 14 as #9.15, grid size 636,840,859, pixel 0.95, shown at
+level 0.31, step 1, values float32
+Opened volume sum 15 as #9.16, grid size 636,840,859, pixel 0.95, shown at
+level 0.31, step 1, values float32
+Opened volume sum 16 as #9.17, grid size 636,840,859, pixel 0.95, shown at
+level 0.31, step 1, values float32
+Opened volume sum 17 as #9.18, grid size 636,840,859, pixel 0.95, shown at
+level 0.31, step 1, values float32
+> close #9.2-18
+> show #!3 models
+> hide #!3 models
+> show #!5 models
+> hide #!5 models
+> show #!3 models
+> hide #!9.1 models
+> hide #!9 models
+> select #6/X:25
+atoms, 23 bonds, 1 residue, 1 model selected
+> select add #6/Y:37@C3'
+atoms, 23 bonds, 2 residues, 1 model selected
+> select add #6/Y:38
+atoms, 43 bonds, 3 residues, 1 model selected
+> select subtract #6/Y:37
+atoms, 43 bonds, 2 residues, 1 model selected
+> hide #!7 models
+> show #!7 models
+> hide #!6 models
+> show #!6 models
+> hide #!7 models
+> ui tool show "Show Sequence Viewer"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> sequence chain #6/X
+Alignment identifier is 6/X
+> sequence chain #6/Y
+Alignment identifier is 6/Y
+> select #6/X:26
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #6/X:26-59
+atoms, 769 bonds, 34 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select #6/Y:34
+atoms, 20 bonds, 1 residue, 1 model selected
+> select #6/Y:34-53
+atoms, 461 bonds, 20 residues, 1 model selected
+> select #6/Y:36
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #6/Y:36-53
+atoms, 415 bonds, 18 residues, 1 model selected
+> select #6/Y:39
+atoms, 24 bonds, 1 residue, 1 model selected
+> select #6/Y:39-53
+atoms, 348 bonds, 15 residues, 1 model selected
+> show #!7 models
+> hide #!6 models
+> hide #!7 models
+> show #!6 models
+> show #!7 models
+> hide #!7 models
+> select #6/Y:38
+atoms, 20 bonds, 1 residue, 1 model selected
+> select #6/Y:15-38
+atoms, 545 bonds, 24 residues, 1 model selected
+> hide #!3 models
+> select #6/Y:36
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #6/Y:15-36
+atoms, 502 bonds, 22 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> show #!9.1 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> select #6/X:15
+atoms, 21 bonds, 1 residue, 1 model selected
+> select clear
+> select #6/X:14
+atoms, 21 bonds, 1 residue, 1 model selected
+> select #6/X:13
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #6/X:9-13
+atoms, 115 bonds, 5 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select #6/Y:53
+atoms, 23 bonds, 1 residue, 1 model selected
+> select #6/Y:49-53
+atoms, 113 bonds, 5 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> ui tool show "Fit in Map"
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> fitmap #6 inMap #9.1
+Fit molecule Zhai_DNA (#6) to map volume sum 0 (#9.1) using 492 atoms
+average map value = 2.428, steps = 112
+shifted from previous position = 2.38
+rotated from previous position = 20.2 degrees
+atoms outside contour = 57, contour level = 0.30965
+Position of Zhai_DNA (#6) relative to volume sum 0 (#9.1) coordinates:
+Matrix rotation and translation
+.84252921 0.47835125 0.24763810 -39.97421560
+-0.52899667 0.64815172 0.54777905 144.67789487
+.10152374 -0.59251958 0.79913296 198.24507755
+Axis -0.74601377 0.09559191 -0.65903387
+Axis point 0.00000000 273.04359310 -103.91847500
+Rotation angle (degrees) 49.84130149
+Shift along axis -86.99886895
+> show #!3 models
+> show #!5 models
+> select #5/I
+atoms, 2903 bonds, 3 pseudobonds, 142 residues, 2 models selected
+> color (#!5 & sel) black
+> select #5/J
+atoms, 2912 bonds, 5 pseudobonds, 141 residues, 2 models selected
+> color (#!5 & sel) dim gray
+> select clear
+> show #!1 models
+> hide #!1 models
+> hide #!3 models
+> show #!3 models
+> select add #3
+atoms, 119480 bonds, 97 pseudobonds, 7337 residues, 3 models selected
+> hide sel atoms
+> show sel cartoons
+> select clear
+> hide #!9.1 models
+> hide #!9 models
+> show #!2 models
+> show #!13 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> combine #3 #6 #5
+Remapping chain ID 'X' in Zhai_DNA #6 to 'Z'
+Remapping chain ID 'Y' in Zhai_DNA #6 to 'a'
+Remapping chain ID 'A' in trimmed_nucleosome #5 to 'K'
+Remapping chain ID 'B' in trimmed_nucleosome #5 to 'L'
+Remapping chain ID 'C' in trimmed_nucleosome #5 to 'M'
+Remapping chain ID 'D' in trimmed_nucleosome #5 to 'N'
+Remapping chain ID 'E' in trimmed_nucleosome #5 to 'O'
+Remapping chain ID 'F' in trimmed_nucleosome #5 to 'P'
+Remapping chain ID 'G' in trimmed_nucleosome #5 to 'Q'
+Remapping chain ID 'H' in trimmed_nucleosome #5 to 'R'
+Remapping chain ID 'I' in trimmed_nucleosome #5 to 'S'
+Remapping chain ID 'J' in trimmed_nucleosome #5 to 'T'
+> hide #!10 models
+> show #!10 models
+> hide #!2 models
+> hide #!3 models
+> hide #!5 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> show #!2 models
+> close #6-7
+> rename #10 extended_structure
+> hide #!10 models
+> show #!10 models
+> select add #10
+atoms, 131991 bonds, 312 pseudobonds, 8456 residues, 4 models selected
+> color zone #2 near sel distance 4.25
+> color zone #2 near sel distance 53.56
+[Repeated 1 time(s)]
+> select clear
+> volume #2 level 0.1833
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+> show #!43 models
+> hide #!43 models
+> show #!43 models
+> hide #!43 models
+> show #!43 models
+> hide #!13 models
+> hide #!10 models
+> hide #!2 models
+Drag select of 6 atoms, 7 residues, 5 bonds
+Drag select of 1 atoms, 4 residues, 1 bonds
+Drag select of 48 atoms, 44 residues, 38 bonds
+Drag select of 66 atoms, 50 residues, 55 bonds
+> select #43/X,Y
+atoms, 2053 bonds, 86 pseudobonds, 90 residues, 2 models selected
+> delete atoms (#!43 & sel)
+> delete bonds (#!43 & sel)
+> show #!2 models
+> hide #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> select #43/I:606
+atoms, 5 bonds, 1 residue, 1 model selected
+> select add #43/I:657
+atoms, 11 bonds, 2 residues, 1 model selected
+> hide #!3 models
+> select clear
+Drag select of 35 atoms, 28 residues, 30 bonds
+Drag select of 14 atoms, 18 residues, 11 bonds
+Drag select of 8 residues
+> select ~sel & ##selected
+atoms, 12085 bonds, 7 pseudobonds, 1480 residues, 3 models selected
+> cartoon hide (#!43 & sel)
+> cartoon (#!43 & sel)
+> ui tool show "Show Sequence Viewer"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> sequence chain #43/I
+Alignment identifier is 43/I
+> select #43/I:605-606
+atoms, 18 bonds, 2 residues, 1 model selected
+> select #43/I:11-606
+atoms, 4671 bonds, 2 pseudobonds, 570 residues, 2 models selected
+> cartoon hide (#!43 & sel)
+> delete atoms (#!43 & sel)
+> delete bonds (#!43 & sel)
+> select #43/I:658
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #43/I:658-781
+atoms, 1089 bonds, 124 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select add #43
+atoms, 6698 bonds, 5 pseudobonds, 831 residues, 3 models selected
+> select #43/2
+atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
+> delete atoms (#!43 & sel)
+> delete bonds (#!43 & sel)
+Drag select of 78 atoms, 55 residues, 65 bonds
+> color sel red
+> combine #43,3
+Remapping chain ID 'I' in full_replisome #3 to 'K'
+> hide #!6 models
+> show #!6 models
+> close #3
+> rename #6 full_replisome
+> combine #5,6
+Remapping chain ID 'A' in full_replisome #6 to 'L'
+Remapping chain ID 'B' in full_replisome #6 to 'M'
+Remapping chain ID 'C' in full_replisome #6 to 'N'
+Remapping chain ID 'D' in full_replisome #6 to 'O'
+Remapping chain ID 'E' in full_replisome #6 to 'P'
+Remapping chain ID 'F' in full_replisome #6 to 'Q'
+Remapping chain ID 'G' in full_replisome #6 to 'R'
+Remapping chain ID 'H' in full_replisome #6 to 'S'
+Remapping chain ID 'I' in full_replisome #6 to 'T'
+Remapping chain ID 'J' in full_replisome #6 to 'U'
+> close #10
+> rename #3 extended_structure
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_2.cxs
+\u2014\u2014\u2014 End of log from Fri Sep 6 19:04:03 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> open /Users/cvetkom/Desktop/extended_structure_old.pdb
+Chain information for extended_structure_old.pdb #7
+---
+Chain | Description
+7 | No description available
+5 AD | No description available
+6 | No description available
+9 | No description available
+AB | No description available
+A | No description available
+AA AC | No description available
+B | No description available
+C | No description available
+D | No description available
+E | No description available
+F G H | No description available
+I | No description available
+J | No description available
+K O | No description available
+L P | No description available
+M Q | No description available
+N R | No description available
+S T | No description available
+X | No description available
+Y | No description available
+Z | No description available
+a | No description available
+> ui tool show Matchmaker
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> matchmaker #7/2 to #3/2 pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain 2 (#3) with extended_structure_old.pdb,
+chain 2 (#7), sequence alignment score = 3554.3
+RMSD between 293 pruned atom pairs is 0.000 angstroms; (across all 293 pairs:
+.000)
+> select #7/a,Z
+atoms, 550 bonds, 24 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 131441 bonds, 58 pseudobonds, 8432 residues, 3 models selected
+> delete atoms (#!7 & sel)
+> delete bonds (#!7 & sel)
