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Opened 2 years ago
Last modified 2 years ago
#10250 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.7rc202311230013 (2023-11-23 00:13:42 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7rc202311230013 (2023-11-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\2_MBCD\\\a_Align.cxs"
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened WT_PIP2_P68_J150_009_volume_map_sharp.mrc as #1, grid size 400,400,400,
pixel 0.848, shown at level 0.143, step 1, values float32
Opened N55H_Chol_P52_J694_007_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.83, shown at level 0.095, step 1, values float32
Opened N55H_MBCD_P74_J90_011_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.848, shown at level 0.152, step 1, values float32
Opened N55H_CBX_P52_J662_003_volume_map_sharp.mrc as #5, grid size
400,400,400, pixel 0.83, shown at level 0.0883, step 1, values float32
restore_snapshot for "Redust" returned None
Log from Mon Nov 20 10:41:15 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\2_MBCD\\\a_Align.cxs"
Opened WT_PIP2_P68_J150_009_volume_map_sharp.mrc as #1, grid size 400,400,400,
pixel 0.848, shown at level 0.164, step 1, values float32
Opened N55H_Chol_P52_J694_007_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.83, shown at level 0.0705, step 1, values float32
Opened N55H_MBCD_P74_J90_011_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.848, shown at level 0.168, step 1, values float32
Opened N55H_MBCD_P76_J149_007_volume_map_sharp as #4, grid size 400,400,400,
pixel 0.848, shown at level 0.0565, step 1, values float32
Opened N55H_CBX_P52_J662_003_volume_map_sharp.mrc as #5, grid size
400,400,400, pixel 0.83, shown at level 0.092, step 1, values float32
Log from Fri Nov 17 14:41:52 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\2_MBCD\\\a_Align.cxs"
Opened WT_PIP2_P68_J150_009_volume_map_sharp.mrc as #1, grid size 400,400,400,
pixel 0.848, shown at level 0.164, step 1, values float32
Opened N55H_Chol_P52_J694_007_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.83, shown at level 0.0705, step 1, values float32
Opened N55H_MBCD_P74_J90_011_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.848, shown at level 0.168, step 1, values float32
Opened N55H_MBCD_P76_J149_007_volume_map_sharp as #4, grid size 400,400,400,
pixel 0.848, shown at level 0.0565, step 1, values float32
Opened N55H_CBX_P52_J662_003_volume_map_sharp.mrc as #5, grid size
400,400,400, pixel 0.83, shown at level 0.092, step 1, values float32
Log from Thu Nov 16 19:13:21 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\2_MBCD\\\a_Align.cxs"
Opened WT_PIP2_P68_J150_009_volume_map_sharp.mrc as #1, grid size 400,400,400,
pixel 0.848, shown at level 0.164, step 1, values float32
Opened N55H_Chol_P52_J694_007_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.83, shown at level 0.0705, step 1, values float32
Opened N55H_MBCD_P74_J90_011_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.848, shown at level 0.168, step 1, values float32
Opened N55H_MBCD_P76_J149_007_volume_map_sharp as #4, grid size 400,400,400,
pixel 0.848, shown at level 0.0565, step 1, values float32
Opened N55H_CBX_P52_J662_003_volume_map_sharp.mrc as #5, grid size
400,400,400, pixel 0.83, shown at level 0.092, step 1, values float32
Log from Thu Nov 16 05:45:38 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\2_MBCD\\\a_Align.cxs"
Opened WT_PIP2_P68_J150_009_volume_map_sharp.mrc as #1, grid size 400,400,400,
pixel 0.848, shown at level 0.164, step 1, values float32
Opened N55H_Chol_P52_J694_007_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.83, shown at level 0.0705, step 1, values float32
Opened N55H_MBCD_P74_J90_011_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.848, shown at level 0.168, step 1, values float32
Opened N55H_MBCD_P76_J149_007_volume_map_sharp as #4, grid size 400,400,400,
pixel 0.848, shown at level 0.0565, step 1, values float32
Opened N55H_CBX_P52_J662_003_volume_map_sharp.mrc as #5, grid size
400,400,400, pixel 0.83, shown at level 0.092, step 1, values float32
Log from Tue Nov 14 06:22:00 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\2_MBCD\\\a_Align.cxs"
Opened WT_PIP2_P68_J150_009_volume_map_sharp.mrc as #1, grid size 400,400,400,
pixel 0.848, shown at level 0.164, step 1, values float32
Opened N55H_Chol_P52_J694_007_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.83, shown at level 0.0705, step 1, values float32
Opened N55H_MBCD_P74_J90_011_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.848, shown at level 0.168, step 1, values float32
Opened N55H_MBCD_P76_J149_007_volume_map_sharp as #4, grid size 400,400,400,
pixel 0.848, shown at level 0.0565, step 1, values float32
Opened N55H_CBX_P52_J662_003_volume_map_sharp.mrc as #5, grid size
400,400,400, pixel 0.83, shown at level 0.092, step 1, values float32
Log from Mon Nov 13 01:25:53 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\2_MBCD\\\a_Align.cxs"
Opened WT_PIP2_P68_J150_009_volume_map_sharp.mrc as #1, grid size 400,400,400,
pixel 0.848, shown at level 0.164, step 1, values float32
Opened N55H_Chol_P52_J694_007_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.83, shown at level 0.0705, step 1, values float32
Opened N55H_MBCD_P74_J90_011_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.848, shown at level 0.168, step 1, values float32
Opened N55H_MBCD_P76_J149_007_volume_map_sharp as #4, grid size 400,400,400,
pixel 0.848, shown at level 0.0565, step 1, values float32
Opened N55H_CBX_P52_J662_003_volume_map_sharp.mrc as #5, grid size
400,400,400, pixel 0.83, shown at level 0.092, step 1, values float32
Log from Fri Nov 10 19:29:33 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\MBCD\\\c_F30.cxs"
Opened WT_PIP2_P68_J150_009_volume_map_sharp.mrc as #1, grid size 400,400,400,
pixel 0.848, shown at level 0.164, step 1, values float32
Opened N55H_Chol_P52_J694_007_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.83, shown at level 0.0799, step 1, values float32
Opened N55H_MBCD_P74_J90_011_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.848, shown at level 0.154, step 1, values float32
Opened N55H_MBCD_P76_J149_007_volume_map_sharp as #4, grid size 400,400,400,
pixel 0.848, shown at level 0.0565, step 1, values float32
Opened N55H_CBX_P52_J662_003_volume_map_sharp.mrc as #5, grid size
400,400,400, pixel 0.83, shown at level 0.092, step 1, values float32
Log from Thu Nov 9 16:49:07 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\MBCD\\\c_F30.cxs"
Opened WT_PIP2_P68_J150_009_volume_map_sharp.mrc as #1, grid size 400,400,400,
pixel 0.848, shown at level 0.164, step 1, values float32
Opened N55H_Chol_P52_J694_007_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.83, shown at level 0.0799, step 1, values float32
Opened N55H_MBCD_P74_J90_011_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.848, shown at level 0.154, step 1, values float32
Opened N55H_MBCD_P76_J149_007_volume_map_sharp as #4, grid size 400,400,400,
pixel 0.848, shown at level 0.0565, step 1, values float32
Opened N55H_CBX_P52_J662_003_volume_map_sharp.mrc as #5, grid size
400,400,400, pixel 0.83, shown at level 0.092, step 1, values float32
Log from Thu Nov 9 08:38:33 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\MBCD\\\b_lipids_position.cxs"
Opened WT_PIP2_P68_J150_009_volume_map_sharp.mrc as #1, grid size 400,400,400,
pixel 0.848, shown at level 0.164, step 1, values float32
Opened N55H_Chol_P52_J694_007_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.83, shown at level 0.0987, step 1, values float32
Opened N55H_MBCD_P74_J90_011_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.848, shown at level 0.127, step 1, values float32
Opened N55H_MBCD_P76_J149_007_volume_map_sharp as #4, grid size 400,400,400,
pixel 0.848, shown at level 0.0505, step 1, values float32
Opened N55H_CBX_P52_J662_003_volume_map_sharp.mrc as #5, grid size
400,400,400, pixel 0.83, shown at level 0.092, step 1, values float32
Log from Thu Nov 9 07:14:57 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\MBCD\\\a_Align.cxs"
Opened WT_PIP2_P68_J150_009_volume_map_sharp.mrc as #1, grid size 400,400,400,
pixel 0.848, shown at level 0.164, step 1, values float32
Opened N55H_Chol_P52_J694_007_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.83, shown at level 0.0705, step 1, values float32
Opened N55H_MBCD_P74_J90_011_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.848, shown at level 0.106, step 1, values float32
Opened N55H_MBCD_P76_J149_007_volume_map_sharp as #4, grid size 400,400,400,
pixel 0.848, shown at level 0.0642, step 1, values float32
Opened N55H_CBX_P52_J662_003_volume_map_sharp.mrc as #5, grid size
400,400,400, pixel 0.83, shown at level 0.092, step 1, values float32
Log from Thu Nov 9 05:24:54 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\Map&Models\\\231011_All_Align_wo_POPE.cxs"
Opened WT_PIP2_P68_J150_009_volume_map_sharp.mrc as #1, grid size 400,400,400,
pixel 0.848, shown at level 0.152, step 1, values float32
Opened N55H_Chol_P52_J694_007_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.83, shown at level 0.0705, step 1, values float32
Opened N55H_MBCD_P74_J90_011_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.848, shown at level 0.106, step 1, values float32
Opened N55H_MBCD_P76_J149_007_volume_map_sharp as #4, grid size 400,400,400,
pixel 0.848, shown at level 0.0642, step 1, values float32
Opened N55H_CBX_P52_J662_003_volume_map_sharp.mrc as #5, grid size
400,400,400, pixel 0.83, shown at level 0.092, step 1, values float32
Log from Tue Nov 7 22:27:07 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\Map&Models\\\231011_All_Align_wo_POPE.cxs"
Opened WT_PIP2_P68_J150_009_volume_map_sharp.mrc as #1, grid size 400,400,400,
pixel 0.848, shown at level 0.152, step 1, values float32
Opened N55H_Chol_P52_J694_007_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.83, shown at level 0.0861, step 1, values float32
Opened N55H_MBCD_P74_J90_011_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.848, shown at level 0.125, step 1, values float32
Opened N55H_CBX_P52_J662_003_volume_map_sharp.mrc as #3, grid size
400,400,400, pixel 0.83, shown at level 0.092, step 1, values float32
Opened cryosparc_P76_J149_007_volume_map_sharp.mrc as #5, grid size
400,400,400, pixel 0.848, shown at level 0.0838, step 1, values float32
Log from Tue Nov 7 00:43:02 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\Map&Models\\\231011_All_Align_wo_POPE.cxs"
Opened WT_PIP2_P68_J150_009_volume_map_sharp.mrc as #1, grid size 400,400,400,
pixel 0.848, shown at level 0.152, step 1, values float32
Opened N55H_Chol_P52_J694_007_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.83, shown at level 0.0938, step 1, values float32
Opened N55H_MBCD_P74_J90_011_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.848, shown at level 0.159, step 1, values float32
Opened N55H_CBX_P52_J662_003_volume_map_sharp.mrc as #3, grid size
400,400,400, pixel 0.83, shown at level 0.092, step 1, values float32
Opened cryosparc_P76_J149_007_volume_map_sharp.mrc as #5, grid size
400,400,400, pixel 0.848, shown at level 0.0838, step 1, values float32
Log from Tue Oct 31 21:23:00 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\Map&Models\\\231011_All_Align_wo_POPE.cxs"
Opened WT_PIP2_P68_J150_009_volume_map_sharp.mrc as #1, grid size 400,400,400,
pixel 0.848, shown at level 0.181, step 1, values float32
Opened N55H_Chol_P52_J694_007_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.83, shown at level 0.115, step 1, values float32
Opened N55H_MBCD_P74_J90_011_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.848, shown at level 0.148, step 1, values float32
Opened N55H_CBX_P52_J662_003_volume_map_sharp.mrc as #3, grid size
400,400,400, pixel 0.83, shown at level 0.092, step 1, values float32
Opened N55H_MBCD_100_P76_J149_007_volume_map_sharp.mrc as #6, grid size
400,400,400, pixel 0.848, shown at level 0.0807, step 1, values float32
