The following bug report has been submitted:
Platform: macOS-14.7.6-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250709_W20_COPI_cyto_alignments.cxs"
Opened W20_J3623_consensus_structure.mrc as #1, grid size 240,240,240, pixel
1.19, shown at level 0.194, step 1, values float32
Opened J3623_auto_sharpened_map.ccp4 as #2, grid size 240,240,240, pixel 1.19,
shown at level 3.17, step 1, values float32
Opened cryosparc_P126_J3623_008_volume_map_half_A.mrc as #3.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened cryosparc_P126_J3623_008_volume_map_half_B.mrc as #3.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32
Opened W20_J3987_consensus_resampled.mrc as #4, grid size 240,240,240, pixel
1.19, shown at level 0.277, step 1, values float32
Opened W20_J3987_halfA_consensus_resampled.mrc as #5.1, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32
Opened W20_J3987_halfB_consensus_resampled.mrc as #5.2, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32
Opened W20_J4021_consensus_resampled.mrc as #6, grid size 240,240,240, pixel
1.19, shown at level 0.227, step 1, values float32
Opened W20_J4021_halfA_consensus_resampled.mrc as #7.1, grid size 240,240,240,
pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4021_halfB_consensus_resampled.mrc as #7.2, grid size 240,240,240,
pixel 1.19, shown at level 0.261, step 1, values float32
Opened W20_J4022_consensus_resampled.mrc as #8, grid size 240,240,240, pixel
1.19, shown at level 0.227, step 1, values float32
Opened W20_J4022_halfA_consensus_resampled.mrc as #9.1, grid size 240,240,240,
pixel 1.19, shown at level 0.257, step 1, values float32
Opened W20_J4022_halfB_consensus_resampled.mrc as #9.2, grid size 240,240,240,
pixel 1.19, shown at level 0.255, step 1, values float32
Opened W20_J4023_consensus_resampled.mrc as #10, grid size 240,240,240, pixel
1.19, shown at level 0.199, step 1, values float32
Opened W20_J4023_halfA_consensus_resampled.mrc as #11.1, grid size
240,240,240, pixel 1.19, shown at level 0.258, step 1, values float32
Opened W20_J4023_halfB_consensus_resampled.mrc as #11.2, grid size
240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32
Opened W20_J4024_consensus_resampled.mrc as #12, grid size 240,240,240, pixel
1.19, shown at level 0.199, step 1, values float32
Opened W20_J4024_halfA_consensus_resampled.mrc as #13.1, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32
Opened W20_J4024_halfB_consensus_resampled.mrc as #13.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32
Opened W20_J4025_consensus_resampled.mrc as #14, grid size 240,240,240, pixel
1.19, shown at level 0.212, step 1, values float32
Opened W20_J4025_halfA_consensus_resampled.mrc as #15.1, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4025_halfB_consensus_resampled.mrc as #15.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4026_consensus_resampled.mrc as #16, grid size 240,240,240, pixel
1.19, shown at level 0.24, step 1, values float32
Opened W20_J4026_halfA_consensus_resampled.mrc as #17.1, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32
Opened W20_J4026_halfB_consensus_resampled.mrc as #17.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4027_consensus_resampled.mrc as #18, grid size 240,240,240, pixel
1.19, shown at level 0.253, step 1, values float32
Opened W20_J4027_halfA_consensus_resampled.mrc as #19.1, grid size
240,240,240, pixel 1.19, shown at level 0.254, step 1, values float32
Opened W20_J4027_halfB_consensus_resampled.mrc as #19.2, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32
Opened W20_J4028_consensus_resampled.mrc as #20, grid size 240,240,240, pixel
1.19, shown at level 0.255, step 1, values float32
Opened W20_J4028_halfA_consensus_resampled.mrc as #21.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4028_halfB_consensus_resampled.mrc as #21.2, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J3988_consensus_resampled.mrc as #22, grid size 240,240,240, pixel
1.19, shown at level 0.286, step 1, values float32
Opened W20_J3988_halfA_consensus_resampled.mrc as #23.1, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32
Opened W20_J3988_halfB_consensus_resampled.mrc as #23.2, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32
Opened composite_map_J4021_J4026.ccp4 as #46, grid size 240,240,240, pixel
1.19, shown at level 4.36, step 1, values float32
Opened J4021_J4027_composite_map.ccp4 as #47, grid size 240,240,240, pixel
1.19, shown at level 4.58, step 1, values float32
Opened cryosparc_P126_J4479_map_locres_J3623.mrc as #48, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32
Opened cryosparc_P126_J4480_map_locres_J3623_v2.mrc as #52, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32
Opened cryosparc_P126_J4481_map_locres_J3623_v3.mrc as #53, grid size
240,240,240, pixel 1.19, shown at level 47.8, step 1, values float32
Opened cryosparc_P126_J4486_map_locres.mrc as #54, grid size 240,240,240,
pixel 2.38, shown at level 59.5, step 1, values float32
Opened relion_locres_filtered.mrc as #55, grid size 292,292,292, pixel 1.71,
shown at level 0.005, step 1, values float32
Log from Wed Jul 9 09:46:30 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments_v2.cxs"
Opened W20_J3623_consensus_structure.mrc as #1, grid size 240,240,240, pixel
1.19, shown at level 0.194, step 1, values float32
Opened J3623_auto_sharpened_map.ccp4 as #2, grid size 240,240,240, pixel 1.19,
shown at level 3.17, step 1, values float32
Opened cryosparc_P126_J3623_008_volume_map_half_A.mrc as #3.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened cryosparc_P126_J3623_008_volume_map_half_B.mrc as #3.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32
Opened W20_J3987_consensus_resampled.mrc as #4, grid size 240,240,240, pixel
1.19, shown at level 0.277, step 1, values float32
Opened W20_J3987_halfA_consensus_resampled.mrc as #5.1, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32
Opened W20_J3987_halfB_consensus_resampled.mrc as #5.2, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32
Opened W20_J4021_consensus_resampled.mrc as #6, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32
Opened W20_J4021_halfA_consensus_resampled.mrc as #7.1, grid size 240,240,240,
pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4021_halfB_consensus_resampled.mrc as #7.2, grid size 240,240,240,
pixel 1.19, shown at level 0.261, step 1, values float32
Opened W20_J4022_consensus_resampled.mrc as #8, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32
Opened W20_J4022_halfA_consensus_resampled.mrc as #9.1, grid size 240,240,240,
pixel 1.19, shown at level 0.257, step 1, values float32
Opened W20_J4022_halfB_consensus_resampled.mrc as #9.2, grid size 240,240,240,
pixel 1.19, shown at level 0.255, step 1, values float32
Opened W20_J4023_consensus_resampled.mrc as #10, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32
Opened W20_J4023_halfA_consensus_resampled.mrc as #11.1, grid size
240,240,240, pixel 1.19, shown at level 0.258, step 1, values float32
Opened W20_J4023_halfB_consensus_resampled.mrc as #11.2, grid size
240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32
Opened W20_J4024_consensus_resampled.mrc as #12, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32
Opened W20_J4024_halfA_consensus_resampled.mrc as #13.1, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32
Opened W20_J4024_halfB_consensus_resampled.mrc as #13.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32
Opened W20_J4025_consensus_resampled.mrc as #14, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32
Opened W20_J4025_halfA_consensus_resampled.mrc as #15.1, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4025_halfB_consensus_resampled.mrc as #15.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4026_consensus_resampled.mrc as #16, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32
Opened W20_J4026_halfA_consensus_resampled.mrc as #17.1, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32
Opened W20_J4026_halfB_consensus_resampled.mrc as #17.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4027_consensus_resampled.mrc as #18, grid size 240,240,240, pixel
1.19, shown at level 0.253, step 1, values float32
Opened W20_J4027_halfA_consensus_resampled.mrc as #19.1, grid size
240,240,240, pixel 1.19, shown at level 0.254, step 1, values float32
Opened W20_J4027_halfB_consensus_resampled.mrc as #19.2, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32
Opened W20_J4028_consensus_resampled.mrc as #20, grid size 240,240,240, pixel
1.19, shown at level 0.255, step 1, values float32
Opened W20_J4028_halfA_consensus_resampled.mrc as #21.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4028_halfB_consensus_resampled.mrc as #21.2, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J3988_consensus_resampled.mrc as #22, grid size 240,240,240, pixel
1.19, shown at level 0.286, step 1, values float32
Opened W20_J3988_halfA_consensus_resampled.mrc as #23.1, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32
Opened W20_J3988_halfB_consensus_resampled.mrc as #23.2, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32
Opened composite_map_J4021_J4026.ccp4 as #46, grid size 240,240,240, pixel
1.19, shown at level 4.36, step 1, values float32
Opened J4021_J4027_composite_map.ccp4 as #47, grid size 240,240,240, pixel
1.19, shown at level 4.58, step 1, values float32
Opened cryosparc_P126_J4479_map_locres_J3623.mrc as #48, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32
Opened cryosparc_P126_J4480_map_locres_J3623_v2.mrc as #52, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32
Opened cryosparc_P126_J4481_map_locres_J3623_v3.mrc as #53, grid size
240,240,240, pixel 1.19, shown at level 47.8, step 1, values float32