+> select #7/a
+atoms, 277 bonds, 12 residues, 1 model selected
+> color sel dim gray
+> select #7/Z
+atoms, 273 bonds, 12 residues, 1 model selected
+> color sel black
+> combine #3,7
+> hide #!10 models
+> show #!10 models
+> hide #!3 models
+> hide #!7 models
+> close #3,7
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!43 models
+> hide #!6 models
+> hide #!10 models
+> show #!10 models
+> rename #10 extended_structure
+> select #10,T
+Expected an objects specifier or a keyword
+> select #10/T
+atoms, 409 bonds, 51 residues, 1 model selected
+> ui tool show "Color Actions"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> color sel medium slate blue
+> color sel slate blue
+> color sel medium slate blue
+[Repeated 2 time(s)]
+> select clear
+> show #!2 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+> select add #10
+atoms, 132400 bonds, 284 pseudobonds, 8507 residues, 4 models selected
+> ui tool show "Color Zone"
+> color zone #2 near #10 distance 1
+> color zone #2 near #10 distance 10
+> color zone #2 near #10 distance 1
+> color zone #2 near #10 distance 15
+> color zone #2 near #10 distance 2
+> color zone #2 near #10 distance 20
+[Repeated 1 time(s)]
+> select clear
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+> volume splitbyzone #2
+Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
+.183, step 1, values float32
+Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
+level 0.183, step 1, values float32
+> volume #3.4 level 0.2577
+> volume #3.4 level 0.1585
+> volume #3.5 level 0.2148
+> volume #3.4 level 0.183
+> volume #3.5 level 0.183
+> volume #3.9 level 0.9634
+> volume #3.9 level 2.784
+> volume #3.10 level 2.78
+> volume #3.11 level 2.78
+> volume #3.13 level 2.78
+> volume #3.14 level 2.78
+> volume #3.16 level 2.78
+> volume #3.17 level 2.78
+> volume #3.18 level 2.78
+> volume #3.15 level 2.78
+> volume #3.12 level 2.78
+> volume copy #3.8
+Opened volume sum 7 copy as #7, grid size 636,840,859, pixel 0.95, shown at
+step 1, values float32
+> volume #3.8 level 2.78
+> volume #7 color #7b68ee7c
+> volume #7 color #7b68ee33
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+[Repeated 1 time(s)]
+> hide #!7 models
+> select #10/T
+atoms, 409 bonds, 51 residues, 1 model selected
+> color zone #7 near sel distance 5.7
+> show #!7 models
+> volume #7 color #ff2600
+> ui tool show "Color Actions"
+> color sel medium slate blue
+> select #7
+models selected
+> color sel medium slate blue
+> volume #7 color #ff260081
+> color sel medium slate blue
+> select #10/T
+atoms, 409 bonds, 51 residues, 1 model selected
+> color sel purple
+> color sel magenta
+> color zone #7 near sel distance 5.7
+> volume splitbyzone #7
+Opened volume sum 7 copy 0 as #11.1, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
+at level 0.183, step 1, values float32
+> close #11.1
+> show #!7 models
+> hide #!3.4 models
+> hide #!3.5 models
+> hide #!3.6 models
+> hide #!3.7 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> show #!5 models
+> select add #5
+atoms, 12370 bonds, 187 pseudobonds, 1146 residues, 4 models selected
+> color zone #13 near sel distance 5.7
+> color zone #13 near sel distance 6.18
+> color zone #13 near sel distance 11.5
+> select clear
+> ui tool show "Hide Dust"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> surface dust #3.3 size 5.7
+> surface dust #3.3 size 5.66
+> surface dust #3.3 size 33
+> surface dust #3.3 size 33.37
+> surface dust #3.3 size 14.12
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240903_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+\u2014\u2014\u2014 End of log from Fri Sep 6 19:48:00 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> hide #!11.2 models
+> show #!11.2 models
+> hide #!11 models
+> show #!11 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> rename #7 Tof1_lower_level
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> hide #!11.2 models
+> show #!11.2 models
+> hide #!11.2 models
+> show #!11.2 models
+> hide #!11.2 models
+> show #!11.2 models
+> hide #!11.2 models
+> show #!11.2 models
+> hide #!11.2 models
+> show #!11.2 models
+> hide #!11.2 models
+> show #!11.2 models
+> hide #!11.2 models
+> show #!11.2 models
+> hide #!11.2 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> show #!11.2 models
+> hide #!11.2 models
+> show #!11.2 models
+> hide #!11 models
+> show #!11 models
+> rename #11 Tof1_HTH_lower_level
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> ui tool show "Hide Dust"
+> hide #!13 models
+> show #!13 models
+> hide #!11 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> surface dust #13 size 5.7
+[Repeated 1 time(s)]
+> surface undust #13
+> surface dust #13 size 5.7
+> show #!3 models
+> hide #!3 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3.2 models
+> show #!3.2 models
+> hide #!3.2 models
+> show #!3.2 models
+> hide #!3.2 models
+> show #!3.2 models
+> hide #!3.2 models
+> show #!3.2 models
+> hide #!3.3 models
+> show #!3.3 models
+> show #!3.1 models
+> hide #!3.1 models
+> surface dust #3.2 size 5.7
+> surface dust #3.2 size 5.68
+> surface dust #3.2 size 13.68
+> surface undust #3.2
+> surface dust #3.2 size 13.68
+> surface dust #3.2 size 14.86
+[Repeated 1 time(s)]
+> surface dust #3.4 size 5.7
+> surface dust #3.3 size 14.12
+> surface dust #3.3 size 14.38
+> surface dust #3.3 size 6.94
+> hide #!3.3 models
+> show #!3.3 models
+> hide #!3.2 models
+> show #!3.2 models
+> hide #!3.2 models
+> hide #!3.3 models
+> show #!3.3 models
+> hide #!3.8 models
+> hide #!3.9 models
+> hide #!3.10 models
+> hide #!3.11 models
+> hide #!3.12 models
+> hide #!3.13 models
+> hide #!3.14 models
+> hide #!3.15 models
+> hide #!3.16 models
+> hide #!3.17 models
+> hide #!3.18 models
+> hide #!13 models
+> surface dust #3.3 size 13.23
+> surface undust #3.3
+> surface dust #3.3 size 13.23
+> ui tool show "Map Eraser"
+> volume erase #3.3 center 191.19,155.01,168.45 radius 10.807
+> show #!3.2 models
+> show #!3.4 models
+> show #!3.5 models
+> show #!3.6 models
+> show #!3.7 models
+> show #!3.8 models
+> show #!3.9 models
+> show #!3.10 models
+> show #!3.11 models
+> show #!3.12 models
+> show #!3.13 models
+> show #!3.14 models
+> show #!3.15 models
+> show #!3.16 models
+> show #!3.17 models
+> show #!3.18 models
+> show #!5 models
+> hide #!5 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> surface dust #3.4 size 5.7
+> surface undust #3.4
+> surface dust #3.4 size 7.66
+> surface dust #3.5 size 5.7
+> surface dust #3.5 size 6.18
+> surface dust #3.5 size 8.89
+> surface dust #3.6 size 5.7
+> surface dust #3.6 size 5.97
+> surface dust #3.6 size 6.94
+> surface dust #3.8 size 7.05
+> surface dust #3.8 size 7.54
+> surface dust #3.8 size 5.15
+> surface dust #3.7 size 5.7
+> surface undust #3.9
+> surface dust #3.9 size 5.7
+> surface undust #3.8
+> surface dust #3.8 size 5.15
+> surface dust #3.9 size 5.7
+> hide #!3.5 models
+> show #!3.5 models
+> surface undust #3.5
+> surface dust #3.5 size 8.89
+> lighting soft
+> hide #!3 models
+> show #!3 models
+> select add #3
+models selected
+> view sel
+> select subtract #3
+Nothing selected
+> lighting soft
+> graphics silhouettes false
+> graphics silhouettes true
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_side.png
+> supersample 6 width 2000 transparentBackground true
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_side_back.png
+> supersample 6 width 2000 transparentBackground true
+> show #!1 models
+> hide #!1 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> surface dust #7 size 5.7
+> surface dust #7 size 6.07
+> surface dust #7 size 11.59
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!3 models
+> hide #!2 models
+> show #!2 models
+> surface dust #2 size 5.7
+> surface dust #2 size 5.97
+> surface dust #2 size 35.17
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!7 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+> hide #!2 models
+> show #!2 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> hide #!2 models
+> show #!2 models
+> show #!8 models
+> hide #!8 models
+> show #!10 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> show #!42 models
+> hide #!2 models
+> show #!2 models
+> hide #!42 models
+> hide #!10 models
+> show #!10 models
+> hide #!2 models
+> show #!2 models
+> ui tool show "Color Zone"
+> color zone #2 near #10 distance 19.41
+> color zone #2 near #10 distance 13.26
+> color zone #2 near #10 distance 1
+> color zone #2 near #10 distance 16
+> color zone #2 near #10 distance 1
+> color zone #2 near #10 distance 18
+> color zone #2 near #10 distance 1
+> color zone #2 near #10 distance 2
+> color zone #2 near #10 distance 20
+> hide #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!2 models
+> show #!13 models
+> hide #!10 models
+> lighting soft
+> lighting simple
+> lighting soft
+> ui tool show "Side View"
+> color zone #2 near #10 distance 2
+> color zone #2 near #10 distance 22
+> color zone #2 near #10 distance 2
+> color zone #2 near #10 distance 24
+> hide #!2 models
+> hide #!13 models
+> show #!8 models
+> hide #!8 models
+> show #!10 models
+> hide #!10 models
+> show #!7 models
+> hide #!7 models
+> show #!2 models
+> hide #!2 models
+> show #!3 models
+> show #!10 models
+> hide #!10 models
+> show #!13 models
+> show #!43 models
+> hide #!43 models
+> show #!10 models