Opened cryosparc_P76_J149_007_volume_map_sharp.mrc as #5, grid size
400,400,400, pixel 0.848, shown at level 0.0965, step 1, values float32
Log from Tue Oct 31 06:40:42 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\Map&Models\\\231011_All_Align_wo_POPE.cxs"
Opened WT_PIP2_P68_J150_009_volume_map_sharp.mrc as #1, grid size 400,400,400,
pixel 0.848, shown at level 0.181, step 1, values float32
Opened N55H_Chol_P52_J694_007_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.83, shown at level 0.0958, step 1, values float32
Opened N55H_MBCD_P74_J90_011_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.848, shown at level 0.148, step 1, values float32
Log from Mon Oct 30 21:11:50 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\Map&Models\\\231011_All_Align_wo_POPE.cxs"
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened WT_PIP2_P68_J150_009_volume_map.mrc as #1, grid size 400,400,400, pixel
0.848, shown at level 0.123, step 1, values float32
Opened WT_PIP2_P68_J150_009_volume_map_sharp.mrc as #2, grid size 400,400,400,
pixel 0.848, shown at level 0.146, step 1, values float32
Opened N55H_CBX_P52_J650_003_volume_map_sharp.mrc as #6, grid size
400,400,400, pixel 0.83, shown at level 0.117, step 1, values float32
Opened N55H_CBX_P52_J650_003_volume_map.mrc as #5, grid size 400,400,400,
pixel 0.83, shown at level 0.0672, step 1, values float32
Opened cryosparc_P52_J654_003_volume_map.mrc as #22, grid size 400,400,400,
pixel 0.83, shown at level 0.0713, step 1, values float32
Opened cryosparc_P52_J576_005_volume_map_sharp.mrc as #23, grid size
400,400,400, pixel 0.83, shown at level 0.141, step 1, values float32
Log from Wed Oct 11 22:08:58 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\Map&Models\\\230903_All_Align.cxs"
Opened WT_PIP2_P68_J150_009_volume_map.mrc as #1, grid size 400,400,400, pixel
0.848, shown at level 0.123, step 1, values float32
Opened WT_PIP2_P68_J150_009_volume_map_sharp.mrc as #2, grid size 400,400,400,
pixel 0.848, shown at level 0.146, step 1, values float32
Opened N55H_CBX_P52_J575_011_volume_map.mrc as #3, grid size 400,400,400,
pixel 0.83, shown at level 0.169, step 1, values float32
Opened N55H_CBX_P52_J575_011_volume_map_sharp.mrc as #4, grid size
400,400,400, pixel 0.83, shown at level 0.19, step 2, values float32
Opened N55H_CBX_P52_J650_003_volume_map_sharp.mrc as #6, grid size
400,400,400, pixel 0.83, shown at level 0.117, step 1, values float32
Opened N55H_CBX_P52_J650_003_volume_map.mrc as #5, grid size 400,400,400,
pixel 0.83, shown at level 0.0672, step 1, values float32
Opened MBCD_P41_J50_013_volume_map_sharp.mrc as #8, grid size 256,256,256,
pixel 0.848, shown at level 0.159, step 1, values float32
Opened MBCD_P41_J50_013_volume_map.mrc as #7, grid size 256,256,256, pixel
0.848, shown at level 0.117, step 1, values float32
Opened M257_POPE_C2_P38_J250.mrc as #15, grid size 360,360,360, pixel 0.842,
shown at level 0.213, step 1, values float32
Opened M257_POPE_C6_P38_J358.mrc as #13, grid size 360,360,360, pixel 0.842,
shown at level 0.167, step 1, values float32
Opened M257_POPE_C6_P38_J358_sharp.mrc as #14, grid size 360,360,360, pixel
0.842, shown at level 0.222, step 1, values float32
Opened M257_POPE_C2_P38_J250_sharp.mrc as #16, grid size 360,360,360, pixel
0.842, shown at level 0.339, step 1, values float32
Opened N55H_POPE_C2_P58_J151_004_volume_map.mrc as #11, grid size 256,256,256,
pixel 1.1, shown at level 0.397, step 1, values float32
Opened N55H_POPE_C2_P58_J151_004_volume_map_sharp.mrc as #12, grid size
256,256,256, pixel 1.1, shown at level 0.81, step 1, values float32
Opened N55H_POPE_C6_P58_J139_004_volume_map.mrc as #9, grid size 256,256,256,
pixel 1.1, shown at level 0.274, step 1, values float32
Opened N55H_POPE_C6_P58_J139_004_volume_map_sharp.mrc as #10, grid size
256,256,256, pixel 1.1, shown at level 0.567, step 1, values float32
Opened cryosparc_P52_J654_003_volume_map.mrc as #22, grid size 400,400,400,
pixel 0.83, shown at level 0.0713, step 1, values float32
Opened cryosparc_P52_J576_005_volume_map_sharp.mrc as #23, grid size
400,400,400, pixel 0.83, shown at level 0.141, step 1, values float32
Log from Mon Oct 9 18:51:11 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\Map&Models\\\230903_All_Align.cxs"
Opened WT_PIP2_P68_J150_009_volume_map.mrc as #1, grid size 400,400,400, pixel
0.848, shown at level 0.0972, step 1, values float32
Opened WT_PIP2_P68_J150_009_volume_map_sharp.mrc as #2, grid size 400,400,400,
pixel 0.848, shown at level 0.173, step 1, values float32
Opened N55H_CBX_P52_J575_011_volume_map.mrc as #3, grid size 400,400,400,
pixel 0.83, shown at level 0.122, step 1, values float32
Opened N55H_CBX_P52_J575_011_volume_map_sharp.mrc as #4, grid size
400,400,400, pixel 0.83, shown at level 0.287, step 2, values float32
Opened N55H_CBX_P52_J650_003_volume_map_sharp.mrc as #6, grid size
400,400,400, pixel 0.83, shown at level 0.137, step 1, values float32
Opened N55H_CBX_P52_J650_003_volume_map.mrc as #5, grid size 400,400,400,
pixel 0.83, shown at level 0.0813, step 1, values float32
Opened MBCD_P41_J50_013_volume_map_sharp.mrc as #8, grid size 256,256,256,
pixel 0.848, shown at level 0.159, step 1, values float32
Opened MBCD_P41_J50_013_volume_map.mrc as #7, grid size 256,256,256, pixel
0.848, shown at level 0.117, step 1, values float32
Opened POPE_C6_P58_J139_004_volume_map.mrc as #9, grid size 256,256,256, pixel
1.1, shown at level 0.465, step 1, values float32
Opened POPE_C6_P58_J139_004_volume_map_sharp.mrc as #10, grid size
256,256,256, pixel 1.1, shown at level 0.851, step 1, values float32
Opened M257_POPE_C2_P38_J250.mrc as #15, grid size 360,360,360, pixel 0.842,
shown at level 0.213, step 1, values float32
Opened M257_POPE_C6_P38_J358.mrc as #13, grid size 360,360,360, pixel 0.842,
shown at level 0.167, step 1, values float32
Opened M257_POPE_C6_P38_J358_sharp.mrc as #14, grid size 360,360,360, pixel
0.842, shown at level 0.222, step 1, values float32
Opened M257_POPE_C2_P38_J250_sharp.mrc as #16, grid size 360,360,360, pixel
0.842, shown at level 0.402, step 1, values float32
Log from Fri Oct 6 04:37:41 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\Map&Models\\\230903_All_Align.cxs"
Opened cryosparc_P41_J50_013_volume_map.mrc as #13, grid size 256,256,256,
pixel 0.848, shown at level 0.0727, step 1, values float32
Opened M257_POPE_Sym_C6_P38_J358.mrc as #14, grid size 360,360,360, pixel
0.842, shown at level 0.178, step 1, values float32
Opened M257_POPE_Asym_C2_P38_J250.mrc as #15, grid size 360,360,360, pixel
0.842, shown at level 0.227, step 1, values float32
Opened N55H_CBX_P52_J575_011_volume_map.mrc as #16, grid size 400,400,400,
pixel 0.83, shown at level 0.101, step 1, values float32
Opened N55H_CBX_P52_J650_003_volume_map.mrc as #17, grid size 400,400,400,
pixel 0.83, shown at level 0.0868, step 1, values float32
Opened WT_PIP2_P68_J150_009_volume_map.mrc as #18, grid size 400,400,400,
pixel 0.848, shown at level 0.104, step 1, values float32
Log from Mon Sep 4 08:40:16 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:\\\Users\\\OJS\\\OneDrive -
> korea.ac.kr\\\MCSB\\\논문\\\230801_Re\\\Map&Models\\\Maps\\\cryosparc_P41_J50_013_volume_map_sharp.mrc"
Opened cryosparc_P41_J50_013_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 0.848, shown at level 0.101, step 1, values float32
> volume #1 level 0.1977
> open
> C:/Users/OJS/Desktop/Phenix/230901_MBCD_Chol_N55H/RealSpaceRefine_6/230901_PIP2_88_Fit_real_space_refined_004-coot-0_real_space_refined_006.pdb
Chain information for
230901_PIP2_88_Fit_real_space_refined_004-coot-0_real_space_refined_006.pdb #2
---
Chain | Description
A B C D E F | No description available
> hide atoms
> show cartoons
> lighting soft
> graphics silhouettes true
> lighting soft
> lighting simple
> lighting soft
> set bgColor white
> transparency 30
> transparency 0
> clip front 0
> clip front 1
[Repeated 3 time(s)]
> transparency 10
> lighting full
> transparency 30
> color #2 #aa55ffff
> show sel atoms
> select
9882 atoms, 10158 bonds, 6 pseudobonds, 1194 residues, 5 models selected
> show sel atoms
> style sel stick
Changed 9882 atom styles
> color sel byhetero
> select clear
> volume #1 level 0.1802
> select #1:301
Nothing selected
> select #2:301
198 atoms, 192 bonds, 6 residues, 1 model selected
> delete sel
> volume #1 level 0.1496
> clip front -1
[Repeated 3 time(s)]
> close #2
> open
> C:/Users/OJS/Desktop/Phenix/230901_MBCD_Chol_N55H/RealSpaceRefine_8/230903_From6-coot-2_real_space_refined_008.pdb
Chain information for 230903_From6-coot-2_real_space_refined_008.pdb #2
---
Chain | Description
A B C D E F | No description available
> hide atoms
> show cartoons
> select ::name="6OU"::name="AV0"::name="CLR"::name="PTY"
1830 atoms, 1860 bonds, 42 residues, 1 model selected
> show sel atoms
> select clear
> volume #1 level 0.1146
> hide #!1 models
> show #!1 models
> close #2
> ~clip
> transparency 0
> close #1
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/cryosparc_P41_J50_013_volume_map.mrc"
Opened cryosparc_P41_J50_013_volume_map.mrc as #1, grid size 256,256,256,
pixel 0.848, shown at level 0.0557, step 1, values float32
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/cryosparc_P52_J654_003_volume_map.mrc"
Opened cryosparc_P52_J654_003_volume_map.mrc as #2, grid size 400,400,400,
pixel 0.83, shown at level 0.0434, step 2, values float32
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/N55H_CBX_P52_J575_011_volume_map.mrc"
Opened N55H_CBX_P52_J575_011_volume_map.mrc as #3, grid size 400,400,400,
pixel 0.83, shown at level 0.0585, step 2, values float32
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/N55H_CBX_P52_J650_003_volume_map.mrc"
Opened N55H_CBX_P52_J650_003_volume_map.mrc as #4, grid size 400,400,400,
pixel 0.83, shown at level 0.0419, step 2, values float32
> hide #!4 models
> hide #!3 models
> close #2
> show #!3 models
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/WT_PIP2_P68_J150_009_volume_map.mrc"
Opened WT_PIP2_P68_J150_009_volume_map.mrc as #2, grid size 400,400,400, pixel
0.848, shown at level 0.0592, step 2, values float32
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/Models/Map/M257_POPE_Asym_C2_P38_J250.mrc"
Opened M257_POPE_Asym_C2_P38_J250.mrc as #5, grid size 360,360,360, pixel
0.842, shown at level 0.129, step 2, values float32
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/Models/Map/M257_POPE_Sym_C6_P38_J247.mrc"
Opened M257_POPE_Sym_C6_P38_J247.mrc as #6, grid size 360,360,360, pixel
0.842, shown at level 0.13, step 2, values float32
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/Models/Map/M257_POPE_Sym_C6_P38_J358.mrc"
Opened M257_POPE_Sym_C6_P38_J358.mrc as #7, grid size 360,360,360, pixel
0.842, shown at level 0.0553, step 2, values float32
> close #5
> ui tool show "Fit in Map"
> volume step 1
> volume sdLevel 7
> select add #2
2 models selected
> ui mousemode right rotate
[Repeated 1 time(s)]
> ui mousemode right translate
> ui mousemode right rotate
> select subtract #2
Nothing selected
> select add #2
2 models selected
> ui mousemode right select
Drag select of 3 N55H_CBX_P52_J575_011_volume_map.mrc , 2
WT_PIP2_P68_J150_009_volume_map.mrc
> select clear
> select add #2
2 models selected
> ui mousemode right translate
> ui mousemode right rotate
[Repeated 1 time(s)]
> select subtract #2
Nothing selected
> select add #7
2 models selected
> ui tool show "Selection Inspector"
[Repeated 1 time(s)]
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.35797,-0.92743,-0.1083,254.06,-0.92274,-0.33363,-0.19298,370.87,0.14284,0.16902,-0.97521,250.63
> select subtract #7
Nothing selected
> select add #2
2 models selected
> view matrix models
> #2,0.99786,-0.051663,0.040024,2.2824,-0.050341,-0.99817,-0.033358,353.13,0.041675,0.031272,-0.99864,329.3
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99786,-0.051663,0.040024,-59.418,-0.050341,-0.99817,-0.033358,291.43,0.041675,0.031272,-0.99864,258.91