Opened cryosparc_P126_J4486_map_locres.mrc as #54, grid size 240,240,240,
pixel 2.38, shown at level 59.5, step 1, values float32
Opened relion_locres_filtered.mrc as #55, grid size 292,292,292, pixel 1.71,
shown at level 0.005, step 1, values float32
Log from Tue Jul 8 14:43:14 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments_v2.cxs"
Opened W20_J3623_consensus_structure.mrc as #1, grid size 240,240,240, pixel
1.19, shown at level 0.194, step 1, values float32
Opened J3623_auto_sharpened_map.ccp4 as #2, grid size 240,240,240, pixel 1.19,
shown at level 3.17, step 1, values float32
Opened cryosparc_P126_J3623_008_volume_map_half_A.mrc as #3.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened cryosparc_P126_J3623_008_volume_map_half_B.mrc as #3.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32
Opened W20_J3987_consensus_resampled.mrc as #4, grid size 240,240,240, pixel
1.19, shown at level 0.277, step 1, values float32
Opened W20_J3987_halfA_consensus_resampled.mrc as #5.1, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32
Opened W20_J3987_halfB_consensus_resampled.mrc as #5.2, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32
Opened W20_J4021_consensus_resampled.mrc as #6, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32
Opened W20_J4021_halfA_consensus_resampled.mrc as #7.1, grid size 240,240,240,
pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4021_halfB_consensus_resampled.mrc as #7.2, grid size 240,240,240,
pixel 1.19, shown at level 0.261, step 1, values float32
Opened W20_J4022_consensus_resampled.mrc as #8, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32
Opened W20_J4022_halfA_consensus_resampled.mrc as #9.1, grid size 240,240,240,
pixel 1.19, shown at level 0.257, step 1, values float32
Opened W20_J4022_halfB_consensus_resampled.mrc as #9.2, grid size 240,240,240,
pixel 1.19, shown at level 0.255, step 1, values float32
Opened W20_J4023_consensus_resampled.mrc as #10, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32
Opened W20_J4023_halfA_consensus_resampled.mrc as #11.1, grid size
240,240,240, pixel 1.19, shown at level 0.258, step 1, values float32
Opened W20_J4023_halfB_consensus_resampled.mrc as #11.2, grid size
240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32
Opened W20_J4024_consensus_resampled.mrc as #12, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32
Opened W20_J4024_halfA_consensus_resampled.mrc as #13.1, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32
Opened W20_J4024_halfB_consensus_resampled.mrc as #13.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32
Opened W20_J4025_consensus_resampled.mrc as #14, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32
Opened W20_J4025_halfA_consensus_resampled.mrc as #15.1, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4025_halfB_consensus_resampled.mrc as #15.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4026_consensus_resampled.mrc as #16, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32
Opened W20_J4026_halfA_consensus_resampled.mrc as #17.1, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32
Opened W20_J4026_halfB_consensus_resampled.mrc as #17.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4027_consensus_resampled.mrc as #18, grid size 240,240,240, pixel
1.19, shown at level 0.253, step 1, values float32
Opened W20_J4027_halfA_consensus_resampled.mrc as #19.1, grid size
240,240,240, pixel 1.19, shown at level 0.254, step 1, values float32
Opened W20_J4027_halfB_consensus_resampled.mrc as #19.2, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32
Opened W20_J4028_consensus_resampled.mrc as #20, grid size 240,240,240, pixel
1.19, shown at level 0.255, step 1, values float32
Opened W20_J4028_halfA_consensus_resampled.mrc as #21.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4028_halfB_consensus_resampled.mrc as #21.2, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J3988_consensus_resampled.mrc as #22, grid size 240,240,240, pixel
1.19, shown at level 0.286, step 1, values float32
Opened W20_J3988_halfA_consensus_resampled.mrc as #23.1, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32
Opened W20_J3988_halfB_consensus_resampled.mrc as #23.2, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32
Opened composite_map_J4021_J4026.ccp4 as #46, grid size 240,240,240, pixel
1.19, shown at level 4.36, step 1, values float32
Opened J4021_J4027_composite_map.ccp4 as #47, grid size 240,240,240, pixel
1.19, shown at level 4.58, step 1, values float32
Opened cryosparc_P126_J4479_map_locres_J3623.mrc as #48, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32
Opened cryosparc_P126_J4480_map_locres_J3623_v2.mrc as #52, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32
Opened cryosparc_P126_J4481_map_locres_J3623_v3.mrc as #53, grid size
240,240,240, pixel 1.19, shown at level 47.8, step 1, values float32
Opened cryosparc_P126_J4486_map_locres.mrc as #54, grid size 240,240,240,
pixel 2.38, shown at level 59.5, step 1, values float32
Opened relion_locres_filtered.mrc as #55, grid size 292,292,292, pixel 1.71,
shown at level 0.005, step 1, values float32
Log from Tue Jul 8 14:25:38 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"
Opened W20_J3623_consensus_structure.mrc as #1, grid size 240,240,240, pixel
1.19, shown at level 0.194, step 1, values float32
Opened J3623_auto_sharpened_map.ccp4 as #2, grid size 240,240,240, pixel 1.19,
shown at level 3.17, step 1, values float32
Opened cryosparc_P126_J3623_008_volume_map_half_A.mrc as #3.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened cryosparc_P126_J3623_008_volume_map_half_B.mrc as #3.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32
Opened W20_J3987_consensus_resampled.mrc as #4, grid size 240,240,240, pixel
1.19, shown at level 0.277, step 1, values float32
Opened W20_J3987_halfA_consensus_resampled.mrc as #5.1, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32
Opened W20_J3987_halfB_consensus_resampled.mrc as #5.2, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32
Opened W20_J4021_consensus_resampled.mrc as #6, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32
Opened W20_J4021_halfA_consensus_resampled.mrc as #7.1, grid size 240,240,240,
pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4021_halfB_consensus_resampled.mrc as #7.2, grid size 240,240,240,
pixel 1.19, shown at level 0.261, step 1, values float32
Opened W20_J4022_consensus_resampled.mrc as #8, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32
Opened W20_J4022_halfA_consensus_resampled.mrc as #9.1, grid size 240,240,240,
pixel 1.19, shown at level 0.257, step 1, values float32
Opened W20_J4022_halfB_consensus_resampled.mrc as #9.2, grid size 240,240,240,
pixel 1.19, shown at level 0.255, step 1, values float32
Opened W20_J4023_consensus_resampled.mrc as #10, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32
Opened W20_J4023_halfA_consensus_resampled.mrc as #11.1, grid size
240,240,240, pixel 1.19, shown at level 0.258, step 1, values float32
Opened W20_J4023_halfB_consensus_resampled.mrc as #11.2, grid size
240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32
Opened W20_J4024_consensus_resampled.mrc as #12, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32
Opened W20_J4024_halfA_consensus_resampled.mrc as #13.1, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32
Opened W20_J4024_halfB_consensus_resampled.mrc as #13.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32
Opened W20_J4025_consensus_resampled.mrc as #14, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32
Opened W20_J4025_halfA_consensus_resampled.mrc as #15.1, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4025_halfB_consensus_resampled.mrc as #15.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4026_consensus_resampled.mrc as #16, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32
Opened W20_J4026_halfA_consensus_resampled.mrc as #17.1, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32
Opened W20_J4026_halfB_consensus_resampled.mrc as #17.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4027_consensus_resampled.mrc as #18, grid size 240,240,240, pixel
1.19, shown at level 0.253, step 1, values float32
Opened W20_J4027_halfA_consensus_resampled.mrc as #19.1, grid size
240,240,240, pixel 1.19, shown at level 0.254, step 1, values float32
Opened W20_J4027_halfB_consensus_resampled.mrc as #19.2, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32
Opened W20_J4028_consensus_resampled.mrc as #20, grid size 240,240,240, pixel
1.19, shown at level 0.255, step 1, values float32
Opened W20_J4028_halfA_consensus_resampled.mrc as #21.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4028_halfB_consensus_resampled.mrc as #21.2, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J3988_consensus_resampled.mrc as #22, grid size 240,240,240, pixel
1.19, shown at level 0.286, step 1, values float32
Opened W20_J3988_halfA_consensus_resampled.mrc as #23.1, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32
Opened W20_J3988_halfB_consensus_resampled.mrc as #23.2, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32
Opened composite_map_J4021_J4026.ccp4 as #46, grid size 240,240,240, pixel
1.19, shown at level 4.36, step 1, values float32
Opened J4021_J4027_composite_map.ccp4 as #47, grid size 240,240,240, pixel
1.19, shown at level 5.81, step 1, values float32
Opened cryosparc_P126_J4479_map_locres_J3623.mrc as #48, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32
Opened cryosparc_P126_J4480_map_locres_J3623_v2.mrc as #52, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32
Opened cryosparc_P126_J4481_map_locres_J3623_v3.mrc as #53, grid size
240,240,240, pixel 1.19, shown at level 47.8, step 1, values float32
Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72
Log from Mon Jul 7 17:31:35 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"
Opened W20_J3623_consensus_structure.mrc as #1, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32
Opened J3623_auto_sharpened_map.ccp4 as #2, grid size 240,240,240, pixel 1.19,
shown at level 3.17, step 1, values float32
Opened cryosparc_P126_J3623_008_volume_map_half_A.mrc as #3.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened cryosparc_P126_J3623_008_volume_map_half_B.mrc as #3.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32
Opened W20_J3987_consensus_resampled.mrc as #4, grid size 240,240,240, pixel
1.19, shown at level 0.277, step 1, values float32
Opened W20_J3987_halfA_consensus_resampled.mrc as #5.1, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32
Opened W20_J3987_halfB_consensus_resampled.mrc as #5.2, grid size 240,240,240,
pixel 1.19, shown at level 0.276, step 1, values float32
Opened W20_J4021_consensus_resampled.mrc as #6, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32
Opened W20_J4021_halfA_consensus_resampled.mrc as #7.1, grid size 240,240,240,
pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4021_halfB_consensus_resampled.mrc as #7.2, grid size 240,240,240,
pixel 1.19, shown at level 0.261, step 1, values float32
Opened W20_J4022_consensus_resampled.mrc as #8, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32
Opened W20_J4022_halfA_consensus_resampled.mrc as #9.1, grid size 240,240,240,
pixel 1.19, shown at level 0.257, step 1, values float32
Opened W20_J4022_halfB_consensus_resampled.mrc as #9.2, grid size 240,240,240,
pixel 1.19, shown at level 0.255, step 1, values float32
Opened W20_J4023_consensus_resampled.mrc as #10, grid size 240,240,240, pixel
1.19, shown at level 0.259, step 1, values float32
Opened W20_J4023_halfA_consensus_resampled.mrc as #11.1, grid size
240,240,240, pixel 1.19, shown at level 0.258, step 1, values float32
Opened W20_J4023_halfB_consensus_resampled.mrc as #11.2, grid size
240,240,240, pixel 1.19, shown at level 0.259, step 1, values float32
Opened W20_J4024_consensus_resampled.mrc as #12, grid size 240,240,240, pixel
1.19, shown at level 0.256, step 1, values float32
Opened W20_J4024_halfA_consensus_resampled.mrc as #13.1, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32
Opened W20_J4024_halfB_consensus_resampled.mrc as #13.2, grid size
240,240,240, pixel 1.19, shown at level 0.257, step 1, values float32
Opened W20_J4025_consensus_resampled.mrc as #14, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32
Opened W20_J4025_halfA_consensus_resampled.mrc as #15.1, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4025_halfB_consensus_resampled.mrc as #15.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4026_consensus_resampled.mrc as #16, grid size 240,240,240, pixel
1.19, shown at level 0.26, step 1, values float32
Opened W20_J4026_halfA_consensus_resampled.mrc as #17.1, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32
Opened W20_J4026_halfB_consensus_resampled.mrc as #17.2, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4027_consensus_resampled.mrc as #18, grid size 240,240,240, pixel
1.19, shown at level 0.253, step 1, values float32
Opened W20_J4027_halfA_consensus_resampled.mrc as #19.1, grid size
240,240,240, pixel 1.19, shown at level 0.254, step 1, values float32
Opened W20_J4027_halfB_consensus_resampled.mrc as #19.2, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32
Opened W20_J4028_consensus_resampled.mrc as #20, grid size 240,240,240, pixel
1.19, shown at level 0.255, step 1, values float32
Opened W20_J4028_halfA_consensus_resampled.mrc as #21.1, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4028_halfB_consensus_resampled.mrc as #21.2, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J3988_consensus_resampled.mrc as #22, grid size 240,240,240, pixel
1.19, shown at level 0.286, step 1, values float32
Opened W20_J3988_halfA_consensus_resampled.mrc as #23.1, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32
Opened W20_J3988_halfB_consensus_resampled.mrc as #23.2, grid size
240,240,240, pixel 1.19, shown at level 0.29, step 1, values float32
Opened composite_map_J4021_J4026.ccp4 as #46, grid size 240,240,240, pixel
1.19, shown at level 4.36, step 1, values float32
Log from Mon Jul 7 09:47:13 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250705_W20_COPI_cyto_alignments.cxs"
Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32
Log from Sat Jul 5 20:47:49 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"
Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32
Log from Fri Jul 4 14:29:17 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"
Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32
Log from Fri Jul 4 10:54:24 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250704_W20_COPI_cyto_alignments.cxs"
Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32
Log from Fri Jul 4 09:53:55 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250703_W20_COPI_cyto_alignments.cxs"
Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32
Log from Thu Jul 3 17:41:19 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"
Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32
Log from Wed Jul 2 17:43:06 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"
Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0132, step 1, values float32
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0117, step 1, values float32
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.0127, step 1, values float32
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.013, step 1, values float32
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.0127, step 1, values float32
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00973, step 1, values float32
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.00816, step 1, values float32
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.0123, step 1, values float32
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0158, step 1, values float32
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0156, step 1, values float32
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.00859, step 1, values float32
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.0145, step 1, values float32
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0137, step 1, values float32
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.0106, step 1, values float32
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.0116, step 1, values float32
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.0133, step 1, values float32
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.0148, step 1, values float32
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.0152, step 1, values float32
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.0134, step 1, values float32
Opened W20_J140_MB_joined as #42, grid size 281,271,305, pixel 1.2, shown at
level 0.0132, step 1, values float32
Opened W20_J145_MB_joined as #43, grid size 285,281,252, pixel 1.2, shown at
level 0.0127, step 1, values float32
Opened W20_J150_MB_joined as #44, grid size 248,255,253, pixel 1.2, shown at
level 0.0158, step 1, values float32
Opened W20_J155_MB_joined as #45, grid size 275,269,255, pixel 1.2, shown at
level 0.0137, step 1, values float32
Opened W20_J160_MB_joined as #46, grid size 299,295,317, pixel 1.2, shown at
level 0.0148, step 1, values float32
Log from Wed Jul 2 15:03:33 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"
Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.00608, step 1, values float32
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.00134, step 1, values float32
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.000955, step 1, values float32
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.000493, step 1, values float32
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.00616, step 1, values float32
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00152, step 1, values float32
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.000716, step 1, values float32
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.000812, step 1, values float32
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0066, step 1, values float32
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0013, step 1, values float32
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.000798, step 1, values float32
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.000426, step 1, values float32
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0064, step 1, values float32
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.00156, step 1, values float32
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.000666, step 1, values float32
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.000439, step 1, values float32
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.00725, step 1, values float32
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.00154, step 1, values float32
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.000864, step 1, values float32
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.000379, step 1, values float32
Log from Tue Jul 1 15:42:09 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250701_W20_COPI_cyto_alignments.cxs"
Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 1.41, step 1, values
float32
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 1.51, step 1, values
float32