+> show #!43 models
+> hide #!43 models
+> show #!43 models
+> hide #!43 models
+> show #!43 models
+> hide #!43 models
+> select #43/I
+atoms, 409 bonds, 51 residues, 1 model selected
+> show #!43 models
+> hide #!10 models
+> hide #!43 models
+> show #!43 models
+> hide #!3 models
+> show #!3 models
+> show #!8 models
+> hide #!8 models
+> show #!10 models
+> hide #!10 models
+> select #43/I
+atoms, 409 bonds, 51 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel magenta
+> hide sel target a
+> select subtract #43
+Nothing selected
+> hide #!43 models
+> hide #!3 models
+> show #!3 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!3 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_low_level.png
+> supersample 6 width 2000 transparentBackground true
+> hide #!2 models
+> show #!2 models
+> show #!3 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!43 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level.png
+> supersample 6 width 2000 transparentBackground true
+> graphics silhouettes false
+> graphics silhouettes true
+> show #!1 models
+> hide #!3 models
+> hide #!13 models
+> hide #!43 models
+> show #!43 models
+> hide #!43 models
+> show #!2 models
+> hide #!2 models
+> show #!3 models
+> hide #!1 models
+> show #!4 models
+> hide #!4 models
+> show #!5 models
+> hide #!5 models
+> show #!6 models
+> hide #!6 models
+> show #!7 models
+> hide #!7 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #7.1 models
+> show #7.1 models
+> show #!13 models
+> show #!43 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #7.1 models
+> show #7.1 models
+> hide #7.1 models
+> hide #!43 models
+> show #!43 models
+> show #!11 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> show #7.1 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> hide #!11 models
+> show #!11 models
+> show #!7 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> color #7 #7b68ee80 models
+> color #7 #7b68ee9e models
+> color #7 #7b68eea0 models
+> color #7 #7b68ee32 models
+> color #7 #7b68ee29 models
+> color #7 #7b68eeab models
+> color #7 #7b68ee89 models
+> color #7 #7b68ee8a models
+> hide #!43 models
+> show #!43 models
+> hide #!43 models
+> hide #!7 models
+> show #!7 models
+> show #!43 models
+> lighting simple
+> lighting full
+> lighting soft
+> hide #!43 models
+> show #!43 models
+> hide #!13 models
+> show #!13 models
+> hide #!7 models
+> hide #!13 models
+> hide #!3 models
+> show #!3 models
+> hide #!3.3 models
+> show #!3.3 models
+> hide #!3.4 models
+> hide #!3.5 models
+> hide #!3.6 models
+> hide #!3.7 models
+> hide #!3.2 models
+> show #!3.2 models
+> hide #!3.3 models
+> show #!3.3 models
+> volume copy #3.2
+Opened volume sum 1 copy as #12, grid size 636,840,859, pixel 0.95, shown at
+step 1, values float32
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> rename #12 leading_strand_vol_3p2
+> volume copy #3.3
+Opened volume sum 2 copy as #14, grid size 636,840,859, pixel 0.95, shown at
+step 1, values float32
+> hide #!14 models
+> show #!14 models
+> rename #14 lagging_strand_vol_3p3
+> hide #!14 models
+> hide #!12 models
+> show #!3.2 models
+> show #!3.3 models
+> hide #!3.3 models
+> hide #!3.2 models
+> show #!12 models
+> show #!11 models
+> hide #!11 models
+> show #!14 models
+> surface dust #12 size 5.7
+> surface dust #12 size 5.59
+> surface dust #12 size 9.82
+> surface dust #12 size 5.68
+[Repeated 1 time(s)]
+> surface undust #12
+> surface dust #12 size 5.68
+> surface dust #14 size 5.7
+> surface dust #14 size 6.18
+> surface dust #14 size 21.74
+> surface dust #14 size 22.85
+> surface dust #14 size 18.43
+> surface dust #14 size 19.68
+> surface dust #14 size 14.62
+> hide #!12 models
+> hide #!14 models
+> show #!3.2 models
+> show #!3.3 models
+> surface undust #3.2
+> surface dust #3.2 size 14.86
+> hide #!3.3 models
+> hide #!3.2 models
+> show #!12 models
+> show #!14 models
+> ui tool show "Map Eraser"
+Can only have one displayed volume when erasing
+[Repeated 1 time(s)]
+> hide #!14 models
+> hide #15 models
+> show #15 models
+> hide #!43 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> hide #15 models
+> show #15 models
+> volume erase #12 center 219.68,211.59,243.35 radius 53.859
+> show #!3 models
+> show #!3.2 models
+> show #!3.3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> volume erase #12 center 202.99,259.45,180.39 radius 53.859
+> volume erase #12 center 157.95,181.67,182.6 radius 53.859
+> volume erase #12 center 178.35,160.14,212.29 radius 53.859
+> volume erase #12 center 206.83,165.32,136.53 radius 18.769
+> show #!14 models
+> hide #!14 models
+> show #!14 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> volume erase #14 center 196.99,177.22,211.99 radius 31.01
+> volume erase #14 center 212.15,214.12,242.94 radius 40.802
+> volume erase #14 center 208.55,248.81,191.88 radius 40.802
+> volume erase #14 center 168.65,198.46,168.27 radius 40.802
+> volume erase #14 center 172.72,159.07,188.6 radius 40.802
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!12 models
+> show #!2 models
+> hide #!2 models
+> show #!3 models
+> hide #!3.2 models
+> hide #!3.3 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+> hide #!3 models
+> show #!3 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> show #!43 models
+> show #!3.2 models
+> hide #!3.2 models
+> show #!3.2 models
+> show #!3.3 models
+> hide #!3.3 models
+> show #!3.3 models
+> hide #!3.3 models
+> show #!3.3 models
+> show #!1 models
+> open 8XGC fromDatabase pdb format mmcif
+xgc title:
+Structure of yeast replisome associated with FACT and histone hexamer,
+Composite map [more info...]
+Chain information for 8xgc #15
+---
+Chain | Description | UniProt
+| DNA replication licensing factor MCM2 | A0A6A5Q1S9_YEASX 1-868
+| DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
+| DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
+| Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
+| DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
+| DNA replication licensing factor MCM7 | A0A8H4BTB2_YEASX 1-845
+| DNA polymerase epsilon catalytic subunit A | DPOE_YEAST 1-2222
+| DNA polymerase epsilon subunit B | DPB2_YEAST 1-689
+A | DNA replication complex GINS protein PSF1 | PSF1_YEAST 1-208
+B | DNA replication complex GINS protein PSF2 |
+C | DNA replication complex GINS protein PSF3 | PSF3_YEAST 1-194
+D | DNA replication complex GINS protein SLD5 | SLD5_YEAST 1-294
+E | Cell division control protein 45 | CDC45_YEAST 1-650
+F G H | DNA polymerase alpha-binding protein | CTF4_YEAST 1-927
+I | Topoisomerase 1-associated factor 1 | TOF1_YEAST 1-1238
+J | Chromosome segregation in meiosis protein 3 | CSM3_YEAST 1-317
+K | Mediator of replication checkpoint protein 1 | MRC1_YEAST 1-1096
+L | FACT complex subunit SPT16 | SPT16_YEAST 1-1035
+M | FACT complex subunit POB3 | POB3_YEAST 1-552
+N R | Histone H3 | A0A6A5Q536_YEASX 1-136
+O S | Histone H4 | H4_YEAST 1-103
+P | Histone H2A.1 | H2A1_YEAST 1-132
+Q | Histone H2B.2 | H2B2_YEAST 1-131
+X | DNA (51-MER) |
+Y | DNA (39-MER) |
+Non-standard residues in 8xgc #15
+---
+ADP \u2014 adenosine-5'-diphosphate
+ZN \u2014 zinc ion
+> show #!177 models
+> hide #!177 models
+> ui tool show Matchmaker
+> matchmaker #15/I to #1/I pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker Zhai, chain I (#1) with 8xgc, chain I (#15), sequence alignment
+score = 5609.4
+RMSD between 745 pruned atom pairs is 0.000 angstroms; (across all 745 pairs:
+.000)
+> select add #15
+atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
+> hide (#!15 & sel) target a
+> cartoon (#!15 & sel)
+> select subtract #15
+Nothing selected
+> select add #15
+atoms, 84406 bonds, 173 pseudobonds, 10421 residues, 4 models selected
+> select subtract #15
+Nothing selected
+> hide #!15 models
+> select #1/N#1/R#15/N#15/R
+atoms, 2766 bonds, 334 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel dodger blue
+[Repeated 2 time(s)]
+> color sel cornflower blue
+[Repeated 1 time(s)]
+> color sel dodger blue
+[Repeated 1 time(s)]
+> color sel deep sky blue
+[Repeated 1 time(s)]
+> color sel cyan
+[Repeated 1 time(s)]
+> color sel deep sky blue
+> color sel dodger blue
+> color sel steel blue
+> color sel slate blue
+> color sel royal blue
+> color sel dodger blue
+> select #1/O#1/S#15/O#15/S
+atoms, 2560 bonds, 316 residues, 2 models selected
+> color sel medium spring green
+> color sel medium aquamarine
+> color sel sea green
+> color sel medium sea green
+> color sel light sea green
+[Repeated 1 time(s)]
+> color sel medium spring green
+[Repeated 1 time(s)]
+> select #1/P#15/P
+atoms, 1422 bonds, 182 residues, 2 models selected
+> select #1/P#15/P
+atoms, 1422 bonds, 182 residues, 2 models selected
+> color sel gold
+[Repeated 1 time(s)]
+> select #1/Q#15/Q
+atoms, 1432 bonds, 182 residues, 2 models selected
+> color sel crimson
+> select #1/L#15/L
+atoms, 7044 bonds, 6 pseudobonds, 986 residues, 4 models selected
+> color sel salmon
+[Repeated 2 time(s)]
+> color sel tomato
+> color sel salmon
+> select #1/M#15/M
+atoms, 3736 bonds, 14 pseudobonds, 758 residues, 4 models selected
+> color sel sienna
+> color sel saddle brown
+> color sel brown
+[Repeated 1 time(s)]
+> color sel tomato
+> color sel fire brick
+> color sel orange red
+> color sel brown
+> color sel sienna
+> select clear
+> lighting simple