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.34319,-0.93825,0.043655,201.36,0.92114,0.32712,-0.21096,-67.738,0.18365,0.11261,0.97652,-116.62
> view matrix models
> #2,0.14617,-0.97572,0.1631,220.71,0.96842,0.10747,-0.22495,-36.114,0.20196,0.19083,0.96062,-130.27
> view matrix models
> #2,0.12082,-0.94128,0.31526,193.16,0.90759,-0.023893,-0.41917,29.683,0.40209,0.33677,0.85142,-170.3
> view matrix models
> #2,-0.11777,-0.9908,0.066684,284.51,0.83184,-0.1351,-0.53832,81.763,0.54238,-0.0079258,0.8401,-133.7
> view matrix models
> #2,0.51184,-0.84324,0.16422,136.03,0.80865,0.40838,-0.42346,-26.114,0.29001,0.34954,0.89091,-160.21
> fitmap #2 inMap #1
Fit map WT_PIP2_P68_J150_009_volume_map.mrc in map
cryosparc_P41_J50_013_volume_map.mrc using 189219 points
correlation = 0.9683, correlation about mean = 0.8907, overlap = 3383
steps = 296, shift = 1.19, angle = 28.8 degrees
Position of WT_PIP2_P68_J150_009_volume_map.mrc (#2) relative to
cryosparc_P41_J50_013_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.32677678 -0.94510154 -0.00002264 213.41584643
0.94510154 0.32677678 0.00009136 -107.18256396
-0.00007895 -0.00005125 0.99999999 -71.13111930
Axis -0.00007545 0.00002979 1.00000000
Axis point 181.93764484 96.20747282 0.00000000
Rotation angle (degrees) 70.92674466
Shift along axis -71.15041417
> view matrix models
> #2,0.34945,-0.93639,-0.03254,213.65,0.93629,0.34768,0.049898,-117.75,-0.03541,-0.047904,0.99822,-56.72
> fitmap #2 inMap #1
Fit map WT_PIP2_P68_J150_009_volume_map.mrc in map
cryosparc_P41_J50_013_volume_map.mrc using 189219 points
correlation = 0.9682, correlation about mean = 0.8905, overlap = 3388
steps = 80, shift = 0.0147, angle = 3.67 degrees
Position of WT_PIP2_P68_J150_009_volume_map.mrc (#2) relative to
cryosparc_P41_J50_013_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.32679113 -0.94509658 0.00000984 213.40712951
0.94509658 0.32679113 0.00004760 -107.17587259
-0.00004820 -0.00000626 0.99999999 -71.15851647
Axis -0.00002849 0.00003071 1.00000000
Axis point 181.93142140 96.20948368 0.00000000
Rotation angle (degrees) 70.92587473
Shift along axis -71.16788833
> select subtract #2
Nothing selected
> select add #3
2 models selected
> view matrix models
> #3,0.72094,0.66141,0.20683,-97.023,0.69182,-0.7043,-0.15922,193.9,0.040358,0.25787,-0.96534,269.32
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.72094,0.66141,0.20683,-123.91,0.69182,-0.7043,-0.15922,99.357,0.040358,0.25787,-0.96534,190.09
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.98393,0.15587,0.087095,-64.224,-0.14701,0.98405,-0.10021,-51.234,-0.10132,0.085791,0.99115,-75.214
> view matrix models
> #3,0.94101,0.28774,-0.17809,-35.969,-0.25639,0.94972,0.17972,-72.791,0.22085,-0.12346,0.96746,-90.117
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.94101,0.28774,-0.17809,-69.081,-0.25639,0.94972,0.17972,-37.412,0.22085,-0.12346,0.96746,-70.59
> fitmap #3 inMap #1
Fit map N55H_CBX_P52_J575_011_volume_map.mrc in map
cryosparc_P41_J50_013_volume_map.mrc using 195940 points
correlation = 0.9335, correlation about mean = 0.7662, overlap = 3373
steps = 152, shift = 5.21, angle = 16 degrees
Position of N55H_CBX_P52_J575_011_volume_map.mrc (#3) relative to
cryosparc_P41_J50_013_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.98611145 0.16608495 -0.00000138 -82.72031950
-0.16608495 0.98611145 -0.00000770 -27.57886542
0.00000008 0.00000782 1.00000000 -63.91314107
Axis 0.00004673 -0.00000439 -1.00000000
Axis point -206.25963015 480.83020006 0.00000000
Rotation angle (degrees) 9.56026706
Shift along axis 63.90939676
> hide #!3 models
> show #!4 models
> select subtract #3
Nothing selected
> select add #4
2 models selected
> show #!3 models
> view matrix models #4,1,0,0,-53.765,0,1,0,-62.394,0,0,1,-59.325
> fitmap #4 inMap #1
Fit map N55H_CBX_P52_J650_003_volume_map.mrc in map
cryosparc_P41_J50_013_volume_map.mrc using 146995 points
correlation = 0.798, correlation about mean = 0.396, overlap = 1819
steps = 232, shift = 7.06, angle = 27.1 degrees
Position of N55H_CBX_P52_J650_003_volume_map.mrc (#4) relative to
cryosparc_P41_J50_013_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.89050330 -0.45497678 -0.00008303 36.24994099
0.45497679 0.89050330 0.00001421 -114.80856765
0.00006747 -0.00005043 1.00000000 -62.76587636
Axis -0.00007103 -0.00016539 0.99999998
Axis point 256.66853373 17.89349568 0.00000000
Rotation angle (degrees) 27.06344103
Shift along axis -62.74946193
> hide #!4 models
> hide #!6 models
> show #!4 models
> show #!6 models
> select subtract #4
Nothing selected
> select add #6
2 models selected
> view matrix models #6,1,0,0,28.419,0,1,0,-13.308,0,0,1,-78.646
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.53513,0.83556,-0.12438,-8.8407,0.8447,-0.5311,0.066407,80.575,-0.01057,-0.1406,-0.99001,246.47
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.53513,0.83556,-0.12438,-80.715,0.8447,-0.5311,0.066407,52.829,-0.01057,-0.1406,-0.99001,267.73
> view matrix models
> #6,0.53513,0.83556,-0.12438,-77.626,0.8447,-0.5311,0.066407,51.241,-0.01057,-0.1406,-0.99001,266.33
> fitmap #6 inMap #1
Fit map M257_POPE_Sym_C6_P38_J247.mrc in map
cryosparc_P41_J50_013_volume_map.mrc using 194488 points
correlation = 0.8514, correlation about mean = 0.5602, overlap = 4849
steps = 72, shift = 6.16, angle = 8.31 degrees
Position of M257_POPE_Sym_C6_P38_J247.mrc (#6) relative to
cryosparc_P41_J50_013_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.56263632 0.82670451 -0.00013411 -101.86896486
0.82670451 -0.56263633 -0.00007213 68.56261639
-0.00013509 -0.00007028 -0.99999999 250.66184416
Axis 0.88409902 0.46729878 -0.00088286
Axis point 0.00000000 61.20312967 125.28008703
Rotation angle (degrees) 179.99994005
Shift along axis -58.24432530
> fitmap #6 inMap #1
Fit map M257_POPE_Sym_C6_P38_J247.mrc in map
cryosparc_P41_J50_013_volume_map.mrc using 194488 points
correlation = 0.8514, correlation about mean = 0.5602, overlap = 4849
steps = 28, shift = 0.021, angle = 0.0247 degrees
Position of M257_POPE_Sym_C6_P38_J247.mrc (#6) relative to
cryosparc_P41_J50_013_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.56262615 0.82671141 0.00024023 -101.94368627
0.82671140 -0.56262619 0.00014085 68.51636515
0.00025160 0.00011936 -0.99999996 250.57455531
Axis -0.88390389 -0.46766855 -0.00020855
Axis point 0.00000000 61.22795765 125.29897553
Rotation angle (degrees) 179.99930373
Shift along axis 58.01321363
> hide #!6 models
> hide #!7 models
> show #!7 models
> show #!6 models
> select subtract #6
Nothing selected
> select add #7
2 models selected
> view matrix models
> #7,0.35797,-0.92743,-0.1083,215.84,-0.92274,-0.33363,-0.19298,329.63,0.14284,0.16902,-0.97521,191.81
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.24212,-0.95262,-0.18408,248.64,-0.96413,-0.2575,0.064476,285.54,-0.10882,0.16187,-0.98079,231.85
> fitmap #7 inMap #1
Fit map M257_POPE_Sym_C6_P38_J358.mrc in map
cryosparc_P41_J50_013_volume_map.mrc using 189657 points
correlation = 0.8119, correlation about mean = 0.4704, overlap = 4338
steps = 116, shift = 10.5, angle = 13.7 degrees
Position of M257_POPE_Sym_C6_P38_J358.mrc (#7) relative to
cryosparc_P41_J50_013_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.38163883 -0.92431153 0.00002283 190.73845572
-0.92431153 -0.38163883 0.00003142 306.34970125
-0.00002033 -0.00003309 -1.00000000 252.17440285
Axis -0.83116088 0.55603200 -0.00000390
Axis point 0.00000000 216.97812902 126.08325375
Rotation angle (degrees) 179.99777625
Shift along axis 11.80490883
> rename #7 id #5
> select clear
> open
> C:/Users/OJS/Desktop/Phenix/230901_MBCD_Chol_N55H/RealSpaceRefine_8/230903_From6-coot-2_real_space_refined_008.pdb
Chain information for 230903_From6-coot-2_real_space_refined_008.pdb #7
---
Chain | Description
A B C D E F | No description available
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/Models/230309_P38_J250_350_M257_C2.pdb"
Chain information for 230309_P38_J250_350_M257_C2.pdb #8
---
Chain | Description
A D | No description available
B E | No description available
C F | No description available
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/Models/230419_P38_J358_M257_C6.pdb"
Chain information for 230419_P38_J358_M257_C6.pdb #9
---
Chain | Description
A B C D E F | No description available
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Models/230810_Chol_HC_124.pdb"
Chain information for 230810_Chol_HC_124.pdb #10
---
Chain | Description
A B C D E F | No description available
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Models/230821_CBX_HC_142.pdb"
Chain information for 230821_CBX_HC_142.pdb #11
---
Chain | Description
A B C D E F | No description available
> rename #7 230903_MBCD
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Models/230829_PIP2_HC_88.pdb"
Chain information for 230829_PIP2_HC_88.pdb #12
---
Chain | Description
A B C D E F | No description available
> color #12 #ff557fff
> color #11 #aa00ffff
> color #11 #aa55ffff
> color #10 #00aaffff
> color #9 #aaff7fff
> color #8 #ffaa00ff
> color #7 yellow
> select
61870 atoms, 63466 bonds, 36 pseudobonds, 7038 residues, 24 models selected
> color sel byhetero
> style sel stick
Changed 61870 atom styles
> hide sel atoms
> show sel cartoons
> ribbon style thickness 0.6
> select clear
> lighting soft
> select clear
> color #1 yellow models
[Repeated 1 time(s)]
> color #2 #ff557fff models
> color #3 #00aaffff models
> color #4 #aa00ffff models
> color #4 #aa55ffff models
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/Models/Map/M257_POPE_Asym_C2_P38_J250.mrc"
Opened M257_POPE_Asym_C2_P38_J250.mrc as #13, grid size 360,360,360, pixel
0.842, shown at level 0.129, step 2, values float32
> close #6
> rename #13 id #6
> color #6 #aaff7fff models
> color #5 #ffaa00ff models
> volume sdLevel 7
> volume step 1
> select clear
> ui mousemode right "rotate selected models"
> select add #6
2 models selected
> view matrix models
> #6,-0.83485,0.51193,0.20237,171.16,-0.39341,-0.29772,-0.86982,381.77,-0.38504,-0.80578,0.44995,259.81
> view matrix models
> #6,-0.60052,0.79644,0.07115,111.52,-0.79405,-0.5835,-0.17033,384.73,-0.094144,-0.15879,0.98281,40.793
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.60052,0.79644,0.07115,78.043,-0.79405,-0.5835,-0.17033,326.61,-0.094144,-0.15879,0.98281,-0.91196
> view matrix models
> #6,-0.60052,0.79644,0.07115,72.898,-0.79405,-0.5835,-0.17033,339.91,-0.094144,-0.15879,0.98281,-7.7399
> fitmap #6 inMap #1
Fit map M257_POPE_Asym_C2_P38_J250.mrc in map
cryosparc_P41_J50_013_volume_map.mrc using 145832 points
correlation = 0.7735, correlation about mean = 0.3914, overlap = 4045
steps = 180, shift = 4.93, angle = 17.5 degrees
Position of M257_POPE_Asym_C2_P38_J250.mrc (#6) relative to
cryosparc_P41_J50_013_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.77273764 0.63472564 -0.00007874 129.46258414
-0.63472566 -0.77273764 -0.00007823 321.74761505
-0.00011050 -0.00001047 1.00000004 -46.82835092
Axis 0.00005337 0.00002502 -1.00000000
Axis point 122.33042087 137.69674210 0.00000000
Rotation angle (degrees) 140.60036250
Shift along axis 46.84331223
> select clear
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> select add #7
11514 atoms, 11832 bonds, 6 pseudobonds, 1230 residues, 2 models selected
> view matrix models #7,1,0,0,6.5244,0,1,0,4.6003,0,0,1,4.7091
> fitmap #7 inMap #1
Fit molecule 230903_MBCD (#7) to map cryosparc_P41_J50_013_volume_map.mrc (#1)
using 11514 atoms
average map value = 0.04257, steps = 212
shifted from previous position = 4.54
rotated from previous position = 10.5 degrees
atoms outside contour = 10033, contour level = 0.10896
Position of 230903_MBCD (#7) relative to cryosparc_P41_J50_013_volume_map.mrc
(#1) coordinates:
Matrix rotation and translation
0.99260754 0.10792896 0.05551232 -8.52696185
-0.11452261 0.98434707 0.13396048 5.69119599
-0.04018517 -0.13932760 0.98943063 20.98601764
Axis -0.74844214 0.26208254 -0.60921843
Axis point 0.00000000 131.92977684 -36.67757226
Rotation angle (degrees) 10.51956531
Shift along axis -4.91156806