Opened W20_J4021_005_volume_map_bprime_local.mrc as #13, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4021_005_volume_map_sharp_bprime_local.mrc as #14, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4022_005_volume_map_bprime_local.mrc as #15, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4022_005_volume_map_sharp_bprime_local.mrc as #16, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4023_003_volume_map_bprime_local.mrc as #17, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4023_003_volume_map_sharp_bprime_local.mrc as #18, grid size
240,240,240, pixel 1.19, shown at level 0.321, step 1, values float32
Opened W20_J4024_005_volume_map_bprime_local.mrc as #19, grid size
240,240,240, pixel 1.19, shown at level 0.256, step 1, values float32
Opened W20_J4024_005_volume_map_sharp_bprime_local.mrc as #20, grid size
240,240,240, pixel 1.19, shown at level 0.291, step 1, values float32
Opened W20_J4025_004_volume_map_bprime_local.mrc as #21, grid size
240,240,240, pixel 1.19, shown at level 0.261, step 1, values float32
Opened W20_J4025_004_volume_map_sharp_bprime_local.mrc as #22, grid size
240,240,240, pixel 1.19, shown at level 0.347, step 1, values float32
Opened W20_J4026_004_volume_map_gammazeta_local.mrc as #23, grid size
240,240,240, pixel 1.19, shown at level 0.26, step 1, values float32
Opened W20_J4026_004_volume_map_sharp_gammazeta_local.mrc as #24, grid size
240,240,240, pixel 1.19, shown at level 0.272, step 1, values float32
Opened W20_J4027_005_volume_map_gammazeta_local.mrc as #25, grid size
240,240,240, pixel 1.19, shown at level 0.253, step 1, values float32
Opened W20_J4027_005_volume_map_sharp_gammazeta_local.mrc as #26, grid size
240,240,240, pixel 1.19, shown at level 0.268, step 1, values float32
Opened W20_J4028_004_volume_map_gammazeta_local.mrc as #27, grid size
240,240,240, pixel 1.19, shown at level 0.255, step 1, values float32
Opened W20_J4028_004_volume_map_sharp_gammazeta_local.mrc as #28, grid size
240,240,240, pixel 1.19, shown at level 0.269, step 1, values float32
Opened W20_J140_run_body001.mrc as #29.1, grid size 240,240,240, pixel 1.2,
shown at level 0.00608, step 1, values float32
Opened W20_J140_run_body002.mrc as #29.2, grid size 240,240,240, pixel 1.2,
shown at level 0.00134, step 1, values float32
Opened W20_J140_run_body003.mrc as #29.3, grid size 240,240,240, pixel 1.2,
shown at level 0.000955, step 1, values float32
Opened W20_J140_run_body004.mrc as #29.4, grid size 240,240,240, pixel 1.2,
shown at level 0.000493, step 1, values float32
Opened W20_J145_run_ct8_body001.mrc as #30.1, grid size 240,240,240, pixel
1.2, shown at level 0.00616, step 1, values float32
Opened W20_J145_run_ct8_body002.mrc as #30.2, grid size 240,240,240, pixel
1.2, shown at level 0.00152, step 1, values float32
Opened W20_J145_run_ct8_body003.mrc as #30.3, grid size 240,240,240, pixel
1.2, shown at level 0.000716, step 1, values float32
Opened W20_J145_run_ct8_body004.mrc as #30.4, grid size 240,240,240, pixel
1.2, shown at level 0.000812, step 1, values float32
Opened W20_J150_run_body001.mrc as #31.1, grid size 240,240,240, pixel 1.2,
shown at level 0.0066, step 1, values float32
Opened W20_J150_run_body002.mrc as #31.2, grid size 240,240,240, pixel 1.2,
shown at level 0.0013, step 1, values float32
Opened W20_J150_run_body003.mrc as #31.3, grid size 240,240,240, pixel 1.2,
shown at level 0.000798, step 1, values float32
Opened W20_J150_run_body004.mrc as #31.4, grid size 240,240,240, pixel 1.2,
shown at level 0.000426, step 1, values float32
Opened W20_J155_run_ct6_body001.mrc as #32.1, grid size 240,240,240, pixel
1.2, shown at level 0.0064, step 1, values float32
Opened W20_J155_run_ct6_body002.mrc as #32.2, grid size 240,240,240, pixel
1.2, shown at level 0.00156, step 1, values float32
Opened W20_J155_run_ct6_body003.mrc as #32.3, grid size 240,240,240, pixel
1.2, shown at level 0.000666, step 1, values float32
Opened W20_J155_run_ct6_body004.mrc as #32.4, grid size 240,240,240, pixel
1.2, shown at level 0.000439, step 1, values float32
Opened W20_J160_run_ct6_body001.mrc as #33.1, grid size 240,240,240, pixel
1.2, shown at level 0.00725, step 1, values float32
Opened W20_J160_run_ct6_body002.mrc as #33.2, grid size 240,240,240, pixel
1.2, shown at level 0.00154, step 1, values float32
Opened W20_J160_run_ct6_body003.mrc as #33.3, grid size 240,240,240, pixel
1.2, shown at level 0.000864, step 1, values float32
Opened W20_J160_run_ct6_body004.mrc as #33.4, grid size 240,240,240, pixel
1.2, shown at level 0.000379, step 1, values float32
Log from Tue Jul 1 13:02:54 2025 Startup Messages
---
warning | No presets found in custom preset folder /Users/becca/Desktop/Postdoc/Computational_references/ChimeraX_presets
note | available bundle cache has not been initialized yet
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> graphics silhouettes true
> set silhouetteWidth 1.5
> ui mousemode right "translate selected models"
> alias t0 transparency 0
> alias t50 transparency 50
> alias t60 transparency 60
> alias t70 transparency 70
> alias t80 transparency 80
> alias t90 transparency 90
> alias fmap ui tool show "Fit in Map"
> alias delh select H; delete sel
> alias ls lighting soft
> alias 0 transp 0; lighting soft
> alias fit transp 50; lighting simple
> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1
> functionkey F1 mousemode right 'rotate selected models'
> functionkey F2 mousemode right 'translate selected models'
> functionkey F3 view sel
> functionkey F5 turn x 1 90
> functionkey F6 turn x -1 90
> functionkey F7 turn y 1 90
> functionkey F8 turn y -1 90
> functionkey F9 turn z 1 90
> functionkey F10 turn z -1 90
> cartoon smooth 1
> style stick
Changed 0 atom styles
> size stickRadius 0.3
Changed 0 bond radii
> set bgColor white
> alias bbh hide @C,N,O
> alias bb show @C,N,O
> cartoon all
> style stick
Changed 0 atom styles
> color all byhetero
> hide atoms
> transparency 0
> lighting soft
> color name alphav1 #5786F5
Color 'alphav1' is opaque: rgb(34.1%, 52.5%, 96.1%) hex: #5786f5
> color name alphav2 #2A4B9B
Color 'alphav2' is opaque: rgb(16.5%, 29.4%, 60.8%) hex: #2a4b9b
> color name betapv1 #53EAF3
Color 'betapv1' is opaque: rgb(32.5%, 91.8%, 95.3%) hex: #53eaf3
> color name betapv2 #759ED9
Color 'betapv2' is opaque: rgb(45.9%, 62%, 85.1%) hex: #759ed9
> color name betav1 #37863D
Color 'betav1' is opaque: rgb(21.6%, 52.5%, 23.9%) hex: #37863d
> color name betav2 #207B35
Color 'betav2' is opaque: rgb(12.5%, 48.2%, 20.8%) hex: #207b35
> color name deltav1 #CE8041
Color 'deltav1' is opaque: rgb(80.8%, 50.2%, 25.5%) hex: #ce8041
> color name deltav2 #E97408
Color 'deltav2' is opaque: rgb(91.4%, 45.5%, 3.14%) hex: #e97408
> color name epsilonv1 #F06969
Color 'epsilonv1' is opaque: rgb(94.1%, 41.2%, 41.2%) hex: #f06969
> color name gammav1 #2AFF3C
Color 'gammav1' is opaque: rgb(16.5%, 100%, 23.5%) hex: #2aff3c
> color name gammav2 #61B230
Color 'gammav2' is opaque: rgb(38%, 69.8%, 18.8%) hex: #61b230
> color name zetav1 #E0C819
Color 'zetav1' is opaque: rgb(87.8%, 78.4%, 9.8%) hex: #e0c819
> color name zetav2 #EFE30C
Color 'zetav2' is opaque: rgb(93.7%, 89%, 4.71%) hex: #efe30c
> color name arf1v1 #FF76AF
Color 'arf1v1' is opaque: rgb(100%, 46.3%, 68.6%) hex: #ff76af
> color name arf1v2 #EB70A8
Color 'arf1v2' is opaque: rgb(92.2%, 43.9%, 65.9%) hex: #eb70a8
> color name label_red #E32723
Color 'label_red' is opaque: rgb(89%, 15.3%, 13.7%) hex: #e32723
> color name label_purple #6C4896
Color 'label_purple' is opaque: rgb(42.4%, 28.2%, 58.8%) hex: #6c4896
> color name alphav3 #57679E
Color 'alphav3' is opaque: rgb(34.1%, 40.4%, 62%) hex: #57679e
> color name betapv3 #7ACADA
Color 'betapv3' is opaque: rgb(47.8%, 79.2%, 85.5%) hex: #7acada
> color name betav3 #447A57
Color 'betav3' is opaque: rgb(26.7%, 47.8%, 34.1%) hex: #447a57
> color name gammav3 #ADE57C
Color 'gammav3' is opaque: rgb(67.8%, 89.8%, 48.6%) hex: #ade57c
> color name deltav3 #E5AF76
Color 'deltav3' is opaque: rgb(89.8%, 68.6%, 46.3%) hex: #e5af76
> color name epsilonv3 #EB8675
Color 'epsilonv3' is opaque: rgb(92.2%, 52.5%, 45.9%) hex: #eb8675
> color name zetav3 #F0E07B
Color 'zetav3' is opaque: rgb(94.1%, 87.8%, 48.2%) hex: #f0e07b
> color name arf1v3 #EB8BCA
Color 'arf1v3' is opaque: rgb(92.2%, 54.5%, 79.2%) hex: #eb8bca
> color name label_red_v3 #E51A16
Color 'label_red_v3' is opaque: rgb(89.8%, 10.2%, 8.63%) hex: #e51a16
> color name label_purple_v3 #691099
Color 'label_purple_v3' is opaque: rgb(41.2%, 6.27%, 60%) hex: #691099
> color name lable_purple_v4 #9057AD
Color 'lable_purple_v4' is opaque: rgb(56.5%, 34.1%, 67.8%) hex: #9057ad
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3623_consensus_structure_sharp.mrc"
Opened W20_J3623_consensus_structure_sharp.mrc as #1, grid size 240,240,240,
pixel 1.19, shown at level 0.264, step 1, values float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3623_consensus_structure.mrc"
Opened W20_J3623_consensus_structure.mrc as #2, grid size 240,240,240, pixel
1.19, shown at level 0.257, step 1, values float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc"
Opened W20_J3985_004_volume_map_csparc_refine_of_relion_job121_bprime_mask.mrc
as #3, grid size 240,240,240, pixel 1.2, shown at level 0.269, step 1, values
float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc"
Opened
W20_J3985_004_volume_map_sharp_csparc_refine_of_relion_job121_bprime_mask.mrc
as #4, grid size 240,240,240, pixel 1.2, shown at level 0.286, step 1, values
float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc"
Opened W20_J3986_004_volume_map_csparc_refine_of_relion_job122_bprime_mask.mrc
as #5, grid size 240,240,240, pixel 1.2, shown at level 0.276, step 1, values
float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc"
Opened
W20_J3986_004_volume_map_sharp_csparc_refine_of_relion_job122_bprime_mask.mrc