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> select #1/2
+atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
+> color (#!1 & sel) hot pink
+> hide #!1 models
+> select add #1
+atoms, 72609 bonds, 163 pseudobonds, 8989 residues, 4 models selected
+> select subtract #1
+Nothing selected
+> ui tool show "Show Sequence Viewer"
+> sequence chain #43/I
+Alignment identifier is 43/I
+> show #!1 models
+> hide #!1 models
+> hide #!12 models
+> show #!12 models
+> hide #!12 models
+> hide #!14 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!3.2 models
+> show #!3.2 models
+> show #!3.4 models
+> hide #!3.4 models
+> show #!3.4 models
+> hide #!3.4 models
+> show #!3.4 models
+> show #!3.5 models
+> show #!3.6 models
+> show #!3.7 models
+> hide #!13 models
+> show #!13 models
+> show #!12 models
+> hide #!12 models
+> show #!11 models
+> hide #!11 models
+> show #!14 models
+> hide #!14 models
+> show #!12 models
+> hide #!12 models
+> hide #!13 models
+> show #!13 models
+> hide #!3.2 models
+> show #!3.2 models
+> hide #!3.2 models
+> show #!3.2 models
+> color #3.2 #00000081 models
+> color #3.2 #0000009d models
+> color #3.2 #00000099 models
+> color #3.3 #696969a7 models
+> color #3.3 #696969a0 models
+> color #3.3 #6969699a models
+> color #3.3 #69696999 models
+> color #3.4 #4682b49a models
+> color #3.4 #4682b499 models
+> color #3.5 #3cb37193 models
+> color #3.5 #3cb37199 models
+> color #3.6 #ffd7009c models
+> color #3.6 #ffd7009a models
+> color #3.6 #ffd70099 models
+> hide #!13 models
+> show #!13 models
+> color #13 #b2ffffbf models
+[Repeated 1 time(s)]
+> color #13 #b2ffffc5 models
+> color #13 #b2ffffc4 models
+> color #13 #b2ffffb0 models
+> color #13 #b2ffff9f models
+> color #13 #b2ffff9b models
+> color #13 #b2ffff98 models
+> color #13 #b2ffff99 models
+> color zone #13 near #10 distance 5.7
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> color #3.7 #b222229c models
+> color #3.7 #b222229b models
+> color #3.7 #b2222297 models
+> color #3.7 #b2222298 models
+> color #3.7 #b2222299 models
+> hide #!3.8 models
+> show #!3.8 models
+> show #!234 models
+> hide #!234 models
+> hide #!13 models
+> show #!13 models
+> color #13 #b2ffffff models
+> show #!9 models
+> hide #!9 models
+> hide #!3.18 models
+> show #!3.18 models
+> hide #!3.17 models
+> show #!3.17 models
+> hide #!3.8 models
+> show #!3.8 models
+> color #3.7 firebrick models
+> color #3.6 gold models
+> color #3.5 mediumseagreen models
+> color #3.4 steelblue models
+> hide #!3.3 models
+> show #!3.3 models
+> color #3.3 dimgrey models
+> color #3.2 black models
+> hide #!13 models
+> show #!13 models
+> color zone #13 near #10 distance 5.7
+[Repeated 1 time(s)]
+> color zone #13 near #10 distance 5.87
+> color zone #13 near #10 distance 12.76
+> ui tool show "Side View"
+> lighting soft
+> hide #!3.2 models
+> show #!3.2 models
+> hide #!3.2 models
+> show #!3.2 models
+> hide #!3.2 models
+> hide #!3.3 models
+> hide #!3.4 models
+> hide #!3.5 models
+> hide #!3.6 models
+> hide #!3.7 models
+> hide #!13 models
+> show #!12 models
+> show #!11 models
+> hide #!11 models
+> show #!14 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level_wo_nucl.png
+> supersample 6 width 2000 transparentBackground true
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> select #43/I:618
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #43/I:618-619
+atoms, 21 bonds, 2 residues, 1 model selected
+> select #43/I:616
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:616-617
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #43/I:609
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:609
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:609,616
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #43/I:609,616,618-619
+atoms, 37 bonds, 4 residues, 1 model selected
+> select #43/I:609,616,618-619,621-622
+atoms, 54 bonds, 6 residues, 1 model selected
+> select #43/I:609,616,618-619,621-622,632
+atoms, 62 bonds, 7 residues, 1 model selected
+> select #43/I:609,616,618-619,621-622,632
+atoms, 62 bonds, 7 residues, 1 model selected
+> select #43/I:609,616,618-619,621-622,632
+atoms, 62 bonds, 7 residues, 1 model selected
+> select #43/I:632
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:632
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:616,632
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #43/I:616,618-619,632
+atoms, 37 bonds, 4 residues, 1 model selected
+> select #43/I:616,618-619,621-622,632
+atoms, 54 bonds, 6 residues, 1 model selected
+> select #43/I:616,618-619,621-622,632
+atoms, 54 bonds, 6 residues, 1 model selected
+> select #43/I:619
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #43/I:619
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #43/I:616,619
+atoms, 18 bonds, 2 residues, 1 model selected
+> select #43/I:616,618-619
+atoms, 29 bonds, 3 residues, 1 model selected
+> select #43/I:616,618-619,621-622
+atoms, 46 bonds, 5 residues, 1 model selected
+> show sel target ab
+> color sel byhetero
+[Repeated 1 time(s)]
+> style sel sphere
+Changed 49 atom styles
+> hide #!12 models
+> show #!12 models
+> ui tool show "Color Actions"
+> color sel cyan
+[Repeated 2 time(s)]
+> color sel byhetero
+[Repeated 1 time(s)]
+> select #43/I:616,618-619,621-622,635-636
+atoms, 63 bonds, 7 residues, 1 model selected
+> select #43/I:635
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #43/I:635-637
+atoms, 26 bonds, 3 residues, 1 model selected
+> select #43/I:627,635-637
+atoms, 34 bonds, 4 residues, 1 model selected
+> select #43/I:627,629,635-637
+atoms, 41 bonds, 5 residues, 1 model selected
+> select #43/I:627,629,635-637,640
+atoms, 48 bonds, 6 residues, 1 model selected
+> select #43/I:627,629,635-637,640,642-643
+atoms, 64 bonds, 8 residues, 1 model selected
+> select #43/I:627,629,635-637,640,642-643,646
+atoms, 71 bonds, 9 residues, 1 model selected
+> color sel orange red
+> show sel target ab
+> color sel byhetero
+> style sel ball
+Changed 77 atom styles
+> style sel sphere
+Changed 77 atom styles
+> color sel orange
+> color sel orange red
+> color sel gold
+> color sel orange
+> color sel byhetero
+> select add #43
+atoms, 409 bonds, 51 residues, 1 model selected
+> select subtract #43
+Nothing selected
+> cartoon style #12,14,43#3.8-18#!3 xsection oval modeHelix default
+> cartoon style #12,14,43#3.8-18#!3 xsection rectangle modeHelix default
+> cartoon style (#12,14,43#3.8-18#!3 & coil) xsection oval
+> cartoon style #12,14,43#3.8-18#!3 xsection barbell modeHelix default
+> cartoon style #12,14,43#3.8-18#!3 modeHelix tube sides 20
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level_wo_nucl_patches.png
+> supersample 6 width 2000 transparentBackground true
+> show #!13 models
+> show #!3.1 models
+> hide #!3.1 models
+> show #!3.2 models
+> show #!3.3 models
+> show #!3.4 models
+> show #!3.5 models
+> show #!3.6 models
+> show #!3.7 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level_wo_nucl_patches_2.png
+> supersample 6 width 2000 transparentBackground true
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level_wo_nucl_patches_3.png
+> supersample 6 width 2000 transparentBackground true
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> select #43/I:607-609
+atoms, 24 bonds, 3 residues, 1 model selected
+> select #43/I
+atoms, 409 bonds, 51 residues, 1 model selected
+> hide sel target a
+> color sel magenta
+> select clear
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_high_level_lighter.png
+> supersample 6 width 2000 transparentBackground true
+> show #!2 models
+> hide #!3 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_low_level_lighter.png
+> supersample 6 width 2000 transparentBackground true
+> hide #!2 models
+> show #!3 models
+> show #!7 models
+> color #7 #7b68ee81 models
+> color #7 #7b68ee80 models
+> color #7 #7b68ee73 models
+> color #7 #7b68ee41 models
+> color #7 #7b68ee96 models
+> color #7 #7b68ee8c models
+> color #7 #7b68ee95 models
+> color #7 #7b68ee9c models
+> color #7 #7b68ee96 models
+> color #7 #7b68ee99 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!7 models
+> hide #!7 models
+> show #!11 models
+> color #11.2 #ff00ff83 models
+> color #11.2 #ff00ff3b models
+> color #11.2 #ff00ff4d models
+> color #11.2 #ff00ff68 models
+> color #11.2 #ff00ff77 models
+> color #11.2 #ff00ff87 models
+> color #11.2 #ff00ff9e models
+> color #11.2 #ff00ff9a models
+> hide #!11.2 models
+> color #11.2 #ff00ff99 models
+> show #!11.2 models
+> hide #!11.2 models
+> show #!11.2 models
+> select #43/I:607
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #43/I
+atoms, 409 bonds, 51 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel dark violet
+> color sel blue violet
+[Repeated 2 time(s)]
+> color sel blue
+> color sel dark blue
+> color sel navy
+[Repeated 2 time(s)]
+> select clear
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_transp.png
+> supersample 6 width 2000 transparentBackground true
+> select #43/I:607
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #43/I:607-656
+atoms, 402 bonds, 50 residues, 1 model selected
+> color sel magenta
+> select clear
+> color #11.2 #ff00ff3b models
+> color #11.2 #ff00ff71 models
+> color #11.2 magenta models
+> color #11.2 white models
+> color #11.2 #ffffff72 models
+> color #11.2 #ffffff5f models
+> color #11.2 #ffffff79 models