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.99261,0.10793,0.055512,-12.751,-0.11452,0.98435,0.13396,4.62,-0.040185,-0.13933,0.98943,21.363
> fitmap #7 inMap #1
Fit molecule 230903_MBCD (#7) to map cryosparc_P41_J50_013_volume_map.mrc (#1)
using 11514 atoms
average map value = 0.1316, steps = 116
shifted from previous position = 5.55
rotated from previous position = 10.5 degrees
atoms outside contour = 5178, contour level = 0.10896
Position of 230903_MBCD (#7) relative to cryosparc_P41_J50_013_volume_map.mrc
(#1) coordinates:
Matrix rotation and translation
0.99999996 0.00022940 0.00013679 -0.03631015
-0.00022941 0.99999997 0.00005237 0.02023641
-0.00013678 -0.00005240 0.99999999 0.01041884
Axis -0.19246222 0.50256079 -0.84284693
Axis point 69.84264452 151.26658368 0.00000000
Rotation angle (degrees) 0.01559453
Shift along axis 0.00837687
> transparency 10
> select clear
> transparency 50
> select clear
> hide #!1 models
> hide #!7 models
> show #!2 models
> select add #12
11454 atoms, 11670 bonds, 6 pseudobonds, 1266 residues, 2 models selected
> view matrix models #12,1,0,0,-56.527,0,1,0,-69.837,0,0,1,-70.002
> fitmap #12 inMap #2
Fit molecule 230829_PIP2_HC_88.pdb (#12) to map
WT_PIP2_P68_J150_009_volume_map.mrc (#2) using 11454 atoms
average map value = 0.1782, steps = 120
shifted from previous position = 9.95
rotated from previous position = 10.9 degrees
atoms outside contour = 1648, contour level = 0.090674
Position of 230829_PIP2_HC_88.pdb (#12) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.49937202 0.86638767 -0.00008925 -62.01524174
-0.86638767 0.49937201 -0.00007139 231.85897875
-0.00001729 0.00011298 1.00000000 -0.01383035
Axis 0.00010640 -0.00004153 -0.99999999
Axis point 169.62015610 169.59133254 0.00000000
Rotation angle (degrees) 60.04153868
Shift along axis -0.00239670
> select clear
> hide #!2 models
> show #!3 models
> hide #!12 models
> hide #!11 models
> hide #!9 models
> show #!7 models
> hide #!8 models
> hide #!7 models
> fitmap #10 inMap #3
Fit molecule 230810_Chol_HC_124.pdb (#10) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11694 atoms
average map value = 0.051, steps = 552
shifted from previous position = 74.3
rotated from previous position = 12.9 degrees
atoms outside contour = 10108, contour level = 0.088068
Position of 230810_Chol_HC_124.pdb (#10) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.94594825 -0.25200136 -0.20414999 92.33500598
0.25542808 0.96677805 -0.00983414 -2.48073845
0.19984595 -0.04284305 0.97889023 -12.63113242
Axis -0.05082584 -0.62205736 0.78132028
Axis point 86.32399546 345.26540146 0.00000000
Rotation angle (degrees) 18.94895328
Shift along axis -13.01880241
> ui mousemode right "translate selected models"
> select add #10
11694 atoms, 11940 bonds, 6 pseudobonds, 1242 residues, 2 models selected
> view matrix models
> #10,0.97523,-0.087934,-0.20295,-15.183,0.094771,0.9952,0.024201,-55.16,0.19985,-0.042836,0.97889,-88.418
> fitmap #10 inMap #3
Fit molecule 230810_Chol_HC_124.pdb (#10) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11694 atoms
average map value = 0.05624, steps = 116
shifted from previous position = 4.57
rotated from previous position = 7.91 degrees
atoms outside contour = 9455, contour level = 0.088068
Position of 230810_Chol_HC_124.pdb (#10) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.90833490 -0.31814026 -0.27150411 99.94197353
0.34655856 0.93592761 0.06274300 -41.10979240
0.23414711 -0.15108373 0.96038994 -6.16642025
Axis -0.24802789 -0.58652911 0.77101606
Axis point 175.74884044 259.27233719 0.00000000
Rotation angle (degrees) 25.53445627
Shift along axis -5.43071598
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.92053,-0.11969,-0.37188,26.917,0.28404,0.85861,0.42674,-133.43,0.26822,-0.49846,0.82438,4.3481
> view matrix models
> #10,0.85536,-0.51335,0.069546,30.326,0.50123,0.78621,-0.36144,-27.558,0.13086,0.34402,0.9298,-130.08
> view matrix models
> #10,0.88149,-0.17558,0.43836,-90.865,0.31253,0.91282,-0.26284,-33.507,-0.35399,0.36869,0.85951,-42.124
> view matrix models
> #10,0.92002,0.33799,-0.19831,-77.58,-0.3164,0.93926,0.13293,1.2522,0.23119,-0.059558,0.97108,-86.543
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.92002,0.33799,-0.19831,-75.079,-0.3164,0.93926,0.13293,-0.63729,0.23119,-0.059558,0.97108,-93.293
> fitmap #10 inMap #3
Fit molecule 230810_Chol_HC_124.pdb (#10) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11694 atoms
average map value = 0.06768, steps = 180
shifted from previous position = 11.9
rotated from previous position = 14.7 degrees
atoms outside contour = 8221, contour level = 0.088068
Position of 230810_Chol_HC_124.pdb (#10) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.95142287 0.30572237 -0.03644682 -40.14595853
-0.28841301 0.92641000 0.24203812 27.52579912
0.10776116 -0.21976886 0.96958196 24.59550090
Axis -0.60272584 -0.18821257 -0.77543381
Axis point 59.45799485 140.87270543 0.00000000
Rotation angle (degrees) 22.52575624
Shift along axis -0.05587768
> view matrix models
> #10,0.89031,0.45534,0.0042569,-113.08,-0.44243,0.86277,0.24472,2.0426,0.10776,-0.21976,0.96958,-45.752
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.91643,0.28888,-0.27697,-43.431,-0.25984,0.95585,0.1372,-25.99,0.30437,-0.053765,0.95103,-102.88
> view matrix models
> #10,0.94767,-0.31633,0.04318,-0.91621,0.3152,0.94852,0.031137,-102.73,-0.050807,-0.015898,0.99858,-58.057
> fitmap #10 inMap #3
Fit molecule 230810_Chol_HC_124.pdb (#10) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11694 atoms
average map value = 0.06734, steps = 136
shifted from previous position = 6.71
rotated from previous position = 3.76 degrees
atoms outside contour = 8164, contour level = 0.088068
Position of 230810_Chol_HC_124.pdb (#10) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.85324131 -0.52019784 0.03706069 103.13577995
0.52020273 0.85398105 0.01027082 -62.11038382
-0.03699198 0.01051558 0.99926024 4.47688143
Axis 0.00023467 0.07099746 0.99747647
Axis point 162.21327500 152.49881288 0.00000000
Rotation angle (degrees) 31.43401976
Shift along axis 0.08010680
> view matrix models
> #10,0.93917,-0.33857,-0.057643,17.177,0.34186,0.93769,0.062247,-112.2,0.032976,-0.078166,0.99639,-55.854
> view matrix models
> #10,0.99054,0.12615,0.05397,-86.888,-0.12721,0.99174,0.016684,-35.818,-0.051419,-0.023392,0.9984,-51.271
> view matrix models
> #10,0.9897,0.14125,-0.023211,-76.535,-0.14108,0.98996,0.0090007,-31.955,0.024249,-0.0056335,0.99969,-66.989
> fitmap #10 inMap #3
Fit molecule 230810_Chol_HC_124.pdb (#10) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11694 atoms
average map value = 0.1628, steps = 60
shifted from previous position = 2.19
rotated from previous position = 2.08 degrees
atoms outside contour = 2683, contour level = 0.088068
Position of 230810_Chol_HC_124.pdb (#10) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999936 0.00113833 0.00000311 -0.18418520
-0.00113833 0.99999935 -0.00013811 0.20161450
-0.00000326 0.00013810 1.00000000 -0.03026483
Axis 0.12043757 0.00277727 -0.99271702
Axis point 176.99996392 162.79492079 0.00000000
Rotation angle (degrees) 0.06569993
Shift along axis 0.00842153
> select clear
> hide #!10 models
> show #!4 models
> hide #!3 models
> show #!11 models
> ui mousemode right "translate selected models"
> select add #11
8598 atoms, 8874 bonds, 6 pseudobonds, 1014 residues, 2 models selected
> view matrix models #11,1,0,0,-58.975,0,1,0,-1.0855,0,0,1,-53.321
> view matrix models #11,1,0,0,-44.78,0,1,0,-32.218,0,0,1,-81.115
> view matrix models #11,1,0,0,-54.182,0,1,0,-36.679,0,0,1,-86.265
> view matrix models #11,1,0,0,-56.354,0,1,0,-56.134,0,0,1,-83.12
> view matrix models #11,1,0,0,-57.204,0,1,0,-64.288,0,0,1,-72.896
> view matrix models #11,1,0,0,-55.543,0,1,0,-52.489,0,0,1,-69.635
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.99501,-0.0018953,-0.099782,-38.446,-0.023336,0.96768,-0.25108,-3.1071,0.097033,0.25216,0.96281,-121.65
> view matrix models
> #11,0.84961,-0.51755,-0.10154,71.57,0.48347,0.84119,-0.24221,-67.655,0.21077,0.15669,0.9649,-125.02
> view matrix models
> #11,0.91893,-0.3931,-0.032101,28.302,0.3828,0.86931,0.31266,-144.33,-0.095001,-0.2996,0.94932,3.9721
> view matrix models
> #11,0.94133,-0.31312,-0.12592,26.308,0.33656,0.84329,0.41903,-149.34,-0.025017,-0.43682,0.8992,23.147
> view matrix models
> #11,0.90948,-0.41458,-0.031209,33.293,0.41457,0.89871,0.14303,-127.36,-0.031247,-0.14302,0.98923,-38.984
> fitmap #11 inMap #3
Fit molecule 230821_CBX_HC_142.pdb (#11) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 8598 atoms
average map value = 0.164, steps = 100
shifted from previous position = 8.61
rotated from previous position = 8.64 degrees
atoms outside contour = 1863, contour level = 0.088068
Position of 230821_CBX_HC_142.pdb (#11) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.80739531 -0.59001086 0.00004459 129.90435110
0.59001086 0.80739531 0.00007172 -65.98298264
-0.00007832 -0.00003160 1.00000000 1.35188729
Axis -0.00008755 0.00010415 0.99999999
Axis point 166.01612466 165.97827380 0.00000000
Rotation angle (degrees) 36.15777893
Shift along axis 1.33364127
> select clear
> hide #!4 models
> show #!5 models
> show #!8 models
> hide #!11 models
> ui mousemode right "rotate selected models"
> select add #8
8962 atoms, 9226 bonds, 6 pseudobonds, 1098 residues, 2 models selected
> view matrix models
> #8,0.99194,0.033207,0.12231,-21.529,-0.034546,0.99936,0.0088462,4.0474,-0.12194,-0.013,0.99245,21.533
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.99194,0.033207,0.12231,-63.712,-0.034546,0.99936,0.0088462,-14.006,-0.12194,-0.013,0.99245,-29.949
> fitmap #8 inMap #5
Fit molecule 230309_P38_J250_350_M257_C2.pdb (#8) to map
M257_POPE_Sym_C6_P38_J358.mrc (#5) using 8962 atoms
average map value = 0.1989, steps = 268
shifted from previous position = 25.4
rotated from previous position = 20 degrees
atoms outside contour = 3899, contour level = 0.15563
Position of 230309_P38_J250_350_M257_C2.pdb (#8) relative to
M257_POPE_Sym_C6_P38_J358.mrc (#5) coordinates:
Matrix rotation and translation
0.68270572 -0.73069340 -0.00023476 158.76444825
-0.73069336 -0.68270576 0.00022163 365.53424739
-0.00032222 0.00002023 -0.99999995 298.74638896
Axis -0.91725455 0.39830148 0.00015338
Axis point 0.00000000 217.24638179 149.37553079
Rotation angle (degrees) 179.99370984
Shift along axis 0.01123796
> select clear
> hide #!8 models
> hide #!5 models
> show #!4 models
> show #!11 models
> fitmap #11 inMap #4
Fit molecule 230821_CBX_HC_142.pdb (#11) to map
N55H_CBX_P52_J650_003_volume_map.mrc (#4) using 8598 atoms
average map value = 0.1165, steps = 48
shifted from previous position = 0.153
rotated from previous position = 0.348 degrees
atoms outside contour = 2582, contour level = 0.075915
Position of 230821_CBX_HC_142.pdb (#11) relative to
N55H_CBX_P52_J650_003_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999788 0.00205104 0.00016791 -0.35684958
-0.00205103 0.99999790 -0.00004972 0.34212674
-0.00016801 0.00004937 0.99999998 0.05188220
Axis 0.02406943 0.08159259 -0.99637509
Axis point 167.91639559 173.77811990 0.00000000
Rotation angle (degrees) 0.11794337
Shift along axis -0.03236829
> fitmap #11 inMap #4
Fit molecule 230821_CBX_HC_142.pdb (#11) to map
N55H_CBX_P52_J650_003_volume_map.mrc (#4) using 8598 atoms
average map value = 0.1165, steps = 40
shifted from previous position = 0.00521
rotated from previous position = 0.0104 degrees
atoms outside contour = 2585, contour level = 0.075915
Position of 230821_CBX_HC_142.pdb (#11) relative to
N55H_CBX_P52_J650_003_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999757 0.00220286 0.00009128 -0.37410629
-0.00220286 0.99999757 0.00001488 0.36040357
-0.00009124 -0.00001508 1.00000000 0.04988797
Axis -0.00679519 0.04139183 -0.99911988
Axis point 164.02793065 170.10819249 0.00000000
Rotation angle (degrees) 0.12632606
Shift along axis -0.03238417
> hide #!4 models
> show #!3 models
> hide #!11 models
> show #!10 models
> fitmap #10 inMap #3
Fit molecule 230810_Chol_HC_124.pdb (#10) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11694 atoms