as #6, grid size 240,240,240, pixel 1.2, shown at level 0.297, step 1, values
float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc"
Opened W20_J3987_004_volume_map_csparc_refine_of_relion_job125_bprime_mask.mrc
as #7, grid size 240,240,240, pixel 1.2, shown at level 0.273, step 1, values
float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc"
Opened
W20_J3987_004_volume_map_sharp_csparc_refine_of_relion_job125_bprime_mask.mrc
as #8, grid size 240,240,240, pixel 1.2, shown at level 0.318, step 1, values
float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc"
Opened
W20_J3988_004_volume_map_csparc_refine_of_relion_job126_gammazeta_mask.mrc as
#9, grid size 240,240,240, pixel 1.2, shown at level 0.282, step 1, values
float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc"
Opened
W20_J3988_004_volume_map_sharp_csparc_refine_of_relion_job126_gammazeta_mask.mrc
as #10, grid size 240,240,240, pixel 1.2, shown at level 0.303, step 1, values
float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc"
Opened
W20_J3989_004_volume_map_csparc_refine_of_relion_job127_gammazeta_mask.mrc as
#11, grid size 240,240,240, pixel 1.2, shown at level 0.729, step 1, values
float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc"
Opened
W20_J3989_004_volume_map_sharp_csparc_refine_of_relion_job127_gammazeta_mask.mrc
as #12, grid size 240,240,240, pixel 1.2, shown at level 0.729, step 1, values
float32
[deleted to fit within ticket limits]
> select subtract #44
Nothing selected
> show #!45 models
> select #45/m
4552 atoms, 4624 bonds, 582 residues, 1 model selected
> color sel gammav3
> select add #45
27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 2 models selected
> select subtract #45
Nothing selected
> hide #!45 models
> show #!1 models
> color zone #1 near #35 distance 6
> volume #1 level 0.1319
> color zone #1 near #35 distance 6.1
> color zone #1 near #35 distance 6.2
> color zone #1 near #35 distance 6.3
> color zone #1 near #35 distance 6.4
> color zone #1 near #35 distance 6.5
> color zone #1 near #35 distance 6.6
> color zone #1 near #35 distance 6.7
> color zone #1 near #35 distance 9
[Repeated 1 time(s)]
> volume #1 level 0.1857
> view view1
Expected an objects specifier or a view name or a keyword
> view name view1
> rotate 90
Unknown command: rotate 90
> turn 90
Expected an axis vector or a keyword
> turn x 90
[Repeated 3 time(s)]
> turn y 90
[Repeated 3 time(s)]
> turn y -90
> view name view2
> turn y 90
> view view2
> turn y 180
> view name view3
> view view3
> turn y 180
> view name view4
[Repeated 1 time(s)]
> view view3
> view name view3
> view name view5
> lighting soft
> set silhouetteWidth 1.5
> ui tool show "Side View"
> save
> /Users/becca/Desktop/Postdoc/Figures/20250707_Poster/J3623_consensus_view5.png
> width 823 height 607 supersample 3 transparentBackground true
> view view3
> save
> /Users/becca/Desktop/Postdoc/Figures/20250707_Poster/J3623_consensus_view3.png
> width 823 height 607 supersample 3 transparentBackground true
> view view4
> save
> /Users/becca/Desktop/Postdoc/Figures/20250707_Poster/J3623_consensus_view4.png
> width 823 height 607 supersample 3 transparentBackground true
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4479_map_locres_J3623.mrc"
Opened cryosparc_P126_J4479_map_locres_J3623.mrc as #48, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32
> ui tool show "Surface Color"
> color sample #1.1 map #48 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766
> color sample #1.1 map #48 palette 2,#ff0000:4,#ffffff:10,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766
> color sample #1.1 map #48 palette 3,#ff0000:4,#ffffff:10,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766
> color sample #1.1 map #48 palette 3,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766
> color sample #1.1 map #48 palette 4,#ff0000:6,#ffffff:8,#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766
> color single #1.1
> key red-white-blue :4 :6 :8 showTool true
> ui mousemode right "color key"
> color sample #1.1 map #48 palette 2.5,#ff0000:6,#ffffff:8,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766
> key red-white-blue :2.5 :6.0 :8.0 showTool true
> color sample #1.1 map #48 palette 2.5,#ff0000:4,#ffffff:8,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766
> key red-white-blue :2.5 :4.0 :8.0 showTool true
> color sample #1.1 map #48 palette 2.5,#ff0000:4,#ffffff:6.5,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766
> key red-white-blue :2.5 :4.0 :6.5 showTool true
> color single #1.1
> color sample #1.1 map #48 palette 2.5,#ff0000:4,#ffffff:6.5,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766
> color sample #1.1 map #48 palette 3,#ff0000:4,#ffffff:6.5,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766
> key red-white-blue :3.0 :4.0 :6.5 showTool true
> color sample #1.1 map #48 palette 3,#ff0000:4.5,#ffffff:6.5,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766
> key red-white-blue :3.0 :4.5 :6.5 showTool true
> color sample #1.1 map #48 palette 3,#ff0000:4.5,#ffffff:6,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766
> key red-white-blue :3.0 :4.5 :6.0 showTool true
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4480_map_locres_J3623_v2.mrc"
Opened cryosparc_P126_J4480_map_locres_J3623_v2.mrc as #52, grid size
240,240,240, pixel 1.19, shown at level 11.6, step 1, values float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4481_map_locres_J3623_v3.mrc"
Opened cryosparc_P126_J4481_map_locres_J3623_v3.mrc as #53, grid size
240,240,240, pixel 1.19, shown at level 47.8, step 1, values float32
> hide #!52 models
> hide #!53 models
> color sample #1.1 map #52 palette 3,#ff0000:4.5,#ffffff:6,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766
> color single #1.1
> color sample #1.1 map #52 palette 3,#ff0000:4.5,#ffffff:6,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766
> color sample #1.1 map #53 palette 3,#ff0000:4.5,#ffffff:6,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766
> color single #1.1
> color sample #1.1 map #53 palette 3,#ff0000:4.5,#ffffff:6,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766
> color sample #1.1 map #53 palette 3,#ff0000:4.5,#ffffff:7,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766
> color sample #1.1 map #53 palette 3,#ff0000:4.5,#ffffff:8,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766
> color single #1.1
> color sample #1.1 map #53 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766
> color sample #1.1 map #53 palette 3,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 2.577, mean 4.107, maximum 7.766
> volume #1 level 0.1937
> view view5
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250707_W20_COPI_cyto_alignments.cxs"
——— End of log from Mon Jul 7 17:31:35 2025 ———
> view name session-start
opened ChimeraX session
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments.cxs"
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2586_007_volume_map.mrc"
Opened cryosparc_P126_J2586_007_volume_map.mrc as #54, grid size 300,300,300,
pixel 1.24, shown at level 0.227, step 1, values float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J4482_map_locres.mrc"
Opened cryosparc_P126_J4482_map_locres.mrc as #55, grid size 400,400,400,
pixel 1.24, shown at level 39.3, step 1, values float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2954_map_locres_v3.mrc"
Opened cryosparc_P126_J2954_map_locres_v3.mrc as #56, grid size 300,300,300,
pixel 1.24, shown at level 6.45, step 1, values float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2953_map_locres_v2.mrc"
Opened cryosparc_P126_J2953_map_locres_v2.mrc as #57, grid size 300,300,300,
pixel 1.24, shown at level 6.45, step 1, values float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2952_map_locres_J2634_v1.mrc"
Opened cryosparc_P126_J2952_map_locres_J2634_v1.mrc as #58, grid size
400,400,400, pixel 1.24, shown at level 39.3, step 1, values float32
> hide #!58 models
> hide #!57 models
> hide #!56 models
> hide #!55 models
> hide #!1 models
> show #!50 models
> hide #51 models
> hide #!50 models
> ui tool show "Surface Color"
> color sample #54.1 map #58 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 2.735, mean 6.524, maximum 41.56
> color single #54.1
> color sample #54.1 map #58 palette 2.735,#ff0000:4,#ffffff:6,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.735, mean 6.524, maximum 41.56
> color single #54.1
> color sample #54.1 map #58 palette 3.5,#ff0000:5,#ffffff:6,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.735, mean 6.524, maximum 41.56
> close #54
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2634_009_volume_map.mrc"
Opened cryosparc_P126_J2634_009_volume_map.mrc as #54, grid size 400,400,400,
pixel 1.24, shown at level 0.224, step 1, values float32
> show #!58 models
> hide #!58 models
> color sample #54.1 map #58 palette 3.5,#ff0000:5,#ffffff:6,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.735, mean 3.894, maximum 29.02
> color single #54.1
> color sample #54.1 map #56 palette 3.5,#ff0000:5,#ffffff:6,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 0.5331, maximum 17.84
> close #54-58
> show #51 models
> show #!1 models
> view view9
Expected an objects specifier or a view name or a keyword
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/cryosparc_P126_J4486_map_locres.mrc"
Opened cryosparc_P126_J4486_map_locres.mrc as #54, grid size 240,240,240,
pixel 2.38, shown at level 59.5, step 1, values float32
> hide #!54 models
> color sample #1.1 map #54 palette 3,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84
> color single #1.1
> color sample #1.1 map #54 palette 2,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84