+> color #11.2 #ffffff4d models
+> color #11.2 #ffffff5e models
+> color #11.2 #ff40ffff models
+> select clear
+[Repeated 1 time(s)]
+> hide #!11.2 models
+> hide #!11 models
+> hide #!43 models
+> lighting flat
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting shadows true intensity 0.5
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_flat.png
+> supersample 6 width 2000 transparentBackground true
+> lighting soft
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_zoom_background.png
+> supersample 6 width 2000 transparentBackground true
+> show #!43 models
+> show #!1 models
+> hide #!3 models
+> hide #!12 models
+> hide #!13 models
+> hide #!14 models
+> hide #!43 models
+> show #!43 models
+> hide #!43 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!3 models
+> color #3.2 black models
+> color #3.3 dimgrey models
+> color #3.4 steelblue models
+> color #3.5 mediumseagreen models
+> color #3.6 #ffd700fd models
+> color #3.6 gold models
+> color #3.7 firebrick models
+> hide #!3 models
+> show #!3 models
+> show #!13 models
+> hide #!13 models
+> show #!13 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!43 models
+> hide #!43 models
+> show #!43 models
+> hide #!43 models
+> show #!43 models
+> hide #!43 models
+> show #!12 models
+> hide #!12 models
+> show #!14 models
+> hide #!14 models
+> select #1/L,M
+atoms, 5390 bonds, 10 pseudobonds, 872 residues, 2 models selected
+> cartoon hide (#!1 & sel)
+> show #!43 models
+> hide #!43 models
+> show #!43 models
+> hide #!43 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_wo_FACT.png
+> supersample 6 width 2000 transparentBackground true
+> select add #12
+atoms, 5390 bonds, 10 pseudobonds, 872 residues, 4 models selected
+> select add #14
+atoms, 5390 bonds, 10 pseudobonds, 872 residues, 6 models selected
+> select subtract #14
+atoms, 5390 bonds, 10 pseudobonds, 872 residues, 4 models selected
+> select subtract #12
+atoms, 5390 bonds, 10 pseudobonds, 872 residues, 2 models selected
+> cartoon (#!1 & sel)
+> select clear
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_with_FACT.png
+> supersample 6 width 2000 transparentBackground true
+> show #!12 models
+> show #!14 models
+> hide #!13 models
+> hide #!3.2 models
+> hide #!3.3 models
+> show #!3.3 models
+> hide #!3.3 models
+> hide #!3.4 models
+> hide #!3.5 models
+> hide #!3.6 models
+> hide #!3.7 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai.png
+> supersample 6 width 2000 transparentBackground true
+> select #1/L,M
+atoms, 5390 bonds, 10 pseudobonds, 872 residues, 2 models selected
+> cartoon hide (#!1 & sel)
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_wo_FACT.png
+> supersample 6 width 2000 transparentBackground true
+> hide #!12 models
+> hide #!14 models
+> show #!14 models
+> show #!12 models
+> hide #!12 models
+> hide #!14 models
+> show #!3.7 models
+> show #!3.6 models
+> show #!3.5 models
+> show #!3.4 models
+> show #!3.3 models
+> show #!3.2 models
+> show #!13 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_wo_FACT_wo_nucl.png
+> supersample 6 width 2000 transparentBackground true
+> cartoon (#!1 & sel)
+> select clear
+> hide #!1 models
+> show #!43 models
+> combine #1
+> select #16/2
+atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 66320 bonds, 158 pseudobonds, 8209 residues, 4 models selected
+> delete atoms (#!16 & sel)
+> delete bonds (#!16 & sel)
+> show #!7 models
+> hide #!7 models
+> show #!11 models
+> show #!11.2 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> color #11.2 #ff40ffde models
+> color #11.2 #ff40ffce models
+> color #11.2 #ff40ffcc models
+> hide #!11.2 models
+> show #!11.2 models
+> hide #!11.2 models
+> show #!11.2 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_Mcm2_Tof1_HTH_density.png
+> supersample 6 width 2000 transparentBackground true
+> hide #!11 models
+> save
+> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_NCP_extended_composit_bottom_Zhai_Mcm2_Tof1_HTH.png
+> supersample 6 width 2000 transparentBackground true
+> show #!1 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+\u2014\u2014\u2014 End of log from Mon Sep 9 04:24:31 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!16 models
+> show #!16 models
+> hide #!1 models
+> hide #!16 models
+> show #!16 models
+> show #!1 models
+> combine #1
+> hide #!1 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> hide #!17 models
+> show #!17 models
+> hide #!3 models
+> hide #!13 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!17 models
+> show #!17 models
+> select #17/L
+atoms, 3522 bonds, 3 pseudobonds, 493 residues, 2 models selected
+> ui tool show Matchmaker
+> matchmaker #17/Q to #10/D pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain D (#10) with copy of Zhai, chain Q (#17),
+sequence alignment score = 586.9
+RMSD between 88 pruned atom pairs is 0.795 angstroms; (across all 91 pairs:
+.028)
+> hide #!10 models
+> select #17/Q,P,O,N,S,R,L,M
+atoms, 9480 bonds, 10 pseudobonds, 1379 residues, 2 models selected
+> select ~sel & ##selected
+atoms, 63129 bonds, 153 pseudobonds, 7610 residues, 4 models selected
+> delete atoms (#!17 & sel)
+> delete bonds (#!17 & sel)
+> show #!8 models
+> hide #!8 models
+> show #!10 models
+> select add #10
+atoms, 132400 bonds, 284 pseudobonds, 8507 residues, 4 models selected
+> view sel
+> select subtract #10
+Nothing selected
+> select #17/L
+atoms, 3522 bonds, 3 pseudobonds, 493 residues, 2 models selected
+> select clear
+> select #17/L
+atoms, 3522 bonds, 3 pseudobonds, 493 residues, 2 models selected
+> ui tool show "Show Sequence Viewer"
+> sequence chain #17/L
+Alignment identifier is 17/L
+> select clear
+> select #17/L:961-996
+atoms, 197 bonds, 36 residues, 1 model selected
+> select #17/L:956
+atoms, 3 bonds, 1 residue, 1 model selected
+> select #17/L:948-956
+atoms, 67 bonds, 9 residues, 1 model selected
+> select #17/L:948-950
+atoms, 23 bonds, 3 residues, 1 model selected
+> select #17/L:948-996
+atoms, 264 bonds, 1 pseudobond, 45 residues, 2 models selected
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!1 models
+> hide #!1 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!15 models
+> hide #!15 models
+> show #!15 models
+> hide #!15 models
+> hide #!17 models
+> hide #!43 models
+> combine #15
+> hide #!18 models
+> select add #17
+atoms, 9480 bonds, 10 pseudobonds, 1379 residues, 2 models selected
+> select subtract #17
+Nothing selected
+> show #!18 models
+> hide #!18 models
+> show #!18 models
+> show #!17 models
+> hide #!17 models
+> hide #!18 models
+> show #!1 models
+> hide #!1 models
+> combine #1
+> select #19/Q,P,O,N,S,R,L,M,2
+atoms, 15769 bonds, 15 pseudobonds, 2159 residues, 3 models selected
+> select ~sel & ##selected
+atoms, 56840 bonds, 148 pseudobonds, 6830 residues, 4 models selected
+> hide (#!19 & sel) target a
+> hide #!19 models
+> show #!19 models
+> cartoon hide (#!19 & sel)
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> show #!9 models
+> hide #!9 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!1 models
+> show #!1 models
+> hide #!3 models
+> hide #!1 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> hide #!10 models
+> show #!16 models
+> hide #!16 models
+> show #!16 models
+> hide #!16 models
+> show #!17 models
+> hide #!17 models
+> show #!16 models
+> hide #!19 models
+> hide #!16 models
+> show #!16 models
+> show #!19 models
+> hide #!16 models
+> show #!16 models
+> hide #!19 models
+> show #!19 models
+> hide #!16 models
+> hide #!19 models
+> show #!19 models
+> cartoon (#!19 & sel)
+> delete atoms (#!19 & sel)
+> delete bonds (#!19 & sel)
+> show #!17 models
+> hide #!17 models
+> show #!17 models
+> hide #!17 models
+> show #!17 models
+> hide #!19 models
+> show #!19 models
+> hide #!17 models
+> show #!17 models
+> ui tool show Matchmaker
+> matchmaker #19/L to #17/L pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker copy of Zhai, chain L (#17) with copy of Zhai, chain L (#19),
+sequence alignment score = 4482.1
+RMSD between 493 pruned atom pairs is 0.000 angstroms; (across all 493 pairs:
+.000)
+> hide #!19 models
+> show #!19 models
+> hide #!17 models
+> show #!17 models
+> hide #!17 models
+> show #!10 models
+> hide #!19 models
+> show #!19 models
+> select #19/L
+atoms, 3522 bonds, 3 pseudobonds, 493 residues, 2 models selected
+> select #19/2
+atoms, 6289 bonds, 5 pseudobonds, 780 residues, 3 models selected
+> select add #19
+atoms, 15769 bonds, 15 pseudobonds, 2159 residues, 3 models selected
+> select subtract #19
+Nothing selected
+> hide #!19 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!10 models
+> show #!10 models
+> hide #!1 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs
+\u2014\u2014\u2014 End of log from Wed Sep 11 12:56:29 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> hide #!10 models
+> show #!10 models
+> show #!19 models
+> hide #!19 models
+> show #!18 models
+> hide #!18 models
+> show #!17 models
+> hide #!17 models
+> show #!17 models
+> hide #!17 models
+> show #!17 models
+> hide #!17 models
+> show #!50 models
+> hide #!50 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J819_005_volume_map_sharp.mrc
+Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
+,588,588, pixel 0.95, shown at level 0.207, step 4, values float32