average map value = 0.1628, steps = 24
shifted from previous position = 0.00349
rotated from previous position = 0.00233 degrees
atoms outside contour = 2686, contour level = 0.088068
Position of 230810_Chol_HC_124.pdb (#10) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999937 0.00112851 -0.00001686 -0.17888625
-0.00112851 0.99999935 -0.00017209 0.20207147
0.00001667 0.00017211 0.99999999 -0.03872896
Axis 0.15074302 -0.01468460 -0.98846391
Axis point 179.07623412 159.73160337 0.00000000
Rotation angle (degrees) 0.06541362
Shift along axis 0.00834899
> fitmap #10 inMap #3
Fit molecule 230810_Chol_HC_124.pdb (#10) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11694 atoms
average map value = 0.1628, steps = 28
shifted from previous position = 0.0238
rotated from previous position = 0.0275 degrees
atoms outside contour = 2684, contour level = 0.088068
Position of 230810_Chol_HC_124.pdb (#10) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999935 0.00113637 -0.00016220 -0.16362150
-0.00113632 0.99999932 0.00028551 0.15178640
0.00016253 -0.00028533 0.99999995 0.01115927
Axis -0.24130270 -0.13726816 -0.96069270
Axis point 134.44857144 142.38133814 0.00000000
Rotation angle (degrees) 0.06777164
Shift along axis 0.00792624
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!10 models
> show #!9 models
> ui mousemode right "rotate selected models"
> select add #9
9648 atoms, 9924 bonds, 6 pseudobonds, 1188 residues, 2 models selected
> view matrix models
> #9,0.93244,0.31782,0.17192,-63.886,0.21879,-0.87525,0.43137,185.76,0.28757,-0.36461,-0.88565,296.58
> view matrix models
> #9,0.88887,-0.091739,-0.44888,98.548,0.14812,-0.86959,0.47104,189.61,-0.43355,-0.48518,-0.75936,404.98
> view matrix models
> #9,0.67196,-0.7362,0.080461,149.05,-0.74058,-0.66789,0.073837,353.66,-0.0006194,-0.1092,-0.99402,317.91
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.67196,-0.7362,0.080461,109.45,-0.74058,-0.66789,0.073837,349.92,-0.0006194,-0.1092,-0.99402,263.59
> view matrix models
> #9,0.67196,-0.7362,0.080461,102.76,-0.74058,-0.66789,0.073837,314.68,-0.0006194,-0.1092,-0.99402,262.04
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.91409,-0.40046,0.063763,17.753,-0.40075,-0.91615,-0.0088264,313.31,0.061951,-0.017485,-0.99793,239.26
> view matrix models
> #9,0.91332,-0.40656,-0.023632,31.998,-0.40516,-0.90125,-0.15359,333.59,0.041144,0.14985,-0.98785,215.54
> view matrix models
> #9,0.87915,-0.47654,-0.0017546,44.467,-0.42504,-0.78247,-0.45505,364.16,0.21548,0.40081,-0.89046,136.41
> view matrix models
> #9,0.75746,-0.64554,-0.097602,102.98,-0.62635,-0.67632,-0.38766,368.38,0.18424,0.35477,-0.91662,152.07
> view matrix models
> #9,0.78083,-0.6242,0.02592,77.546,-0.61291,-0.77342,-0.16176,346.92,0.12102,0.11042,-0.98649,209.21
> fitmap #9 inMap #6
Fit molecule 230419_P38_J358_M257_C6.pdb (#9) to map
M257_POPE_Asym_C2_P38_J250.mrc (#6) using 9648 atoms
average map value = 0.1342, steps = 120
shifted from previous position = 8.76
rotated from previous position = 3.53 degrees
atoms outside contour = 7324, contour level = 0.19869
Position of 230419_P38_J358_M257_C6.pdb (#9) relative to
M257_POPE_Asym_C2_P38_J250.mrc (#6) coordinates:
Matrix rotation and translation
-0.25899727 0.96455166 0.05060050 33.23953776
0.95379827 0.24714741 0.17084183 -62.05069974
0.15227999 0.09251025 -0.98399827 261.49338132
Axis -0.60815068 -0.78941918 -0.08348712
Axis point 35.17041874 0.00000000 134.79263482
Rotation angle (degrees) 176.30751284
Shift along axis 6.93803496
> view matrix models
> #9,0.31505,-0.92613,0.20745,168.94,-0.90846,-0.35754,-0.2165,339.85,0.27468,-0.12025,-0.95399,223.8
> view matrix models
> #9,0.28314,-0.95902,0.010277,208.55,-0.95025,-0.28197,-0.13237,322.02,0.12984,0.027714,-0.99115,228.94
> view matrix models
> #9,0.29318,-0.95587,0.019039,205.23,-0.9498,-0.29348,-0.10842,320.07,0.10923,0.013705,-0.99392,234.6
> fitmap #9 inMap #6
Fit molecule 230419_P38_J358_M257_C6.pdb (#9) to map
M257_POPE_Asym_C2_P38_J250.mrc (#6) using 9648 atoms
average map value = 0.2359, steps = 116
shifted from previous position = 7.05
rotated from previous position = 8.26 degrees
atoms outside contour = 4832, contour level = 0.19869
Position of 230419_P38_J358_M257_C6.pdb (#9) relative to
M257_POPE_Asym_C2_P38_J250.mrc (#6) coordinates:
Matrix rotation and translation
0.29219050 0.95635994 0.00051878 -37.74090997
0.95636003 -0.29219026 -0.00052326 50.95499440
-0.00034884 0.00064904 -0.99999969 298.64796823
Axis 0.80380283 0.59489579 0.00005773
Axis point 0.00000000 39.37581696 149.33689714
Rotation angle (degrees) 179.95821849
Shift along axis -0.00609690
> fitmap #9 inMap #6
Fit molecule 230419_P38_J358_M257_C6.pdb (#9) to map
M257_POPE_Asym_C2_P38_J250.mrc (#6) using 9648 atoms
average map value = 0.2359, steps = 36
shifted from previous position = 0.00681
rotated from previous position = 0.0115 degrees
atoms outside contour = 4832, contour level = 0.19869
Position of 230419_P38_J358_M257_C6.pdb (#9) relative to
M257_POPE_Asym_C2_P38_J250.mrc (#6) coordinates:
Matrix rotation and translation
0.29218992 0.95636020 0.00033708 -37.70657169
0.95636021 -0.29218979 -0.00043798 50.94394241
-0.00032038 0.00045035 -0.99999981 298.67380088
Axis 0.80380342 0.59489500 0.00001163
Axis point 0.00000000 39.37395886 149.34592861
Rotation angle (degrees) 179.96833943
Shift along axis 0.00109977
> select clear
> hide #!9 models
> hide #!6 models
> show #!7 models
> show #!1 models
> select clear
> select
61870 atoms, 63466 bonds, 36 pseudobonds, 7038 residues, 24 models selected
> ui tool show "Selection Inspector"
> setattr =sel p display false
Assigning display attribute to 36 items
> select clear
> hide #!1 models
> show #!8 models
> show #!9 models
> show #!10 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> show #!12 models
> view orient
> turn x 90
> view name 1
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/230903_All_Align.pdb"
> view 1
> rename #1 id #13
> rename #5 id #14
> rename #5 id #15
> rename #6 id #15
> rename #3 id #16
> rename #4 id #17
> rename #2 id #18
> hide #!12 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> show #!12 models
> hide #!11 models
> show #!11 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> show #!8 models
> color #8 #aaff7fff
> color #8 #aaff00ff
> color #9 #ffaa00ff
> show #!9 models
> rename #7 id #1
> rename #9 id #2
> rename #8 id 3
> rename #10 id E 4
Invalid "id" argument: Expected an integer
> rename #10 id #4
> rename #11 id #5
> rename #12 id #6
> select clear
> hide #!2 models
> select #3/a,d
3162 atoms, 3254 bonds, 2 pseudobonds, 390 residues, 2 models selected
> color sel dark green
> rename #3/b,e
No name or id option specified for renaming
> rename #3/b,e
No name or id option specified for renaming
> select #3/b,e
2884 atoms, 2970 bonds, 2 pseudobonds, 352 residues, 2 models selected
> color sel lime
> select clear
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select clear
> view 1
> hide #!3 models
> show #!2 models
> view 1
> select #1,2,3,4,5,6/b,c,e,f
41072 atoms, 42130 bonds, 24 pseudobonds, 4668 residues, 12 models selected
> hide sel ribbons
> select clear
> ui mousemode right "rotate selected models"
> select add #2
9648 atoms, 9924 bonds, 6 pseudobonds, 1188 residues, 2 models selected
> view matrix models
> #2,0.67349,-0.65832,0.33619,55.417,-0.69421,-0.71954,-0.018286,325.44,0.25394,-0.22107,-0.94162,238.03
> view matrix models
> #2,0.89421,-0.43077,-0.12179,56.671,-0.44491,-0.88528,-0.13538,330.45,-0.049497,0.17524,-0.98328,230.27
> view matrix models
> #2,0.95996,-0.26839,0.080245,-8.4255,-0.25031,-0.95045,-0.18438,318.23,0.12575,0.15691,-0.97957,205.92
> view matrix models
> #2,0.97289,-0.22018,0.070787,-16.261,-0.2196,-0.97546,-0.01592,291.91,0.072555,-5.6005e-05,-0.99736,240.46
> view matrix models
> #2,0.98174,-0.18755,0.031669,-16.637,-0.18758,-0.98225,-0.0022455,286.02,0.031528,-0.0037359,-0.9995,247.56
> fitmap #2 inMap #14
Fit molecule 230419_P38_J358_M257_C6.pdb (#2) to map
M257_POPE_Sym_C6_P38_J358.mrc (#14) using 9648 atoms
average map value = 0.2429, steps = 56
shifted from previous position = 0.309
rotated from previous position = 3.72 degrees
atoms outside contour = 2597, contour level = 0.15563
Position of 230419_P38_J358_M257_C6.pdb (#2) relative to
M257_POPE_Sym_C6_P38_J358.mrc (#14) coordinates:
Matrix rotation and translation
0.50018653 0.86591768 0.00014979 -55.48528275
-0.86591769 0.50018650 0.00022098 206.83619813
0.00011642 -0.00024024 0.99999998 0.04043401
Axis -0.00026631 0.00001927 -0.99999996
Axis point 151.42731421 151.48172201 0.00000000
Rotation angle (degrees) 59.98766087
Shift along axis -0.02167230
> fitmap #2 inMap #14
Fit molecule 230419_P38_J358_M257_C6.pdb (#2) to map
M257_POPE_Sym_C6_P38_J358.mrc (#14) using 9648 atoms
average map value = 0.2429, steps = 40
shifted from previous position = 0.0121
rotated from previous position = 0.00816 degrees
atoms outside contour = 2597, contour level = 0.15563
Position of 230419_P38_J358_M257_C6.pdb (#2) relative to
M257_POPE_Sym_C6_P38_J358.mrc (#14) coordinates:
Matrix rotation and translation
0.50020278 0.86590831 0.00000897 -55.45295793
-0.86590829 0.50020276 0.00021099 206.83113615
0.00017821 -0.00011331 0.99999999 0.01182515
Axis -0.00018726 -0.00009772 -0.99999998
Axis point 151.44297786 151.45222884 0.00000000
Rotation angle (degrees) 59.98658468
Shift along axis -0.02165298
> hide #!2 models
> select subtract #2
Nothing selected
> show #!3 models
> select add #3
8962 atoms, 9226 bonds, 6 pseudobonds, 1098 residues, 2 models selected
> view matrix models
> #3,0.93752,0.34654,0.031208,-90.518,-0.34793,0.93441,0.076322,8.5761,-0.0027128,-0.082411,0.99659,-33.144
> fitmap #3 inMap #15
Fit molecule 230309_P38_J250_350_M257_C2.pdb (#3) to map
M257_POPE_Asym_C2_P38_J250.mrc (#15) using 8962 atoms
average map value = 0.2026, steps = 156
shifted from previous position = 2.46
rotated from previous position = 7.63 degrees
atoms outside contour = 5186, contour level = 0.19869
Position of 230309_P38_J250_350_M257_C2.pdb (#3) relative to
M257_POPE_Asym_C2_P38_J250.mrc (#15) coordinates:
Matrix rotation and translation
-0.49694846 -0.86027216 -0.11390306 371.99233453
0.85758834 -0.50692067 0.08702625 87.23052198
-0.13260609 -0.05443439 0.98967289 31.47420956
Axis -0.08206437 0.01085003 0.99656797
Axis point 162.26877173 150.22088392 0.00000000
Rotation angle (degrees) 120.47073094
Shift along axis 1.78532625
> view matrix models
> #3,0.91212,0.39795,0.098334,-101.94,-0.40957,0.89467,0.17837,8.8886,-0.016996,-0.20297,0.97904,-8.8336
> view matrix models
> #3,0.90962,0.41168,-0.055805,-81.153,-0.4015,0.90562,0.13656,12.108,0.10676,-0.10181,0.98906,-44.363
> view matrix models
> #3,0.99757,0.043137,-0.054758,-38.804,-0.039696,0.99726,0.062447,-45.759,0.057302,-0.060121,0.99654,-44.279
> view matrix models
> #3,0.99166,0.039979,0.12251,-63.298,-0.053675,0.99241,0.11062,-49.937,-0.11716,-0.11627,0.98628,-7.8515
> view matrix models
> #3,0.85384,0.50173,0.13868,-114.72,-0.48982,0.86458,-0.11219,68,-0.17619,0.027863,0.98396,-20.403
> view matrix models
> #3,0.88175,0.46716,-0.065442,-83.929,-0.47121,0.86577,-0.16853,73.221,-0.022072,0.17943,0.98352,-66.642
> view matrix models
> #3,0.97412,0.22074,-0.048623,-63.049,-0.22371,0.97229,-0.067809,4.9008,0.032308,0.076931,0.99651,-61.248
> view matrix models
> #3,0.97215,0.23144,0.036784,-76.835,-0.22979,0.97224,-0.044121,2.3742,-0.045974,0.03444,0.99835,-43.222
> fitmap #3 inMap #15
Fit molecule 230309_P38_J250_350_M257_C2.pdb (#3) to map
M257_POPE_Asym_C2_P38_J250.mrc (#15) using 8962 atoms
average map value = 0.2026, steps = 164
shifted from previous position = 0.254
rotated from previous position = 9.81 degrees
atoms outside contour = 5186, contour level = 0.19869
Position of 230309_P38_J250_350_M257_C2.pdb (#3) relative to
M257_POPE_Asym_C2_P38_J250.mrc (#15) coordinates:
Matrix rotation and translation
-0.49695452 -0.86026790 -0.11390884 371.99254190