> color sample #1.1 map #54 palette 1,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84
> color sample #1.1 map #54 palette 1,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84
> color single #1.1
> color sample #1.1 map #54 palette 1,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84
> color single #1.1
> color sample #1.1 map #54 palette 1,#ff0000:10,#ffffff:20,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84
> color single #1.1
> color sample #1.1 map #54 palette 3,#ff0000:10,#ffffff:30,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84
> color single #1.1
> color sample #1.1 map #54 palette 4,#ff0000:10,#ffffff:30,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84
> color sample #1.1 map #54 palette 1,#ff0000:10,#ffffff:30,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84
> color single #1.1
> color sample #1.1 map #54 palette 1,#ff0000:20,#ffffff:50,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84
> key red-white-blue :1 :20 :50 showTool true
> ui mousemode right "color key"
> color sample #1.1 map #54 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 7.493, mean 26.23, maximum 62.84
> key red-white-blue :7.5 :35.2 :62.8 showTool true
> ui mousemode right "color key"
> color single #1.1
> color sample #1.1 map #48 palette 7.493,#ff0000:35.17,#ffffff:62.84,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72
> color sample #1.1 map #48 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72
> key red-white-blue :2.58 :5.15 :7.72 showTool true
> ui mousemode right "color key"
> color sample #1.1 map #48 palette 3,#ff0000:5,#ffffff:8,#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72
> color sample #1.1 map #48 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72
> color sample #1.1 map #48 palette 2.5,#ff0000:5.1,#ffffff:7.7,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72
> color sample #1.1 map #48 palette 2.5,#ff0000:5.1,#ffffff:7.7,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72
> key red-white-blue :2.5 :5.1 :7.7 showTool true
> ui mousemode right "color key"
> hide #51 models
> hide #!1 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2586_007_volume_map.mrc"
Opened cryosparc_P126_J2586_007_volume_map.mrc as #55, grid size 300,300,300,
pixel 1.24, shown at level 0.227, step 1, values float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J4484_map_locres_J2586.mrc"
Opened cryosparc_P126_J4484_map_locres_J2586.mrc as #56, grid size
300,300,300, pixel 2.48, shown at level 7.7, step 1, values float32
> hide #!56 models
> color sample #55.1 map #56 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 0, mean 0.01555, maximum 9.579
> color sample #55.1 map #56 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 0, mean 0.01555, maximum 9.579
> color sample #55.1 map #56 palette 0,#ff0000:4.79,#ffffff:9.579,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 0.01555, maximum 9.579
> color single #55.1
> close #56
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W33_COPI_budding_p23_ergic/cryosparc_P126_J2953_map_locres_v2.mrc"
Opened cryosparc_P126_J2953_map_locres_v2.mrc as #56, grid size 300,300,300,
pixel 1.24, shown at level 6.45, step 1, values float32
> color sample #55.1 map #56 palette 0,#ff0000:4.79,#ffffff:9.579,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283
> hide #!55 models
> show #!55 models
> hide #!56 models
> color sample #55.1 map #56 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283
> color single #55.1
> color sample #55.1 map #56 palette 3,#ff0000:4,#ffffff:7.5,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283
> color sample #55.1 map #56 palette 3,#ff0000:4,#ffffff:7,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283
> color single #55.1
> color sample #55.1 map #56 palette 3,#ff0000:4,#ffffff:7,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283
> color sample #55.1 map #56 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283
> color sample #55.1 map #56 palette 0,#ff0000:3.642,#ffffff:7,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283
> color sample #55.1 map #56 palette 2,#ff0000:4,#ffffff:7,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283
> color sample #55.1 map #56 palette 2.5,#ff0000:4,#ffffff:7,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283
> color sample #55.1 map #56 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283
> color sample #55.1 map #56 palette 2,#ff0000:4,#ffffff:7.283,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 2.645, maximum 7.283
> volume #55 level 0.1387
> volume #55 level 0.2647
> volume #56 level 5.608
> hide #!56 models
> volume #55 level 0.196
> color sample #55.1 map #56 palette 2,#ff0000:3,#ffffff:7.283,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 2.469, maximum 10.19
> color sample #55.1 map #56 palette 2,#ff0000:5,#ffffff:7.283,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 2.469, maximum 10.19
> color sample #55.1 map #56 palette 2,#ff0000:3.5,#ffffff:7.283,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 2.469, maximum 10.19
> key red-white-blue :2.00 :3.50 :7.28 showTool true
> ui mousemode right "color key"
> show #51 models
> color sample #55.1 map #56 palette 2,#ff0000:3.5,#ffffff:6,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 2.469, maximum 10.19
> color sample #55.1 map #56 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 0, mean 2.469, maximum 10.19
> color sample #55.1 map #56 palette 2,#ff0000:4,#ffffff:7.2,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 2.469, maximum 10.19
> close #55
> close #56
> hide #51 models
> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Final maps and
> model/job073_local_res_filtered_map/relion_locres_filtered.mrc"
Opened relion_locres_filtered.mrc as #55, grid size 292,292,292, pixel 1.71,
shown at level 0.00473, step 1, values float32
> select add #55
2 models selected
> show #!1 models
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> view matrix models #55,1,0,0,-49.466,0,1,0,19.546,0,0,1,-35.582
> view matrix models #55,1,0,0,-125.29,0,1,0,-27.177,0,0,1,-72.202
> view matrix models #55,1,0,0,-131.08,0,1,0,-78.985,0,0,1,-39.391
> ui mousemode right "rotate selected models"
> view matrix models
> #55,-0.38231,0.6929,0.61133,-29.962,0.21577,0.71024,-0.67007,84.421,-0.89849,-0.12426,-0.42104,593.37
> view matrix models
> #55,-0.86508,-0.091241,-0.49327,551.34,0.025332,-0.99001,0.1387,320.67,-0.501,0.10749,0.85875,116.81
> ui mousemode right "translate selected models"
> view matrix models
> #55,-0.86508,-0.091241,-0.49327,563.32,0.025332,-0.99001,0.1387,328.73,-0.501,0.10749,0.85875,49.963
> view matrix models
> #55,-0.86508,-0.091241,-0.49327,502.1,0.025332,-0.99001,0.1387,335.45,-0.501,0.10749,0.85875,10.384
> ui mousemode right "rotate selected models"
> view matrix models
> #55,-0.7625,0.17437,-0.62305,444.83,-0.32722,-0.93469,0.13888,425.79,-0.55814,0.30977,0.76975,3.7603
> ui mousemode right "translate selected models"
> view matrix models
> #55,-0.7625,0.17437,-0.62305,440.55,-0.32722,-0.93469,0.13888,403.93,-0.55814,0.30977,0.76975,-7.0818
> fitmap #55 inMap #1
Fit map relion_locres_filtered.mrc in map W20_J3623_consensus_structure.mrc
using 248012 points
correlation = 0.446, correlation about mean = 0.2993, overlap = 121.7
steps = 328, shift = 23.5, angle = 15 degrees
Position of relion_locres_filtered.mrc (#55) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:
Matrix rotation and translation
-0.64805723 0.29760230 -0.70103830 399.38555473
-0.32266507 -0.94108474 -0.10122635 486.21101125
-0.68986164 0.16060010 0.70590263 74.18713432
Axis 0.38883752 -0.01659842 -0.92115682
Axis point 261.23669220 207.73357377 0.00000000
Rotation angle (degrees) 160.32536182
Shift along axis 78.88777001
> select subtract #55
Nothing selected
> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Final maps and model/Model_files/COPI_GOLPH3_combined_model_v14.mmcif"
Summary of feedback from opening /Users/becca/Desktop/Postdoc/Grants and paper
drafts/Golph3 paper/Final maps and
model/Model_files/COPI_GOLPH3_combined_model_v14.mmcif
---
warnings | Unknown polymer entity '1' on line 142
Unknown polymer entity '2' on line 206
Unknown polymer entity '3' on line 1183
Unknown polymer entity '4' on line 3547
Unknown polymer entity '5' on line 4479
11 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for COPI_GOLPH3_combined_model_v14.mmcif #56
---
Chain | Description
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
R S T | No description available
> hide #!56 atoms
> show #!56 cartoons
> show #!24 models
> hide #!24 models
> select add #56
17013 atoms, 16995 bonds, 4 pseudobonds, 4252 residues, 2 models selected
> view matrix models #56,1,0,0,-57.326,0,1,0,-94.635,0,0,1,-152.05
> view matrix models #56,1,0,0,-96.675,0,1,0,-128.13,0,0,1,-110.53
> hide #!1 models
> color #55 #929292ff models
> color #55 #92929240 models
> view matrix models #56,1,0,0,-87.633,0,1,0,-75.202,0,0,1,-105.19
> ui mousemode right "rotate selected models"
> view matrix models
> #56,-0.57627,0.2909,-0.76373,403.39,-0.3025,-0.94406,-0.13134,514.31,-0.75921,0.15534,0.63203,127.54
> ui mousemode right "translate selected models"
> view matrix models
> #56,-0.57627,0.2909,-0.76373,414.45,-0.3025,-0.94406,-0.13134,516.62,-0.75921,0.15534,0.63203,106.07
> view matrix models
> #56,-0.57627,0.2909,-0.76373,421.71,-0.3025,-0.94406,-0.13134,495.85,-0.75921,0.15534,0.63203,110.7
> fitmap #56 inMap #55
Fit molecule COPI_GOLPH3_combined_model_v14.mmcif (#56) to map
relion_locres_filtered.mrc (#55) using 17013 atoms
average map value = 0.005565, steps = 148
shifted from previous position = 12.3
rotated from previous position = 7.06 degrees
atoms outside contour = 9511, contour level = 0.0047295