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J819_005_volume_map.mrc
+Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
+pixel 0.95, shown at level 0.108, step 4, values float32
+> hide #!10 models
+> hide #!20 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!20 models
+> volume #20 step 1
+> volume #20 level 0.6282
+> volume #20 level 0.5581
+> volume #21 step 1
+> volume #21 level 0.3191
+> show #!50 models
+> hide #!20 models
+> show #!10 models
+> hide #!10 models
+> show #!20 models
+> select add #20
+models selected
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #20,0.99684,0.061516,0.050168,-28.958,-0.064381,0.99626,0.057647,4.4916,-0.046434,-0.060695,0.99708,30.666
+> lighting simple
+> view matrix models
+> #20,0.73598,-0.4705,-0.48679,329.31,0.6768,0.52918,0.51178,-191.97,0.01681,-0.70611,0.7079,265.3
+> view matrix models
+> #20,0.12559,-0.15204,-0.98036,539.99,-0.57343,0.79527,-0.1968,269.08,0.80957,0.58689,0.012694,-138.71
+> view matrix models
+> #20,-0.16726,-0.54653,-0.82057,691.05,-0.96595,-0.075783,0.24736,507.43,-0.19738,0.83401,-0.51525,212.61
+> view matrix models
+> #20,-0.44936,-0.35876,-0.81815,718.23,-0.88005,0.3352,0.33637,346.68,0.15357,0.87116,-0.46636,90.611
+> view matrix models
+> #20,-0.44063,-0.37463,-0.81578,719.55,-0.88716,0.32048,0.33201,353.87,0.13706,0.87003,-0.47357,97.439
+> ui mousemode right "translate selected models"
+> view matrix models
+> #20,-0.44063,-0.37463,-0.81578,705.11,-0.88716,0.32048,0.33201,144.71,0.13706,0.87003,-0.47357,26.598
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #20,-0.33684,-0.44475,-0.8299,698.78,-0.91245,0.37165,0.17118,178.84,0.2323,0.81491,-0.531,29.613
+> ui mousemode right "translate selected models"
+> view matrix models
+> #20,-0.33684,-0.44475,-0.8299,696.83,-0.91245,0.37165,0.17118,160.27,0.2323,0.81491,-0.531,22.667
+> ui tool show "Fit in Map"
+> fitmap #20 inMap #50
+Fit map cryosparc_P17_J819_005_volume_map_sharp.mrc in map
+J842_005_volume_map_EMReady.mrc using 218333 points
+correlation = 0.9383, correlation about mean = 0.6201, overlap = 1.633e+06
+steps = 320, shift = 3.21, angle = 32.8 degrees
+Position of cryosparc_P17_J819_005_volume_map_sharp.mrc (#20) relative to
+J842_005_volume_map_EMReady.mrc (#50) coordinates:
+Matrix rotation and translation
+-0.97651784 -0.21085655 -0.04418632 623.63633661
+-0.20170911 0.96689998 -0.15626218 100.15142454
+.07567265 -0.14368002 -0.98672676 575.82401984
+Axis 0.10410159 -0.99168284 0.07568362
+Axis point 308.30489723 0.00000000 301.22875456
+Rotation angle (degrees) 176.53538416
+Shift along axis 9.18353169
+> select subtract #20
+Nothing selected
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> show #!50 models
+> hide #!50 models
+> volume #20 level 0.55
+> volume #20 level 0.52
+> ui mousemode right zoom
+> select add #20
+models selected
+> view sel
+> select subtract #20
+Nothing selected
+> show #!10 models
+> hide #!20 models
+> show #!20 models
+> volume #20 level 0.5
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> ui tool show "Color Zone"
+> color zone #20 near #10 distance 5.7
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!20 models
+> show #!20 models
+> hide #!10 models
+> show #!10 models
+> hide #!20 models
+> show #!20 models
+> open
+> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_13_mrc1_mcm265_cdc45/fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif
+Chain information for fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif #22
+---
+Chain | Description
+A | .
+B | .
+C | .
+D | .
+E | .
+> ui tool show Matchmaker
+> matchmaker #22/B to #10/5 pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain 5 (#10) with
+fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain B (#22), sequence
+alignment score = 3612.5
+RMSD between 349 pruned atom pairs is 0.656 angstroms; (across all 376 pairs:
+.211)
+> select add #22
+atoms, 35428 bonds, 4406 residues, 1 model selected
+> hide sel target a
+> cartoon sel
+> lighting soft
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> select subtract #22
+Nothing selected
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> fitmap #21 inMap #50
+Fit map cryosparc_P17_J819_005_volume_map.mrc in map
+J842_005_volume_map_EMReady.mrc using 385073 points
+correlation = -0.002927, correlation about mean = 0.004409, overlap = -0.0752
+steps = 684, shift = 150, angle = 30.2 degrees
+Position of cryosparc_P17_J819_005_volume_map.mrc (#21) relative to
+J842_005_volume_map_EMReady.mrc (#50) coordinates:
+Matrix rotation and translation
+.57579874 0.59202822 -0.56387799 140.55370059
+.23007257 0.54448263 0.80660106 227.62276282
+.78455237 -0.59417273 0.17730296 170.40181219
+Axis -0.70827102 -0.68180470 -0.18301506
+Axis point 0.00000000 142.99311800 40.24521085
+Rotation angle (degrees) 81.44306259
+Shift along axis -285.93048023
+> hide #!20 models
+> show #!20 models
+> lighting simple
+> select add #21
+models selected
+> ui mousemode right "translate selected models"
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> view matrix models
+> #21,0.97135,-0.052031,-0.23188,161.6,0.15157,0.88715,0.43587,-376.59,0.18303,-0.45853,0.86962,210.47
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #21,0.19048,0.81338,-0.54967,226.48,0.29087,0.48802,0.82294,-405.4,0.93761,-0.31663,-0.14363,216.66
+> view matrix models
+> #21,-0.32552,0.21775,-0.92012,629.77,-0.85556,0.34648,0.38467,69.087,0.40256,0.91244,0.073519,-23.833
+> view matrix models
+> #21,-0.53454,-0.15623,-0.83058,768.38,-0.79246,0.43422,0.42833,16.109,0.29374,0.88715,-0.35592,123.32
+> view matrix models
+> #21,-0.53754,0.14132,-0.83131,687.98,-0.53102,0.70909,0.46391,-142.08,0.65503,0.69082,-0.30612,62.244
+> view matrix models
+> #21,-0.084069,-0.50373,-0.85976,743.6,-0.50818,0.76385,-0.39785,56.165,0.85714,0.40347,-0.3202,87.35
+> ui mousemode right "translate selected models"
+> view matrix models
+> #21,-0.084069,-0.50373,-0.85976,600,-0.50818,0.76385,-0.39785,93.73,0.85714,0.40347,-0.3202,23.425
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #21,-0.11912,-0.5728,-0.81099,616.38,-0.60623,0.68884,-0.39748,141.88,0.78632,0.44429,-0.4293,60.08
+> ui mousemode right "translate selected models"
+> view matrix models
+> #21,-0.11912,-0.5728,-0.81099,641.5,-0.60623,0.68884,-0.39748,134.93,0.78632,0.44429,-0.4293,-49.603
+> select subtract #21
+Nothing selected
+> fitmap #21 inMap #50
+Fit map cryosparc_P17_J819_005_volume_map.mrc in map
+J842_005_volume_map_EMReady.mrc using 385073 points
+correlation = 0.9655, correlation about mean = 0.736, overlap = 1.153e+06
+steps = 428, shift = 23.7, angle = 35.9 degrees
+Position of cryosparc_P17_J819_005_volume_map.mrc (#21) relative to
+J842_005_volume_map_EMReady.mrc (#50) coordinates:
+Matrix rotation and translation
+-0.97650910 -0.21085482 -0.04438713 623.66015597
+-0.20170409 0.96695488 -0.15592857 100.07508728
+.07579864 -0.14331260 -0.98677052 575.69053694
+Axis 0.10409896 -0.99169665 0.07550605
+Axis point 308.29085690 0.00000000 301.17618213
+Rotation angle (degrees) 176.52597465
+Shift along axis 9.14636480
+> ui mousemode right zoom
+> lighting soft
+[Repeated 1 time(s)]
+> lighting simple
+> hide #!20 models
+> color #21 #ffffb2b1 models
+> color #21 #ffffb2c3 models
+> color #21 #ffffb2cd models
+> lighting soft
+> hide #!21 models
+> show #!20 models
+> hide #!10 models
+> hide #!20 models
+> show #!21 models
+> color #21 #ffffb2ff models
+> volume #21 level 0.3
+> show #!10 models
+> hide #22 models
+> hide #!21 models
+> show #!21 models
+> volume #21 color #ffffb2a7
+> volume #21 color #ffffb2c7
+> volume #21 level 0.2436
+> lighting simple
+> volume #21 level 0.1591
+> show #22 models
+> volume #21 level 0.1281
+> volume #21 level 0.1788
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> select #22/1
+Nothing selected
+> hide #22 models
+> show #22 models
+> select #22/A
+atoms, 8850 bonds, 1096 residues, 1 model selected
+> color sel red
+> ui tool show "Color Actions"
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> color sel fire brick
+[Repeated 1 time(s)]
+> select clear
+> hide #22 models
+> show #22 models
+> hide #!21 models
+> show #!21 models
+> hide #22 models
+> show #22 models
+> hide #!21 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> matchmaker #22/E to #10/P pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain P (#10) with
+fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain E (#22), sequence
+alignment score = 3080.7
+RMSD between 540 pruned atom pairs is 0.670 angstroms; (across all 564 pairs:
+.017)
+> show #!21 models
+> hide #22 models
+> show #22 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> color #21 #ffffb2bd models
+> color #21 #ffffb2b5 models
+> color #21 #ffffb2b2 models
+> color #21 #ffffb2b3 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> show #!20 models
+> hide #!21 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> open
+> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J842_005_volume_map.mrc
+Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
+pixel 0.95, shown at level 0.12, step 4, values float32
+> select add #23
+models selected
+> lighting simple
+> ui mousemode right "translate selected models"
+> view matrix models #23,1,0,0,-7.0847,0,1,0,-197.97,0,0,1,-109.28
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #23,0.98683,-0.1075,-0.12084,64.211,0.093694,0.98898,-0.11463,-186.41,0.13184,0.1018,0.98603,-171.46