0.85759158 -0.50692450 0.08697205 87.23712688
-0.13256246 -0.05446612 0.98967699 31.46725035
Axis -0.08205150 0.01082139 0.99656934
Axis point 162.26659190 150.22405949 0.00000000
Rotation angle (degrees) 120.47092339
Shift along axis 1.78077838
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.92789,0.36427,0.079507,-96.484,-0.37239,0.89488,0.24601,-6.6418,0.018463,-0.25787,0.966,-3.9903
> view matrix models
> #3,0.85823,0.49328,0.14185,-114.57,-0.50624,0.85909,0.075415,43.945,-0.084662,-0.13653,0.98701,-9.8149
> view matrix models
> #3,0.86799,0.49657,-0.00053615,-95.772,-0.49622,0.86741,0.037011,46.771,0.018844,-0.031859,0.99931,-43.143
> view matrix models
> #3,0.96507,0.25419,0.063415,-83.094,-0.2455,0.96197,-0.1198,17.354,-0.091454,0.10004,0.99077,-45.169
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.96507,0.25419,0.063415,-83.736,-0.2455,0.96197,-0.1198,16.996,-0.091454,0.10004,0.99077,-47.732
> fitmap #3 inMap #15
Fit molecule 230309_P38_J250_350_M257_C2.pdb (#3) to map
M257_POPE_Asym_C2_P38_J250.mrc (#15) using 8962 atoms
average map value = 0.2026, steps = 192
shifted from previous position = 2.61
rotated from previous position = 10.6 degrees
atoms outside contour = 5191, contour level = 0.19869
Position of 230309_P38_J250_350_M257_C2.pdb (#3) relative to
M257_POPE_Asym_C2_P38_J250.mrc (#15) coordinates:
Matrix rotation and translation
-0.49691445 -0.86029323 -0.11389232 371.98822184
0.85761606 -0.50688253 0.08697528 87.22497694
-0.13255428 -0.05445662 0.98967861 31.46783226
Axis -0.08204552 0.01082592 0.99656978
Axis point 162.26646217 150.22271298 0.00000000
Rotation angle (degrees) 120.46814280
Shift along axis 1.78421546
> view matrix models
> #3,0.92835,0.34305,0.14314,-108.84,-0.3473,0.93774,0.0050039,16.68,-0.13251,-0.054356,0.98969,-16.12
> select #3
8962 atoms, 9226 bonds, 6 pseudobonds, 1098 residues, 2 models selected
> show sel ribbons
> show #!15 models
> view matrix models
> #3,0.92835,0.34305,0.14314,-106.94,-0.3473,0.93774,0.0050039,15.879,-0.13251,-0.054356,0.98969,-16.248
> view matrix models
> #3,0.92835,0.34305,0.14314,-105.43,-0.3473,0.93774,0.0050039,16.247,-0.13251,-0.054356,0.98969,-15.879
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.88356,0.45031,-0.12864,-75.552,-0.45251,0.89166,0.013266,37.968,0.12068,0.046491,0.9916,-69.781
> view matrix models
> #3,0.96657,0.25606,0.013258,-79.24,-0.25592,0.96033,0.11073,-16.318,0.015621,-0.11042,0.99376,-30.413
> view matrix models
> #3,0.94972,0.28287,0.13424,-98.259,-0.28755,0.95762,0.016436,2.531,-0.1239,-0.05421,0.99081,-17.368
> view matrix models
> #3,0.89392,0.44316,0.067281,-104.39,-0.44594,0.89444,0.033515,33.621,-0.045326,-0.059963,0.99717,-29.318
> fitmap #3 inMap #15
Fit molecule 230309_P38_J250_350_M257_C2.pdb (#3) to map
M257_POPE_Asym_C2_P38_J250.mrc (#15) using 8962 atoms
average map value = 0.2026, steps = 156
shifted from previous position = 3.43
rotated from previous position = 7.82 degrees
atoms outside contour = 5182, contour level = 0.19869
Position of 230309_P38_J250_350_M257_C2.pdb (#3) relative to
M257_POPE_Asym_C2_P38_J250.mrc (#15) coordinates:
Matrix rotation and translation
-0.49682474 -0.86030510 -0.11419368 372.01524848
0.85761224 -0.50684689 0.08722027 87.18910567
-0.13291477 -0.05460072 0.98962232 31.55887157
Axis -0.08226929 0.01085996 0.99655096
Axis point 162.29598887 150.21876168 0.00000000
Rotation angle (degrees) 120.46584743
Shift along axis 1.79146272
> hide #!1 models
> view matrix models
> #3,0.47472,0.86673,-0.15304,-70.362,-0.88,0.46439,-0.099659,185.77,-0.015306,0.18198,0.98318,-68.005
> view matrix models
> #3,-0.36883,0.88854,-0.27288,71.453,-0.83749,-0.44503,-0.3171,348.55,-0.4032,0.11158,0.90828,12.253
> view matrix models
> #3,-0.49925,0.85487,-0.14126,77.256,-0.85109,-0.5144,-0.10508,330.43,-0.1625,0.067763,0.98438,-28.582
> view matrix models
> #3,-0.51684,0.85484,-0.046079,66.149,-0.8481,-0.51861,-0.10849,331.11,-0.11664,-0.016992,0.99303,-23.942
> view matrix models
> #3,-0.59603,0.79548,0.10938,64.634,-0.79182,-0.60489,0.08444,307.73,0.13334,-0.036285,0.99041,-58.505
> view matrix models
> #3,-0.81519,0.57868,-0.024283,150.02,-0.57918,-0.81473,0.027862,315.49,-0.0036606,0.036777,0.99932,-50.11
> fitmap #3 inMap #15
Fit molecule 230309_P38_J250_350_M257_C2.pdb (#3) to map
M257_POPE_Asym_C2_P38_J250.mrc (#15) using 8962 atoms
average map value = 0.3294, steps = 84
shifted from previous position = 2.73
rotated from previous position = 4.49 degrees
atoms outside contour = 2379, contour level = 0.19869
Position of 230309_P38_J250_350_M257_C2.pdb (#3) relative to
M257_POPE_Asym_C2_P38_J250.mrc (#15) coordinates:
Matrix rotation and translation
0.99999946 0.00094995 0.00021438 -0.16461288
-0.00094996 0.99999950 -0.00002203 0.14619147
-0.00021439 0.00002183 0.99999993 0.02742264
Axis 0.02251545 0.22008632 -0.97522052
Axis point 153.41150945 173.40219209 0.00000000
Rotation angle (degrees) 0.05581132
Shift along axis 0.00172529
> select clear
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> color #15 #00aa7f80 models
> color #15 #aaff7f80 models
> select clear
> hide #!15 models
> show #!4 models
> hide #!3 models
> show #!1 models
> show #!2 models
> show #!5 models
> show #!6 models
> hide #!5 models
> hide #!4 models
> hide #!6 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> view 1
> undo
> select clear
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> view orient
> turn x90
Expected an axis vector or a keyword
> turn x 90
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/230903_All_Align.pdb"
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #!4 models
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select #1,2,3,4,5,6
61870 atoms, 63466 bonds, 36 pseudobonds, 7038 residues, 12 models selected
> select #1,2,3,4,5,6/b,c,e,f
41072 atoms, 42130 bonds, 24 pseudobonds, 4668 residues, 12 models selected
> hide sel ribbons
> select clear
> hide #!1 models
> show #!6 models
> select #1-6:52-55
1332 atoms, 1350 bonds, 144 residues, 6 models selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 0
Assigning ss_type attribute to 144 items
> select clear
> view 1
> turn y 10
[Repeated 1 time(s)]
> view name 1
> select
61870 atoms, 63466 bonds, 36 pseudobonds, 7038 residues, 24 models selected
> show sel ribbons
> select clear
> view orient
> turn x 90
> select #1-6/b,c,e,f
41072 atoms, 42130 bonds, 24 pseudobonds, 4668 residues, 12 models selected
> hide sel ribbons
> view name 1
> select clear
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> show #!6 models
> hide #!6 models
> show #!6 models
> select #1-6:200
288 atoms, 252 bonds, 36 residues, 6 models selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 0
Assigning ss_type attribute to 36 items
> select clear
> show #!5 models
> select clear
> show #!1 models
> view 1
> hide #!4 models
> hide #!5 models
> show #!4 models
> view 1
> select clear
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/230903_All_Align.cxs"
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #6.1 models
> hide #!4 models
> hide #!1 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!6 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> show #!1 models
> show #!2 models
> ui mousemode right "rotate selected models"
[Repeated 1 time(s)]
> select add #2
9648 atoms, 9924 bonds, 6 pseudobonds, 1188 residues, 2 models selected
> view matrix models
> #2,0.67025,-0.66278,0.33391,56.923,-0.67525,-0.7313,-0.096148,336.11,0.30791,-0.16103,-0.93769,220.15
> view matrix models
> #2,0.88861,-0.45242,-0.075396,53.781,-0.45434,-0.89077,-0.0096914,313.72,-0.062777,0.042868,-0.99711,254.43
> view matrix models
> #2,0.93123,-0.36439,0.0045883,21.896,-0.36363,-0.92997,-0.054075,312.61,0.023972,0.048688,-0.99853,240.61
> view matrix models
> #2,0.95181,-0.30583,0.022694,7.1667,-0.30646,-0.94578,0.10766,281.91,-0.011462,-0.10942,-0.99393,269.25
> fitmap #2 inMap #14
Fit molecule 230419_P38_J358_M257_C6.pdb (#2) to map
M257_POPE_Sym_C6_P38_J358.mrc (#14) using 9648 atoms
average map value = 0.2429, steps = 104
shifted from previous position = 0.329
rotated from previous position = 12.1 degrees
atoms outside contour = 2601, contour level = 0.15563
Position of 230419_P38_J358_M257_C6.pdb (#2) relative to
M257_POPE_Sym_C6_P38_J358.mrc (#14) coordinates:
Matrix rotation and translation
0.50032441 0.86583802 0.00017424 -55.48359217
-0.86583803 0.50032438 0.00020311 206.79352059
0.00008868 -0.00025248 0.99999998 0.04677101
Axis -0.00026309 0.00004941 -0.99999996
Axis point 151.42413692 151.46775929 0.00000000
Rotation angle (degrees) 59.97853710
Shift along axis -0.02195655
> fitmap #2 inMap #14
Fit molecule 230419_P38_J358_M257_C6.pdb (#2) to map
M257_POPE_Sym_C6_P38_J358.mrc (#14) using 9648 atoms
average map value = 0.2429, steps = 40
shifted from previous position = 0.0216
rotated from previous position = 0.0113 degrees
atoms outside contour = 2597, contour level = 0.15563
Position of 230419_P38_J358_M257_C6.pdb (#2) relative to
M257_POPE_Sym_C6_P38_J358.mrc (#14) coordinates:
Matrix rotation and translation
0.50016981 0.86592733 0.00022058 -55.49263770
-0.86592735 0.50016979 0.00013201 206.85928912
0.00000399 -0.00025704 0.99999998 0.05876135
Axis -0.00022464 0.00012507 -0.99999997
Axis point 151.43964570 151.49856948 0.00000000
Rotation angle (degrees) 59.98876661
Shift along axis -0.02042415
> select clear
> show #!14 models
> hide #!4 models
> hide #!2 models
> hide #!14 models
> show #!13 models
> hide #!13 models
> show #!3 models
> show #!15 models
> hide #!1 models
> fitmap #3 inMap #15
Fit molecule 230309_P38_J250_350_M257_C2.pdb (#3) to map
M257_POPE_Asym_C2_P38_J250.mrc (#15) using 8962 atoms
average map value = 0.2026, steps = 256
shifted from previous position = 2.39
rotated from previous position = 8.22 degrees
atoms outside contour = 5190, contour level = 0.19869
Position of 230309_P38_J250_350_M257_C2.pdb (#3) relative to
M257_POPE_Asym_C2_P38_J250.mrc (#15) coordinates:
Matrix rotation and translation
-0.49693105 -0.86029952 0.11377235 342.11910563
0.85762765 -0.50687817 -0.08688631 109.45436385
0.13241697 0.05439780 0.98970022 -25.15337376
Axis 0.08195952 -0.01081583 0.99657697
Axis point 140.68126701 152.71695907 0.00000000
Rotation angle (degrees) 120.46783129
Shift along axis 1.78880617
> select add #3
8962 atoms, 9226 bonds, 6 pseudobonds, 1098 residues, 2 models selected
> view matrix models
> #3,0.9695,0.24431,0.019477,-80.463,-0.24507,0.96731,0.065271,-10.235,-0.0028941,-0.068054,0.99768,-34.122
> view matrix models
> #3,0.94626,0.29074,0.14166,-101.82,-0.30542,0.94739,0.09577,-2.532,-0.10637,-0.13389,0.98527,-6.6646
> view matrix models
> #3,0.82519,0.56434,0.024021,-107.74,-0.56475,0.82346,0.054518,61.545,0.010987,-0.058554,0.99822,-37.743
> view matrix models
> #3,0.95204,0.20343,0.22858,-102.17,-0.22066,0.97395,0.05228,-13.041,-0.21199,-0.10021,0.97212,6.1526
> view matrix models
> #3,0.99574,0.091153,-0.014144,-56.326,-0.091255,0.99581,-0.0067013,-27.337,0.013474,0.0079634,0.99988,-48.437
> view matrix models
> #3,0.98826,0.14735,-0.040427,-59.866,-0.14722,0.98908,0.0061686,-19.722,0.040895,-0.0001446,0.99916,-51.258
> fitmap #3 inMap #15
Fit molecule 230309_P38_J250_350_M257_C2.pdb (#3) to map
M257_POPE_Asym_C2_P38_J250.mrc (#15) using 8962 atoms
average map value = 0.2026, steps = 224
shifted from previous position = 0.243
rotated from previous position = 13.3 degrees
atoms outside contour = 5190, contour level = 0.19869
Position of 230309_P38_J250_350_M257_C2.pdb (#3) relative to
M257_POPE_Asym_C2_P38_J250.mrc (#15) coordinates:
Matrix rotation and translation
-0.49696593 -0.86028834 0.11370447 342.13112617
0.85761986 -0.50690085 -0.08683084 109.45193221
0.13233645 0.05436324 0.98971289 -25.13894262
Axis 0.08190855 -0.01080866 0.99658124
Axis point 140.68782596 152.71603446 0.00000000
Rotation angle (degrees) 120.46932361
Shift along axis 1.78743698
> view matrix models
> #3,0.21378,0.92847,0.3037,-111.14,-0.96537,0.24839,-0.079832,228.96,-0.14956,-0.27611,0.94942,26.656
> view matrix models