Position of COPI_GOLPH3_combined_model_v14.mmcif (#56) relative to
relion_locres_filtered.mrc (#55) coordinates:
Matrix rotation and translation
0.99861221 0.04491552 0.02749984 -28.06097041
-0.04715481 0.99508491 0.08707710 -7.47857239
-0.02345356 -0.08825301 0.99582194 24.76832483
Axis -0.85742564 0.24917997 -0.45025617
Axis point 0.00000000 330.55403154 136.14787847
Rotation angle (degrees) 5.86829908
Shift along axis 11.04459412
> select subtract #56
Nothing selected
> select add #56
17013 atoms, 16995 bonds, 4 pseudobonds, 4252 residues, 2 models selected
> view matrix models
> #56,-0.64475,0.3289,-0.69002,379.8,-0.27547,-0.94202,-0.19162,491.22,-0.71303,0.066527,0.69797,103.59
> fitmap #56 inMap #55
Fit molecule COPI_GOLPH3_combined_model_v14.mmcif (#56) to map
relion_locres_filtered.mrc (#55) using 17013 atoms
average map value = 0.005776, steps = 92
shifted from previous position = 4.45
rotated from previous position = 3.4 degrees
atoms outside contour = 9140, contour level = 0.0047295
Position of COPI_GOLPH3_combined_model_v14.mmcif (#56) relative to
relion_locres_filtered.mrc (#55) coordinates:
Matrix rotation and translation
0.99783486 0.06315960 -0.01834221 -2.15609454
-0.06052615 0.99097184 0.11963015 -14.59510136
0.02573241 -0.11826095 0.99264907 30.83542514
Axis -0.87549404 -0.16220473 -0.45519206
Axis point 0.00000000 213.68284829 151.38980884
Rotation angle (degrees) 7.80841410
Shift along axis -9.78099817
> view matrix models
> #56,-0.68271,0.33689,-0.6484,381.54,-0.26761,-0.941,-0.20715,505.03,-0.67992,0.032098,0.73258,104.14
> fitmap #56 inMap #55
Fit molecule COPI_GOLPH3_combined_model_v14.mmcif (#56) to map
relion_locres_filtered.mrc (#55) using 17013 atoms
average map value = 0.01255, steps = 84
shifted from previous position = 7.68
rotated from previous position = 7.81 degrees
atoms outside contour = 1181, contour level = 0.0047295
Position of COPI_GOLPH3_combined_model_v14.mmcif (#56) relative to
relion_locres_filtered.mrc (#55) coordinates:
Matrix rotation and translation
0.99999995 0.00017955 -0.00021830 0.02553185
-0.00017956 0.99999997 -0.00007215 0.05642662
0.00021829 0.00007219 0.99999997 -0.06358059
Axis 0.24739544 -0.74829798 -0.61550437
Axis point 282.18300475 0.00000000 113.24807650
Rotation angle (degrees) 0.01671451
Shift along axis 0.00322666
> select subtract #56
Nothing selected
> color #56/a label_purple_v3
> color #56/b label_purple_v3
> color #56/d navy
> color #56/e navy
> color #56/f betapv3
> color #56/g betapv3
> color #56/h betav1
> color #56/i betav1
> color #56/j betav1
> color #56/k betav1
> color #56/l deltav1
> color #56/l deltav3
> color #56/m gammav3
> color #56/n gammav3
> color #56/o gammav3
> color #56/s arf1v3
> color #56/r arf1v3
> color #56/t arf1v3
> hide #!56 models
> hide #!55 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments_v2.cxs"
> show #!24 models
> select add #24.13
4552 atoms, 4624 bonds, 582 residues, 1 model selected
> color sel gammav3
> select subtract #24.13
Nothing selected
> select add #25.13
4552 atoms, 4624 bonds, 582 residues, 1 model selected
> color sel gammav3
> select subtract #25.13
Nothing selected
> hide #!24 models
> show #!26 models
> select add #26.13
4552 atoms, 4624 bonds, 582 residues, 1 model selected
> color sel gammav3
> select add #26
27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 15 models selected
> select subtract #26
Nothing selected
> show #!27 models
> select add #26.13
4552 atoms, 4624 bonds, 582 residues, 1 model selected
> select add #26
27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 15 models selected
> select subtract #26
Nothing selected
> select add #27.13
4552 atoms, 4624 bonds, 582 residues, 1 model selected
> color sel gammav3
> select add #27
27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 15 models selected
> select subtract #27
Nothing selected
> hide #!26 models
> hide #!27 models
> select add #28.13
4552 atoms, 4624 bonds, 582 residues, 1 model selected
> color sel gammav3
> select subtract #28.13
Nothing selected
> select add #29.13
4552 atoms, 4624 bonds, 582 residues, 1 model selected
> color sel gammav3
> select add #29
27347 atoms, 27860 bonds, 1 pseudobond, 3435 residues, 15 models selected
> select subtract #29
Nothing selected
> select add #30.13
4552 atoms, 4624 bonds, 582 residues, 1 model selected
> color sel gammav3
> select subtract #30.13
Nothing selected
> select add #32.13
4552 atoms, 4624 bonds, 582 residues, 1 model selected
> color sel gammav3
> select subtract #32.13
Nothing selected
> show #!33.13 models
> select add #33.13
2744 atoms, 2786 bonds, 1 pseudobond, 354 residues, 2 models selected
> color sel gammav3
> select subtract #33.13
Nothing selected
> show #34.13 models
> select add #34.13
4552 atoms, 4624 bonds, 582 residues, 1 model selected
> color sel gammav3
> select subtract #34.13
Nothing selected
> hide #!33 models
> hide #!34 models
> show #!33 models
> hide #!33 models
> show #!35 models
> hide #!35 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
> show #!41 models
> hide #!41 models
> show #!42 models
> hide #!42 models
> show #!43 models
> hide #!43 models
> show #!44 models
> hide #!44 models
> show #!45 models
> hide #!45 models
> show #!46 models
> hide #!46 models
> show #!47 models
> hide #!47 models
> show #!49 models
> show #!50 models
> hide #!50 models
> show #!50 models
> hide #!49 models
> hide #!50 models
> show #!50 models
> hide #!50 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments_v2.cxs"
> show #!55 models
> show #!56 models
> view view1
> view view2
> view view3
> view view4
> view view5
> view view6
Expected an objects specifier or a view name or a keyword
> view view7
Expected an objects specifier or a view name or a keyword
> view view8
Expected an objects specifier or a view name or a keyword
> volume #55 level 0.0055
> volume #55 level 0.005
> color #55 darkgrey models
> color #55 #929292ff models
> color #55 #92929267 models
> ui tool show "Side View"
> view name view8
> hide #!56 models
> hide #!55 models
> show #!50 models
> show #!47 models
> color #47 #929292ff models
> color #47 #92929266 models
> ui mousemode right select
> select clear
[Repeated 2 time(s)]
> hide #!50 models
> show #!50 models
Drag select of 2 residues
> select up
166 atoms, 167 bonds, 24 residues, 1 model selected
> delete sel
Drag select of 7 residues
> select up
149 atoms, 150 bonds, 18 residues, 1 model selected
> delete sel
> select #50/L:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #50/L:2
9 atoms, 8 bonds, 1 residue, 1 model selected
> delete sel
> select #50/L:3
5 atoms, 4 bonds, 1 residue, 1 model selected
> delete sel
> select #50/L:4
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #47
3 models selected
> select clear
> select #50/L:5
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> hide #!50 models
> show #!49 models
> hide #!47 models
> show #!46 models
> select #49/L:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> \
Unknown command: \
> delete sel
> select #46
2 models selected
> select clear
> select #46
2 models selected
> hide #!46 models
> select subtract #46
Nothing selected
> select #49/L:2
9 atoms, 8 bonds, 1 residue, 1 model selected
> delete sel
> select #49/L:3
5 atoms, 4 bonds, 1 residue, 1 model selected
> delete sel
> show #!46 models
> select #49/L:4
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #49/L:5
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
Drag select of 3 residues
> select up
149 atoms, 150 bonds, 18 residues, 1 model selected
> delete sel
> select clear
[Repeated 1 time(s)]Drag select of 4 residues
> select up
166 atoms, 167 bonds, 24 residues, 1 model selected
> delete sel
> hide #!49 models
> hide #!46 models
> color #46 #929292ff models
> color #46 #92929266 models
> show #!46 models
> show #!49 models
> view view8
> hide #!49 models
> hide #!46 models
> show #!55 models
> show #!56 models
> view name view8
> hide #!56 models
> hide #!55 models
> show #!50 models
> show #!47 models
> volume #47 level 4.58
> view view8
> hide #!50 models
> hide #!47 models
> show #!56 models
> show #!55 models
> hide #!56 models
> hide #!55 models
> show #!55 models
> show #!46 models
> hide #!46 models
> show #!46 models
> color #55 #d4fb79ff models
> select add #55
3 models selected
Drag select of 46 composite_map_J4021_J4026.ccp4 , 55
relion_locres_filtered.mrc
> select add #55
5 models selected
> select subtract #55
2 models selected
> ui mousemode right "translate selected models"
> select add #55
5 models selected
> select subtract #55
2 models selected
> select add #46
3 models selected
> select subtract #46
Nothing selected
> select add #55
3 models selected
> view matrix models
> #55,-0.64806,0.2976,-0.70104,404.74,-0.32267,-0.94108,-0.10123,483.04,-0.68986,0.1606,0.7059,77.297
> ui mousemode right "rotate selected models"
> view matrix models
> #55,-0.73178,0.069047,-0.67804,474.38,-0.12094,-0.99222,0.029485,404.07,-0.67073,0.10358,0.73444,77.507
> fitmap #55 inMap #1
Fit map relion_locres_filtered.mrc in map W20_J3623_consensus_structure.mrc
using 191343 points
correlation = 0.5091, correlation about mean = 0.3117, overlap = 135.7
steps = 196, shift = 24.8, angle = 11.2 degrees
Position of relion_locres_filtered.mrc (#55) relative to
W20_J3623_consensus_structure.mrc (#1) coordinates:
Matrix rotation and translation
-0.75253459 0.06710395 -0.65512499 473.61243410
0.00933094 -0.99360872 -0.11249292 428.86098374
-0.65848662 -0.09076775 0.74709878 117.70957595
Axis 0.35145885 0.05438278 -0.93462249
Axis point 262.44867657 214.17046526 0.00000000
Rotation angle (degrees) 178.22886921
Shift along axis 79.76391490
> select subtract #55
Nothing selected