+> view matrix models
+> #23,0.94591,0.31213,-0.088466,-59.663,-0.29926,0.73415,-0.60948,142.32,-0.12529,0.60298,0.78785,-193.05
+> view matrix models
+> #23,0.82112,-0.20887,0.53116,-52.333,0.43246,0.83502,-0.34017,-166.12,-0.37248,0.50903,0.77598,-94.238
+> ui mousemode right "translate selected models"
+> view matrix models
+> #23,0.82112,-0.20887,0.53116,-76.409,0.43246,0.83502,-0.34017,-186.01,-0.37248,0.50903,0.77598,-92.077
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #23,0.83793,-0.011709,0.54565,-144.2,0.24675,0.89989,-0.35961,-149.17,-0.48681,0.43596,0.75693,-33.526
+> ui mousemode right "translate selected models"
+> view matrix models
+> #23,0.83793,-0.011709,0.54565,-128.24,0.24675,0.89989,-0.35961,-146.49,-0.48681,0.43596,0.75693,-40.894
+> fitmap #23 inMap #50
+Fit map cryosparc_P17_J842_005_volume_map.mrc in map
+J842_005_volume_map_EMReady.mrc using 31738 points
+correlation = 0.8988, correlation about mean = 0.8848, overlap = 2.616e+04
+steps = 240, shift = 14.4, angle = 16.1 degrees
+Position of cryosparc_P17_J842_005_volume_map.mrc (#23) relative to
+J842_005_volume_map_EMReady.mrc (#50) coordinates:
+Matrix rotation and translation
+.99999950 -0.00093282 -0.00036048 0.38612693
+.00093288 0.99999955 0.00017577 -0.28600473
+.00036032 -0.00017611 0.99999992 -0.03720041
+Axis -0.17327202 -0.35493124 0.91869507
+Axis point 306.61813627 413.85199204 0.00000000
+Rotation angle (degrees) 0.05817852
+Shift along axis 0.00043119
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> volume #23 step 1
+> select subtract #23
+Nothing selected
+> show #!20 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> show #!21 models
+> hide #!21 models
+> volume #20 level 0.4302
+> volume #20 level 0.3778
+> volume #20 level 0.35
+> color zone #20 near #10 distance 5.7
+> color single #20
+> color #20 #b2b2b2d5 models
+> color #20 #b2b2b2be models
+> color #20 #b2b2b2bf models
+> hide #!10 models
+> show #!10 models
+> hide #22 models
+> show #22 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> fitmap #23 inMap #50
+Fit map cryosparc_P17_J842_005_volume_map.mrc in map
+J842_005_volume_map_EMReady.mrc using 2030930 points
+correlation = 0.8962, correlation about mean = 0.8821, overlap = 1.677e+06
+steps = 40, shift = 0.0507, angle = 0.0557 degrees
+Position of cryosparc_P17_J842_005_volume_map.mrc (#23) relative to
+J842_005_volume_map_EMReady.mrc (#50) coordinates:
+Matrix rotation and translation
+.00000000 -0.00007868 -0.00004863 0.03041624
+.00007868 0.99999998 -0.00016626 0.01451905
+.00004864 0.00016625 0.99999998 -0.05718112
+Axis 0.87385342 -0.25564418 0.41355321
+Axis point 0.00000000 342.00873970 86.09530376
+Rotation angle (degrees) 0.01090079
+Shift along axis -0.00077981
+> volume #23 level 0.2075
+> hide #!23 models
+> show #!23 models
+> show #!21 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!21 models
+> show #!21 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!23 models
+> show #!21 models
+> hide #!23 models
+> hide #!21 models
+> hide #22 models
+> show #22 models
+> select clear
+> hide #22 models
+> show #22 models
+> hide #!21 models
+> show #!21 models
+> hide #22 models
+> show #!20 models
+> hide #!21 models
+> volume #20 level 0.38
+> volume #20 level 0.4
+> volume #20 level 0.45
+> show #22 models
+> hide #22 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> hide #!20 models
+> show #!20 models
+> hide #!20 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> show #22 models
+> hide #22 models
+> hide #!23 models
+> show #!23 models
+> hide #!21 models
+> color #23 #b2ffffcc models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #!23 models
+> show #!23 models
+> show #!21 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!21 models
+> ui mousemode right zoom
+> hide #!23 models
+> open /Users/cvetkom/Downloads/cryosparc_P17_J1282_volume_map.mrc
+Opened cryosparc_P17_J1282_volume_map.mrc as #24, grid size 588,588,588, pixel
+.95, shown at level 0.156, step 4, values float32
+> close #24
+> show #22 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #22 models
+> show #22 models
+> matchmaker #22/B to #10/AD pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain AD (#10) with
+fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain B (#22), sequence
+alignment score = 3101.9
+RMSD between 14 pruned atom pairs is 1.061 angstroms; (across all 27 pairs:
+.919)
+> matchmaker #22/C to #10/AD pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain AD (#10) with
+fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain C (#22), sequence
+alignment score = 468.1
+RMSD between 6 pruned atom pairs is 1.308 angstroms; (across all 25 pairs:
+.655)
+> hide #22 models
+> show #22 models
+> matchmaker #22/B to #10/AD pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain AD (#10) with
+fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain B (#22), sequence
+alignment score = 3101.9
+RMSD between 14 pruned atom pairs is 1.061 angstroms; (across all 27 pairs:
+.919)
+> hide #!23 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> matchmaker #22/E to #10/P pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain P (#10) with
+fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain E (#22), sequence
+alignment score = 3080.7
+RMSD between 540 pruned atom pairs is 0.670 angstroms; (across all 564 pairs:
+.017)
+> matchmaker #22/B to #10/2 pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain 2 (#10) with
+fold_2024_09_13_mrc1_mcm265_cdc45_model_0.cif, chain B (#22), sequence
+alignment score = 3481.1
+RMSD between 244 pruned atom pairs is 0.690 angstroms; (across all 293 pairs:
+.338)
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> show #!21 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!21 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> volume #23 level 0.18
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #!21 models
+> show #22 models
+> hide #!21 models
+> show #!21 models
+> hide #!21 models
+> show #!21 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #!23 models
+> volume #21 level 0.16
+> show #!23 models
+> hide #!23 models
+> show #!23 models
+> hide #22 models
+> show #22 models
+> hide #!21 models
+> hide #!23 models
+> hide #22 models
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
+> open
+> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif
+Chain information for
+fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif #24
+---
+Chain | Description
+A | .
+B | .
+C | .
+D E | .
+F G | .
+H I J | .
+K | .
+> select add #24
+atoms, 35097 bonds, 4327 residues, 1 model selected
+> hide sel target a
+> cartoon sel
+> select subtract #24
+Nothing selected
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> matchmaker #24/B to #10/P pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain P (#10) with
+fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif, chain B
+(#24), sequence alignment score = 3082.5
+RMSD between 545 pruned atom pairs is 0.663 angstroms; (across all 564 pairs:
+.931)
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> matchmaker #24/C to #10/2 pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain 2 (#10) with
+fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif, chain C
+(#24), sequence alignment score = 3488.9
+RMSD between 245 pruned atom pairs is 0.669 angstroms; (across all 293 pairs:
+.945)
+> select #24/A
+atoms, 1527 bonds, 185 residues, 1 model selected
+> color sel red
+> select #10/M:96
+atoms, 21 bonds, 1 residue, 1 model selected
+> select clear
+> color #10,24 hot pink
+> undo
+> select #24/C
+atoms, 7047 bonds, 868 residues, 1 model selected
+> select clear
+> select #24/C
+atoms, 7047 bonds, 868 residues, 1 model selected
+> color sel hot pink
+> select clear
+> select #24/C
+atoms, 7047 bonds, 868 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel deep pink
+> color sel blue violet
+> color sel orchid
+> color sel deep pink
+> select clear
+> select #24/C
+atoms, 7047 bonds, 868 residues, 1 model selected
+> color sel medium violet red
+> select clear
+> select #24/C
+atoms, 7047 bonds, 868 residues, 1 model selected
+> color sel magenta
+> select clear
+> select #24/C
+atoms, 7047 bonds, 868 residues, 1 model selected
+> color sel dark orchid
+> select clear
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #24 models
+> hide #22 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #!10 models
+> show #!4 models
+> hide #!4 models
+> show #!5 models
+> hide #!5 models
+> show #!4 models
+> hide #!4 models
+> select #24/D,E
+atoms, 2190 bonds, 272 residues, 1 model selected
+> color sel dodger blue
+> color sel steel blue
+> color sel dodger blue
+> select clear
+> show #!10 models
+> select #24/K
+atoms, 6153 bonds, 775 residues, 1 model selected
+> select clear
+> select #24/K
+atoms, 6153 bonds, 775 residues, 1 model selected
+> color sel yellow green
+> color sel orange
+> select clear
+[Repeated 1 time(s)]
+> hide #!10 models
+> show #!8 models
+> hide #!8 models
+> show #!10 models
+> open
+> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_741_925_mcm2_cdc45_ctf4ctdx3_mcm5_model_0.cif
+Chain information for fold_mrc1_741_925_mcm2_cdc45_ctf4ctdx3_mcm5_model_0.cif
+#25
+---
+Chain | Description
+A | .
+B | .
+C | .
+D E F | .
+G | .