> #3,0.068524,0.99501,-0.072573,-44.251,-0.99756,0.069309,0.0083453,248.08,0.013334,0.071825,0.99733,-57.718
> fitmap #3 inMap #15
Fit molecule 230309_P38_J250_350_M257_C2.pdb (#3) to map
M257_POPE_Asym_C2_P38_J250.mrc (#15) using 8962 atoms
average map value = 0.1921, steps = 80
shifted from previous position = 2.36
rotated from previous position = 6.79 degrees
atoms outside contour = 5405, contour level = 0.19869
Position of 230309_P38_J250_350_M257_C2.pdb (#3) relative to
M257_POPE_Asym_C2_P38_J250.mrc (#15) coordinates:
Matrix rotation and translation
0.50220100 -0.86474117 -0.00409126 206.89559466
0.86473940 0.50221309 -0.00276939 -55.21962549
0.00444949 -0.00214709 0.99998775 0.38089494
Axis 0.00035981 -0.00493828 0.99998774
Axis point 151.40754348 152.09730652 0.00000000
Rotation angle (degrees) 59.85427878
Shift along axis 0.72802340
> select #3
8962 atoms, 9226 bonds, 6 pseudobonds, 1098 residues, 2 models selected
> show sel ribbons
> view matrix models
> #3,0.17938,0.97739,0.11194,-82.85,-0.98169,0.18525,-0.044382,235.7,-0.064115,-0.10193,0.99272,-19.914
> view matrix models
> #3,0.73864,-0.65378,-0.16427,119.53,0.62957,0.75615,-0.17853,-75.399,0.24093,0.028451,0.97013,-82.593
> view matrix models
> #3,0.75232,-0.6586,-0.016243,96.741,0.6586,0.75247,-0.0056854,-104.28,0.015967,-0.0064203,0.99985,-47.543
> fitmap #3 inMap #15
Fit molecule 230309_P38_J250_350_M257_C2.pdb (#3) to map
M257_POPE_Asym_C2_P38_J250.mrc (#15) using 8962 atoms
average map value = 0.3294, steps = 56
shifted from previous position = 0.738
rotated from previous position = 2.1 degrees
atoms outside contour = 2379, contour level = 0.19869
Position of 230309_P38_J250_350_M257_C2.pdb (#3) relative to
M257_POPE_Asym_C2_P38_J250.mrc (#15) coordinates:
Matrix rotation and translation
-0.99999944 -0.00099918 0.00001826 303.09055990
0.00099920 -0.99999945 0.00005887 302.78483583
0.00001819 0.00005888 0.99999995 -0.01352554
Axis 0.00000965 0.00003403 1.00000000
Axis point 151.46964488 151.46812966 0.00000000
Rotation angle (degrees) 179.94275045
Shift along axis -0.00029615
> fitmap #3 inMap #15
Fit molecule 230309_P38_J250_350_M257_C2.pdb (#3) to map
M257_POPE_Asym_C2_P38_J250.mrc (#15) using 8962 atoms
average map value = 0.3294, steps = 36
shifted from previous position = 0.00821
rotated from previous position = 0.00955 degrees
atoms outside contour = 2376, contour level = 0.19869
Position of 230309_P38_J250_350_M257_C2.pdb (#3) relative to
M257_POPE_Asym_C2_P38_J250.mrc (#15) coordinates:
Matrix rotation and translation
-0.99999949 -0.00094463 0.00008854 303.07370935
0.00094464 -0.99999950 -0.00008200 302.80529257
0.00008861 -0.00008191 0.99999995 -0.00275835
Axis 0.00004486 -0.00003612 1.00000000
Axis point 151.46534488 151.47421948 0.00000000
Rotation angle (degrees) 179.94587660
Shift along axis -0.00009990
> fitmap #3 inMap #15
Fit molecule 230309_P38_J250_350_M257_C2.pdb (#3) to map
M257_POPE_Asym_C2_P38_J250.mrc (#15) using 8962 atoms
average map value = 0.3294, steps = 36
shifted from previous position = 0.00395
rotated from previous position = 0.00561 degrees
atoms outside contour = 2378, contour level = 0.19869
Position of 230309_P38_J250_350_M257_C2.pdb (#3) relative to
M257_POPE_Asym_C2_P38_J250.mrc (#15) coordinates:
Matrix rotation and translation
-0.99999949 -0.00094863 0.00003438 303.08485255
0.00094865 -0.99999950 -0.00000051 302.79580550
0.00003437 -0.00000047 0.99999996 -0.00689447
Axis 0.00001776 0.00000459 1.00000000
Axis point 151.47061518 151.46978247 0.00000000
Rotation angle (degrees) 179.94564686
Shift along axis -0.00012149
> select clear
> volume sdLevel 8
> select clear
> show #!4 models
> hide #!3 models
> show #!16 models
> hide #!15 models
> fitmap #4 inMap #16
Fit molecule 230810_Chol_HC_124.pdb (#4) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#16) using 11694 atoms
average map value = 0.1628, steps = 28
shifted from previous position = 0.0219
rotated from previous position = 0.028 degrees
atoms outside contour = 3402, contour level = 0.10065
Position of 230810_Chol_HC_124.pdb (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#16) coordinates:
Matrix rotation and translation
0.99999936 0.00113941 -0.00003054 -0.18003217
-0.00113942 0.99999934 -0.00018487 0.20741262
0.00003033 0.00018491 0.99999999 -0.04449163
Axis 0.16011472 -0.02635443 -0.98674653
Axis point 182.16265209 159.45849446 0.00000000
Rotation angle (degrees) 0.06616063
Shift along axis 0.00960992
> fitmap #4 inMap #16
Fit molecule 230810_Chol_HC_124.pdb (#4) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#16) using 11694 atoms
average map value = 0.1628, steps = 28
shifted from previous position = 0.0212
rotated from previous position = 0.0269 degrees
atoms outside contour = 3410, contour level = 0.10065
Position of 230810_Chol_HC_124.pdb (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#16) coordinates:
Matrix rotation and translation
0.99999935 0.00113329 -0.00012946 -0.16723827
-0.00113325 0.99999933 0.00027334 0.15272530
0.00012976 -0.00027319 0.99999996 0.01400239
Axis -0.23297818 -0.11050075 -0.96618360
Axis point 135.51443044 145.88786128 0.00000000
Rotation angle (degrees) 0.06720410
Shift along axis 0.00855773
> fitmap #4 inMap #16
Fit molecule 230810_Chol_HC_124.pdb (#4) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#16) using 11694 atoms
average map value = 0.1628, steps = 28
shifted from previous position = 0.0209
rotated from previous position = 0.0276 degrees
atoms outside contour = 3403, contour level = 0.10065
Position of 230810_Chol_HC_124.pdb (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#16) coordinates:
Matrix rotation and translation
0.99999936 0.00113921 -0.00003748 -0.17944806
-0.00113922 0.99999934 -0.00019887 0.20985345
0.00003725 0.00019891 0.99999998 -0.04801347
Axis 0.17189392 -0.03229528 -0.98458595
Axis point 184.38884046 159.08116339 0.00000000
Rotation angle (degrees) 0.06629393
Shift along axis 0.00965008
> show #!5 models
> hide #!4 models
> show #!17 models
> hide #!16 models
> hide #!5 models
> show #!6 models
> show #!18 models
> hide #!17 models
> hide #!18 models
> show #!5 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!1 models
> view orient
> turn x 90
> turn y 10
[Repeated 1 time(s)]
> view name 1
> select clear
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/230903_All_Align.cxs"
> hide #!5 models
> hide #!6 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!5 models
> hide #!1 models
> show #!4 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!4 models
> select #3: 184-187, 196-199
384 atoms, 384 bonds, 48 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 2
Assigning ss_type attribute to 48 items
> setattr sel r ss_id 1
Assigning ss_id attribute to 48 items
> select clear
> select #3/E:184
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 0
Assigning ss_type attribute to 1 item
> undo
> select clear
> show #!6 models
> hide #!6 models
> select #2 show sel ribbon
Expected a keyword
> select #2
9648 atoms, 9924 bonds, 6 pseudobonds, 1188 residues, 2 models selected
> show sel ribbons
> show #!2 models
> select subtract #2
Nothing selected
> view 1
> view orient
> turn x 180
> turn y 180
> undo
[Repeated 2 time(s)]
> view orient
> turn x 90
[Repeated 1 time(s)]
> clip back 0
> hide #!2 models
> hide #!3 models
> show #!13 models
> hide #!13 models
> show #!1 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/230903_All_Align.cxs"
> select #1
11514 atoms, 11832 bonds, 6 pseudobonds, 1230 residues, 2 models selected
> show sel ribbons
> select
> ::name="6OU"::name="AV0"::name="CBO"::name="CLR"::name="MC3"::name="PTY"::name="Y01"
6168 atoms, 6114 bonds, 204 residues, 4 models selected
> show sel atoms
> ~clip
> select clear
> select
> ::name="6OU"::name="AV0"::name="CBO"::name="CLR"::name="MC3"::name="PTY"::name="Y01"
6168 atoms, 6114 bonds, 204 residues, 4 models selected
> color sel light gray
> color sel byhetero
> select clear
> select #1/b,c,e,f
7676 atoms, 7886 bonds, 4 pseudobonds, 820 residues, 2 models selected
> hide sel
> hide sel atoms
> hide sel ribbons
> show #!13 models
> volume #13 level 0.08867
> transparency 0
> volume #13 level 0.07274
> view orient
> turn x 90
> clip front 0
> clip front 1
[Repeated 3 time(s)]
> color #1 #bfbfbfff
> undo
> color #13 #bfbfbfff models
> transparency 30
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/MBCD.cxs"
> select #
Expected an objects specifier or a keyword
> select #1
11514 atoms, 11832 bonds, 6 pseudobonds, 1230 residues, 2 models selected
> show sel ribbons
> ~clip
> view orient
> turn x 90
> clip front 0
> clip front 1
[Repeated 8 time(s)]
> turn x 90
[Repeated 1 time(s)]
> select clear
> ~clip
> show #!6 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!6 models
> select #1,6:1-5
384 atoms, 396 bonds, 48 residues, 2 models selected
> show sel atoms
> undo
> select #1,6:4
168 atoms, 180 bonds, 12 residues, 2 models selected
> show sel atoms
> select clear
> hide #!6 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/230903_All_Align.cxs"
——— End of log from Mon Sep 4 08:40:16 2023 ———
opened ChimeraX session
> show #!16 models
> hide #!16 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!13 models
> show #!16 models
> hide #!16 models
> hide #!4 models
> hide #!1 models
> show #!6 models
> show #!1 models
> hide #!1 models
> show #!18 models
> volume #18 level 0.1492
> select #6
11454 atoms, 11670 bonds, 6 pseudobonds, 1266 residues, 2 models selected
> show sel atoms
> select clear
> show #!4 models
> el #4
Unknown command: el #4
> select #4
11694 atoms, 11940 bonds, 6 pseudobonds, 1242 residues, 2 models selected
> show sel atoms
> select clear
> show #!16 models
> volume #16 level 0.1209
> volume #16 level 0.1095
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!18 models
> volume #16 level 0.09812
> show #!1 models
> select
> ::name="6OU"::name="AV0"::name="CBO"::name="CLR"::name="MC3"::name="PTY"::name="Y01"
6168 atoms, 6114 bonds, 204 residues, 4 models selected
> show sel atoms
> select clear
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> close #1
> show #!2 models
> hide #!2 models
> show #!4 models
> close #4
> close #5
> close #6
> transparency 0
> select clear
[Repeated 1 time(s)]
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/N55H_CBX_P52_J575_011_volume_map_sharp.mrc"
Opened N55H_CBX_P52_J575_011_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 0.83, shown at level 0.0684, step 2, values float32
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/N55H_CBX_P52_J650_003_volume_map_sharp.mrc"
Opened N55H_CBX_P52_J650_003_volume_map_sharp.mrc as #4, grid size
400,400,400, pixel 0.83, shown at level 0.0535, step 2, values float32
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/WT_PIP2_P68_J150_009_volume_map_sharp.mrc"
Opened WT_PIP2_P68_J150_009_volume_map_sharp.mrc as #5, grid size 400,400,400,
pixel 0.848, shown at level 0.0605, step 2, values float32
> rename #1 id #20
> rename #2 id #1
> rename #3 id #3
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2858, in run
self._process_keyword_arguments(final, prev_annos)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2784, in
_process_keyword_arguments
value, text = self._parse_arg(anno, text, session, final)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2488, in _parse_arg
value, replacement, rest = annotation.parse(text, session)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 532, in parse
value, consumed, rest = self.annotation.parse(text,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 723, in parse
value, new_text, rest = self.anno.parse(text, session)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 981, in parse
token, text, rest = next_token(text)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 1816, in next_token
assert text and not text[0].isspace()
AssertionError
AssertionError
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 1816, in next_token
assert text and not text[0].isspace()
See log for complete Python traceback.