> color #55 #929292ff models
> color #55 #92929266 models
> hide #!46 models
> view view8
> show #!56 models
> hide #!56 models
> hide #!55 models
> show #!50 models
> show #!47 models
> hide #!50 models
> hide #!47 models
> show #!49 models
> show #!46 models
> view name view8a
> hide #!49 models
> hide #!46 models
> show #!46 models
> show #!49 models
> view name view9
> hide #!49 models
> hide #!46 models
> show #!47 models
> show #!50 models
> hide #!50 models
> view name view10
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments_v2.cxs"
——— End of log from Tue Jul 8 14:25:38 2025 ———
opened ChimeraX session
> show #!1 models
> hide #!47 models
> view view1
> show #51 models
> ui tool show "Surface Color"
> color sample #1.1 map #48 palette 2.5,#ff0000:5.1,#ffffff:7.7,#0000ff
Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72
> key red-white-blue :2.5 :5.1 :7.7 showTool true
> ui mousemode right "color key"
> ui mousemode right "translate selected models"
> key red-white-blue :2.5 :5.0 :7.0 showTool true
> ui mousemode right "color key"
> key red-white-blue :2.5 :5.0 :7.0
> ui mousemode right "translate selected models"
> color sample #1.1 map #48 palette 2.5,#ff0000:5,#ffffff:7,#0000ff
Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72
> view view1
> view view2
> view view3
> view view4
> view view5
> color sample #1.1 map #48 palette #ff0000:#ffffff:#0000ff
Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72
> color sample #1.1 map #48 palette #ff0000:#ffffff:#0000ff
Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72
> color sample #1.1 map #48 palette 3,#ff0000:5,#ffffff:8,#0000ff
Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72
> color sample #1.1 map #48 palette 3,#ff0000:5,#ffffff:8,#0000ff
Map values for surface "surface": minimum 2.577, mean 4.088, maximum 7.72
> key red-white-blue :3 :5 :8 showTool true
> ui mousemode right "color key"
> ui mousemode right "translate selected models"
> save
> /Users/becca/Desktop/Postdoc/Figures/20250707_Poster/chimerax_images/J3623_consensus_view5_locales_color_v2.png
> width 866 height 597 supersample 3 transparentBackground true
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/Files from
> csparc/J3740_betaprime_3Dclass/J3740_betaprime_3Dclass_aligned.py"
Failed opening file /Users/becca/Desktop/Postdoc/COPI notebooks and
resources/Processing/Files from
csparc/J3740_betaprime_3Dclass/J3740_betaprime_3Dclass_aligned.py:
ChimeraX cannot open a regular Chimera session. An exporter from Chimera to
ChimeraX is available in the latest Chimera release. Use its File->Export
Scene
menu item, and change the resulting dialog's "File Type" to ChimeraX.
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250708_W20_COPI_cyto_alignments_v2.cxs"
——— End of log from Tue Jul 8 14:43:14 2025 ———
> view name session-start
opened ChimeraX session
> hide #!1 models
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> presentations/20250702_research_update/Figures/J4021_betaprime_focused_grey.png"
> width 866 height 597 supersample 3 transparentBackground true
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> presentations/20250702_research_update/Figures/J4023_betaprime_focused_grey.png"
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> presentations/20250702_research_update/Figures/J4023_J4024_J4025_betaprime_focused_superimposed_lightgrey_darkgrey.png"
> width 866 height 597 supersample 3 transparentBackground true
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[Repeated 1 time(s)]
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> color #16 silver models
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> save "/Users/becca/Desktop/Postdoc/Group meeting
> presentations/20250702_research_update/Figures/J4027_J4026_gammazeta_focused_superimposed_lightgrey_darkgrey.png"
> width 866 height 597 supersample 3 transparentBackground true
> hide #!18 models
> hide #!16 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/W20_MM_cyto_COPI/20250709_W20_COPI_cyto_alignments.cxs"
——— End of log from Wed Jul 9 09:46:30 2025 ———
opened ChimeraX session
> show #!49 models
> hide #!49 models
> show #!50 models
> show #!49 models
> hide #!49 models
> hide #!50 models
> ui tool show XMAS
Traceback (most recent call last):
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/pandas/core/indexes/base.py", line 3805, in get_loc
return self._engine.get_loc(casted_key)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "index.pyx", line 167, in pandas._libs.index.IndexEngine.get_loc
File "index.pyx", line 196, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 7081, in
pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 7089, in
pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'PSMID'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/tool.py", line 290, in <lambda>
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/tool.py", line 447, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/tool.py", line 460, in map_crosslinks
evidence = Evidence(evidence_file)
^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 37, in __init__
evidence = cls(evidence_file)
^^^^^^^^^^^^^^^^^^
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 105, in __init__
self.engines[engine][1](df)
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 131, in
parse_xlinkx_xi_seqs_scores
function(peptide_pairs, df, xi_alternative)
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 218, in parse_xi_pos_ids
params[key] = df[col_name].tolist()
~~^^^^^^^^^^
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/pandas/core/frame.py", line 4102, in __getitem__
indexer = self.columns.get_loc(key)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/pandas/core/indexes/base.py", line 3812, in get_loc
raise KeyError(key) from err
KeyError: 'PSMID'
KeyError: 'PSMID'
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/pandas/core/indexes/base.py", line 3812, in get_loc
raise KeyError(key) from err
See log for complete Python traceback.
Traceback (most recent call last):
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/pandas/core/indexes/base.py", line 3805, in get_loc
return self._engine.get_loc(casted_key)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "index.pyx", line 167, in pandas._libs.index.IndexEngine.get_loc
File "index.pyx", line 196, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 7081, in
pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 7089, in
pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'PSMID'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/tool.py", line 290, in <lambda>
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/tool.py", line 447, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/tool.py", line 460, in map_crosslinks
evidence = Evidence(evidence_file)
^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 37, in __init__
evidence = cls(evidence_file)
^^^^^^^^^^^^^^^^^^
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 105, in __init__
self.engines[engine][1](df)
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 131, in
parse_xlinkx_xi_seqs_scores
function(peptide_pairs, df, xi_alternative)
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 218, in parse_xi_pos_ids
params[key] = df[col_name].tolist()
~~^^^^^^^^^^
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/pandas/core/frame.py", line 4102, in __getitem__
indexer = self.columns.get_loc(key)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/pandas/core/indexes/base.py", line 3812, in get_loc
raise KeyError(key) from err
KeyError: 'PSMID'
KeyError: 'PSMID'
File "/Users/becca/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/pandas/core/indexes/base.py", line 3812, in get_loc
raise KeyError(key) from err
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16S000N6D/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.121.1
OS Loader Version: 10151.140.19.700.2
Software:
System Software Overview:
System Version: macOS 14.7.6 (23H626)
Kernel Version: Darwin 23.6.0
Time since boot: 6 days, 18 hours, 15 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
biopython: 1.85
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.6.0
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.24.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.9
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-locscalesurfer: 0.1.1
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.3.7
ChimeraX-PickBlobs: 1.0.1
ChimeraX-PICKLUSTER: 2.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RIBFIND: 0.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-XMAS: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
einops: 0.3.2
et_xmlfile: 2.0.0
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
fsspec: 2025.5.1
funcparserlib: 2.0.0a0
geomdl: 5.3.1
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
mpmath: 1.3.0
mrcfile: 1.3.0
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.24.4
numpy: 1.26.4
openpyxl: 3.1.5
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
pandas: 2.2.3
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pyarrow: 19.0.1
pycollada: 0.8
pydantic: 2.11.1
pydantic_core: 2.33.0
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
QtRangeSlider: 0.1.5
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
ribfind: 2.0.2
scipy: 1.10.1
scipy: 1.14.0
seaborn: 0.13.2
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
starfile: 0.5.12
superqt: 0.6.3
sympy: 1.14.0
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
timm: 0.4.12
tinyarray: 1.2.4
tomli: 2.0.1
torch: 2.2.2
torchvision: 0.17.2
tornado: 6.4.2
tqdm: 4.66.6
traitlets: 5.14.3
typeguard: 4.3.0
typing-inspection: 0.4.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