+> hide #25 models
+> show #25 models
+> hide #25 models
+> show #25 models
+> select add #25
+atoms, 31289 bonds, 3849 residues, 1 model selected
+> select subtract #25
+Nothing selected
+> select add #25
+atoms, 31289 bonds, 3849 residues, 1 model selected
+> hide sel target a
+> cartoon sel
+> select subtract #25
+Nothing selected
+> matchmaker #25/B to #24/B pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif,
+chain B (#24) with fold_mrc1_741_925_mcm2_cdc45_ctf4ctdx3_mcm5_model_0.cif,
+chain B (#25), sequence alignment score = 3315.9
+RMSD between 585 pruned atom pairs is 0.430 angstroms; (across all 650 pairs:
+.003)
+> hide #!10 models
+> matchmaker #25/C to #24/C pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker fold_mrc1_741_925_mcm2_cdc45_h3h4tet_ctf4ctdx3_mcm5_model_0.cif,
+chain C (#24) with fold_mrc1_741_925_mcm2_cdc45_ctf4ctdx3_mcm5_model_0.cif,
+chain C (#25), sequence alignment score = 4205.3
+RMSD between 670 pruned atom pairs is 0.557 angstroms; (across all 868 pairs:
+.308)
+> hide #24 models
+> show #24 models
+> hide #24 models
+> select #25/A
+atoms, 1527 bonds, 185 residues, 1 model selected
+> color sel red
+> color sel orange red
+> select clear
+> show #24 models
+> select #25/C
+atoms, 7047 bonds, 868 residues, 1 model selected
+> color sel magenta
+> select clear
+[Repeated 1 time(s)]
+> select #25/G
+atoms, 6153 bonds, 775 residues, 1 model selected
+> color sel coral
+> color sel sienna
+> select clear
+[Repeated 1 time(s)]
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> hide #25 models
+> select #24/H,I,J
+atoms, 11241 bonds, 1371 residues, 1 model selected
+> color sel slate gray
+> color sel cadet blue
+> select add #24
+atoms, 35097 bonds, 4327 residues, 1 model selected
+> select subtract #24
+Nothing selected
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #25 models
+> select #25/D,E,F
+atoms, 11241 bonds, 1371 residues, 1 model selected
+> color sel medium aquamarine
+> color sel cyan
+> select clear
+> show #24 models
+> show #!10 models
+> hide #25 models
+> hide #24 models
+> hide #!10 models
+> show #24 models
+> show #25 models
+> hide #25 models
+> show #25 models
+> hide #24 models
+> show #!10 models
+> hide #!10 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> hide #24 models
+> show #24 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> show #22 models
+> hide #22 models
+> hide #24 models
+> hide #25 models
+> open
+> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_323_337_tof1_model_0.cif
+Chain information for fold_mrc1_323_337_tof1_model_0.cif #26
+---
+Chain | Description
+A | .
+B | .
+> select #26/B
+atoms, 10133 bonds, 1238 residues, 1 model selected
+> color sel slate blue
+> color sel medium slate blue
+[Repeated 4 time(s)]
+> color sel dark slate blue
+[Repeated 1 time(s)]
+> color sel rebecca purple
+[Repeated 4 time(s)]
+> select clear
+> show #!10 models
+> matchmaker #26/B to #10/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain X (#10) with
+fold_mrc1_323_337_tof1_model_0.cif, chain B (#26), sequence alignment score =
+.8
+RMSD between 514 pruned atom pairs is 0.989 angstroms; (across all 665 pairs:
+.879)
+> open
+> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_469_492_tof1_mcm2_mcm6_model_0.cif
+Chain information for fold_mrc1_469_492_tof1_mcm2_mcm6_model_0.cif #27
+---
+Chain | Description
+A | .
+B | .
+C | .
+D | .
+> matchmaker #27/B to #10/X pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain X (#10) with
+fold_mrc1_469_492_tof1_mcm2_mcm6_model_0.cif, chain B (#27), sequence
+alignment score = 5344.2
+RMSD between 523 pruned atom pairs is 0.976 angstroms; (across all 665 pairs:
+.339)
+> select #27/B
+atoms, 10133 bonds, 1238 residues, 1 model selected
+> color sel blue violet
+> select #27/A
+atoms, 202 bonds, 24 residues, 1 model selected
+> color sel red
+> select #27/C
+atoms, 7047 bonds, 868 residues, 1 model selected
+> color sel orchid
+> color sel medium orchid
+[Repeated 1 time(s)]
+> color sel dark orchid
+> color sel medium orchid
+> select clear
+> select #27/D
+atoms, 8057 bonds, 1017 residues, 1 model selected
+> color sel light coral
+> select clear
+> hide #26 models
+> open
+> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_385_456_mcm6_model_0.cif
+Chain information for fold_mrc1_385_456_mcm6_model_0.cif #28
+---
+Chain | Description
+A | .
+B | .
+> hide #27 models
+> hide #28 models
+> show #28 models
+> select #28/A
+atoms, 562 bonds, 72 residues, 1 model selected
+> color sel red
+> select clear
+> matchmaker #28/B to #10/AB pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain AB (#10) with
+fold_mrc1_385_456_mcm6_model_0.cif, chain B (#28), sequence alignment score =
+.2
+RMSD between 300 pruned atom pairs is 0.858 angstroms; (across all 332 pairs:
+.385)
+> hide #28 models
+> show #28 models
+> hide #!10 models
+> show #!10 models
+> matchmaker #28/B to #10/8 pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain 8 (#10) with
+fold_mrc1_385_456_mcm6_model_0.cif, chain B (#28), sequence alignment score =
+.4
+RMSD between 253 pruned atom pairs is 0.826 angstroms; (across all 305 pairs:
+.667)
+> hide #!10 models
+> show #!10 models
+> hide #!10 models
+> show #!10 models
+> select #28/A
+atoms, 562 bonds, 72 residues, 1 model selected
+> color sel dark red
+> select #28/B
+atoms, 8057 bonds, 1017 residues, 1 model selected
+> color sel orange
+> select clear
+> open
+> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_813_865_mcm2_cdc45_model_0.cif
+Chain information for fold_mrc1_813_865_mcm2_cdc45_model_0.cif #29
+---
+Chain | Description
+A | .
+B | .
+C | .
+> select #29/A
+atoms, 451 bonds, 53 residues, 1 model selected
+> color sel red
+> select clear
+> select #29/B
+atoms, 5321 bonds, 650 residues, 1 model selected
+> color sel pale violet red
+> select clear
+> matchmaker #29/B to #10/2 pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain 2 (#10) with
+fold_mrc1_813_865_mcm2_cdc45_model_0.cif, chain B (#29), sequence alignment
+score = 13
+Fewer than 3 residues aligned; cannot match extended_structure, chain 2 with
+fold_mrc1_813_865_mcm2_cdc45_model_0.cif, chain B
+> select #29/B
+atoms, 5321 bonds, 650 residues, 1 model selected
+> select #29/C
+atoms, 7047 bonds, 868 residues, 1 model selected
+> matchmaker #29/C to #10/2 pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain 2 (#10) with
+fold_mrc1_813_865_mcm2_cdc45_model_0.cif, chain C (#29), sequence alignment
+score = 3493.1
+RMSD between 246 pruned atom pairs is 0.605 angstroms; (across all 293 pairs:
+.580)
+> color sel pale violet red
+> select #29/B
+atoms, 5321 bonds, 650 residues, 1 model selected
+> color sel gray
+[Repeated 5 time(s)]
+> color sel light gray
+> color sel gray
+> color sel light yellow
+[Repeated 1 time(s)]
+> color sel old lace
+[Repeated 1 time(s)]
+> color sel antique white
+[Repeated 1 time(s)]
+> color sel ghost white
+> color sel mint cream
+> color sel white smoke
+[Repeated 1 time(s)]
+> color sel beige
+[Repeated 1 time(s)]
+> color sel azure
+> color sel wheat
+[Repeated 1 time(s)]
+> select clear
+> hide #28 models
+> hide #29 models
+> show #29 models
+> hide #29 models
+> show #29 models
+> hide #29 models
+> show #29 models
+> hide #29 models
+> show #29 models
+> hide #29 models
+> open
+> /Users/cvetkom/Documents/AlphaFold/Oliver/fold_mrc1_908_925_cdc45_model_0.cif
+Chain information for fold_mrc1_908_925_cdc45_model_0.cif #30
+---
+Chain | Description
+A | .
+B | .
+> select #30/B
+atoms, 5321 bonds, 650 residues, 1 model selected
+> color sel lavender
+> color sel gainsboro
+> color sel dim gray
+> color sel gray
+> color sel light gray
+> color sel thistle
+[Repeated 1 time(s)]
+> select #30/A
+atoms, 146 bonds, 18 residues, 1 model selected
+> color sel red
+> select clear
+> matchmaker #30/B to #10/P pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain P (#10) with
+fold_mrc1_908_925_cdc45_model_0.cif, chain B (#30), sequence alignment score =
+.5
+RMSD between 536 pruned atom pairs is 0.657 angstroms; (across all 564 pairs:
+.134)
+> save
+> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs
+\u2014\u2014\u2014 End of log from Mon Sep 16 15:36:42 2024 \u2014\u2014\u2014
+opened ChimeraX session
+> open
+> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_0.cif
+Chain information for
+fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_0.cif #31
+---
+Chain | Description
+A | .
+B | .
+C | .
+D | .
+E | .
+F | .
+> open
+> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_1.cif
+Chain information for
+fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_1.cif #32
+---
+Chain | Description
+A | .
+B | .
+C | .
+D | .
+E | .
+F | .
+> open
+> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927/fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_2.cif
+Chain information for
+fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_2.cif #33
+---
+Chain | Description
+A | .
+B | .
+C | .
+D | .
+E | .
+F | .
+> hide #30 models
+> hide #32 models
+> hide #33 models
+> hide #31 models
+> show #31 models
+> ui tool show Matchmaker
+> matchmaker #31/A to #10/2 pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker extended_structure, chain 2 (#10) with
+fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_0.cif, chain A (#31),
+sequence alignment score = 3496.1
+RMSD between 253 pruned atom pairs is 0.662 angstroms; (across all 293 pairs:
+.847)
+The cached device pixel ratio value was stale on window expose. Please file a
+QTBUG which explains how to reproduce.
+> select add #31
+atoms, 38162 bonds, 4714 residues, 1 model selected
+> show #32 models
+> show #33 models
+> select add #32
+atoms, 76324 bonds, 9428 residues, 2 models selected
+> select add #33
+atoms, 114486 bonds, 14142 residues, 3 models selected
+> hide sel target a
+> cartoon sel
+> select subtract #33
+atoms, 76324 bonds, 9428 residues, 2 models selected
+> select subtract #32
+atoms, 38162 bonds, 4714 residues, 1 model selected
+> select subtract #31
+Nothing selected
+> hide #32 models
+> hide #33 models
+> show #32 models
+> show #33 models
+> select #31/A #32/A #33/A
+atoms, 21141 bonds, 2604 residues, 3 models selected
+[deleted to fit within ticket limits]
 > color sel hot pink