> rename #3 id #30
> rename #1 id #31
> volume #4 step 1
> volume #5 step 1
> color #4 #ff557fff models
> rename #18 id #1
> rename #5 id #2
> rename #16 id #3
> rename #4 id #5
> rename #20 id #4
> volume #5 level 0.09795
> select clear
> color #2 #ff557fff models
> color #4 #00aaffff models
> color #5 #aa55ffff models
> rename #5 id #6
> rename #17 id #5
> select clear
> show #!31 models
> hide #!31 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> rename #13 id #7
> ui tool show "Fit in Map"
> hide #!4 models
> show #!4 models
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> select add #4
2 models selected
> select subtract #4
Nothing selected
> select add #4
2 models selected
> view matrix models #4,1,0,0,-150.64,0,1,0,-144.25,0,0,1,-50.389
> volume #4 level 0.2122
> view matrix models #4,1,0,0,-135.17,0,1,0,-128.66,0,0,1,-63.971
> view matrix models #4,1,0,0,-74.564,0,1,0,-55.349,0,0,1,-35.428
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12611 points
correlation = 0.566, correlation about mean = 0.07368, overlap = 281.7
steps = 144, shift = 8.44, angle = 8.69 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.97142270 -0.19986219 -0.12803534 47.55102644
0.19161482 0.97868349 -0.07390799 -18.24089784
0.14007748 0.04726243 0.98901191 -6.20771939
Axis 0.24743038 -0.54748720 0.79939726
Axis point 70.26112301 207.08693842 0.00000000
Rotation angle (degrees) 14.17341924
Shift along axis 16.78979278
> view matrix models
> #4,0.98976,-0.034542,-0.13853,-16.623,0.027614,0.99828,-0.051624,-57.062,0.14008,0.04727,0.98901,-90.6
> view matrix models
> #4,0.98976,-0.034542,-0.13853,-20.711,0.027614,0.99828,-0.051624,-59.81,0.14008,0.04727,0.98901,-98.378
> view matrix models
> #4,0.98976,-0.034542,-0.13853,-23.761,0.027614,0.99828,-0.051624,-58.658,0.14008,0.04727,0.98901,-100.87
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12611 points
correlation = 0.7097, correlation about mean = 0.2041, overlap = 569.8
steps = 140, shift = 7.11, angle = 13.1 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99971188 -0.02400344 -0.00000118 4.03258728
0.02400344 0.99971188 -0.00000036 -3.93668959
0.00000118 0.00000033 1.00000000 -5.01802421
Axis 0.00001442 -0.00004915 1.00000000
Axis point 166.00817820 166.01071000 0.00000000
Rotation angle (degrees) 1.37542809
Shift along axis -5.01777260
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12611 points
correlation = 0.7097, correlation about mean = 0.2043, overlap = 570.2
steps = 28, shift = 0.013, angle = 0.00292 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99971290 -0.02396092 0.00002047 4.02190904
0.02396092 0.99971290 0.00001744 -3.93279034
-0.00002089 -0.00001695 1.00000000 -4.99849903
Axis -0.00071754 0.00086308 0.99999937
Axis point 165.93886282 165.71465837 0.00000000
Rotation angle (degrees) 1.37299200
Shift along axis -5.00477608
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12611 points
correlation = 0.7097, correlation about mean = 0.2041, overlap = 569.9
steps = 40, shift = 0.0106, angle = 0.00246 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99971372 -0.02392683 0.00000087 4.01924224
0.02392683 0.99971372 0.00000035 -3.92438522
-0.00000088 -0.00000033 1.00000000 -5.01519921
Axis -0.00001424 0.00003646 1.00000000
Axis point 165.99456737 165.99143247 0.00000000
Rotation angle (degrees) 1.37103717
Shift along axis -5.01539949
> view matrix models
> #4,0.9898,0.14244,-4.6291e-07,-78.88,-0.14244,0.9898,-7.4975e-06,-34.524,-6.0977e-07,7.487e-06,1,-61.157
> view matrix models
> #4,0.9898,0.14244,-4.6291e-07,-79.387,-0.14244,0.9898,-7.4975e-06,-34.479,-6.0977e-07,7.487e-06,1,-61.814
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12611 points
correlation = 0.9587, correlation about mean = 0.7509, overlap = 1067
steps = 64, shift = 3.18, angle = 1.4 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999987 0.00051706 0.00000932 -0.09443579
-0.00051706 0.99999987 -0.00000388 0.09120000
-0.00000932 0.00000387 1.00000000 -0.01620720
Axis 0.00749297 0.01802491 -0.99980946
Axis point 175.73777878 182.93451275 0.00000000
Rotation angle (degrees) 0.02963088
Shift along axis 0.01714038
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12611 points
correlation = 0.9587, correlation about mean = 0.7508, overlap = 1067
steps = 24, shift = 0.00307, angle = 0.00397 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999987 0.00050374 -0.00005677 -0.08307581
-0.00050374 0.99999988 0.00001220 0.08461456
0.00005678 -0.00001217 1.00000000 -0.02657311
Axis -0.02403010 -0.11196666 -0.99342137
Axis point 172.13618584 164.05853150 0.00000000
Rotation angle (degrees) 0.02905344
Shift along axis 0.01892060
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12611 points
correlation = 0.9587, correlation about mean = 0.7507, overlap = 1067
steps = 24, shift = 0.00324, angle = 0.00465 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999987 0.00049069 -0.00013546 -0.07099614
-0.00049069 0.99999988 -0.00000258 0.08318564
0.00013546 0.00000265 0.99999999 -0.04309415
Axis 0.00514243 -0.26610458 -0.96393045
Axis point 179.81793266 144.93413768 0.00000000
Rotation angle (degrees) 0.02916634
Shift along axis 0.01903859
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12611 points
correlation = 0.9587, correlation about mean = 0.7507, overlap = 1067
steps = 28, shift = 0.0234, angle = 0.0226 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999986 0.00045900 0.00025585 -0.10470745
-0.00045900 0.99999990 0.00003178 0.07111576
-0.00025584 -0.00003190 0.99999997 0.02647488
Axis -0.06047569 0.48597616 -0.87187721
Axis point 136.02649021 225.81743099 0.00000000
Rotation angle (degrees) 0.03016334
Shift along axis 0.01780998
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12611 points
correlation = 0.9587, correlation about mean = 0.7508, overlap = 1067
steps = 28, shift = 0.0231, angle = 0.0285 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999985 0.00049981 -0.00023739 -0.05593434
-0.00049981 0.99999988 -0.00001471 0.08606075
0.00023738 0.00001483 0.99999997 -0.06129699
Axis 0.02667770 -0.42886754 -0.90297339
Axis point 186.70250507 112.87431743 0.00000000
Rotation angle (degrees) 0.03171387
Shift along axis 0.01694869
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12611 points
correlation = 0.9587, correlation about mean = 0.7507, overlap = 1067
steps = 24, shift = 0.00184, angle = 0.00252 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999984 0.00050050 -0.00027397 -0.05138794
-0.00050049 0.99999988 0.00000962 0.08327743
0.00027397 -0.00000948 0.99999997 -0.06436354
Axis -0.01673043 -0.48009792 -0.87705535
Axis point 182.98790105 102.15437563 0.00000000
Rotation angle (degrees) 0.03269601
Shift along axis 0.01732881
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12611 points
correlation = 0.9587, correlation about mean = 0.7507, overlap = 1067
steps = 28, shift = 0.0234, angle = 0.0277 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999985 0.00052032 0.00020881 -0.10824212
-0.00052032 0.99999987 0.00002645 0.08212967
-0.00020880 -0.00002656 0.99999998 0.01945093
Axis -0.04722335 0.37201213 -0.92702585
Axis point 145.18238879 206.47405714 0.00000000
Rotation angle (degrees) 0.03215898
Shift along axis 0.01763327
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12611 points
correlation = 0.9586, correlation about mean = 0.7503, overlap = 1066
steps = 28, shift = 0.0156, angle = 0.0136 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999982 0.00058733 0.00012275 -0.11625961
-0.00058731 0.99999981 -0.00018433 0.12289576
-0.00012286 0.00018426 0.99999998 -0.04058302
Axis 0.29361339 0.19564077 -0.93569005
Axis point 199.89590109 211.94434509 0.00000000
Rotation angle (degrees) 0.03596388
Shift along axis 0.02788117
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12611 points
correlation = 0.9587, correlation about mean = 0.7508, overlap = 1067
steps = 44, shift = 0.0169, angle = 0.0201 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999986 0.00052729 -0.00000625 -0.08587506
-0.00052728 0.99999985 0.00013701 0.07412074
0.00000632 -0.00013701 0.99999999 0.00276735
Axis -0.25147674 -0.01153353 -0.96779462
Axis point 140.92209352 154.28498966 0.00000000
Rotation angle (degrees) 0.03121660
Shift along axis 0.01806248
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12611 points
correlation = 0.9587, correlation about mean = 0.7508, overlap = 1067
steps = 24, shift = 0.00155, angle = 0.0016 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999988 0.00050193 -0.00001176 -0.08101802
-0.00050193 0.99999987 0.00014714 0.06981900
0.00001183 -0.00014713 0.99999999 0.00375471
Axis -0.28122723 -0.02254551 -0.95937633
Axis point 139.85056452 151.58173138 0.00000000
Rotation angle (degrees) 0.02997629
Shift along axis 0.01760819
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12611 points
correlation = 0.9587, correlation about mean = 0.7508, overlap = 1067
steps = 24, shift = 0.000724, angle = 0.00078 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999988 0.00050390 -0.00000915 -0.08147056
-0.00050390 0.99999986 0.00016035 0.06870207
0.00000923 -0.00016035 0.99999999 0.00631042
Axis -0.30318362 -0.01738486 -0.95277356
Axis point 136.90181249 151.18802068 0.00000000
Rotation angle (degrees) 0.03030257
Shift along axis 0.01749376
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12611 points
correlation = 0.9587, correlation about mean = 0.7508, overlap = 1067
steps = 24, shift = 0.000717, angle = 0.000689 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999988 0.00050444 -0.00000942 -0.08144605
-0.00050444 0.99999986 0.00017237 0.06754947
0.00000950 -0.00017236 0.99999999 0.00801953
Axis -0.32328864 -0.01774544 -0.94613400
Axis point 134.48505551 150.24829528 0.00000000
Rotation angle (degrees) 0.03054773
Shift along axis 0.01754434
> hide #!4 models
> select subtract #4
Nothing selected
> select add #2
2 models selected
> view matrix models #2,1,0,0,-58.696,0,1,0,-12.967,0,0,1,-6.6108
> view matrix models #2,1,0,0,-81.089,0,1,0,-113.09,0,0,1,-99.949
> volume #2 level 0.2715
> view matrix models #2,1,0,0,-49.814,0,1,0,-63.08,0,0,1,-82.861
> view matrix models #2,1,0,0,-56.104,0,1,0,-62.628,0,0,1,-83.714
> fitmap #2 inMap #3
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 59234 points
correlation = 0.933, correlation about mean = 0.5608, overlap = 5503
steps = 152, shift = 13.6, angle = 11 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#2) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.93622630 -0.35139758 0.00023499 66.78045556
0.35139760 0.93622632 -0.00005626 -52.37394220
-0.00020024 0.00013525 0.99999997 -7.23552155
Axis 0.00027250 0.00061929 0.99999977
Axis point 177.67096159 157.80329811 0.00000000
Rotation angle (degrees) 20.57282665
Shift along axis -7.24975688
> fitmap #2 inMap #3
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 59234 points
correlation = 0.933, correlation about mean = 0.5609, overlap = 5503
steps = 28, shift = 0.00483, angle = 0.0216 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#2) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.93609694 -0.35174208 0.00019473 66.86606025
0.35174209 0.93609696 0.00001226 -52.41982065
-0.00018660 0.00005702 0.99999998 -7.22865825
Axis 0.00006363 0.00054207 0.99999985
Axis point 177.68987261 157.81903145 0.00000000
Rotation angle (degrees) 20.59390887
Shift along axis -7.25281791
> fitmap #2 inMap #3
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 59234 points
correlation = 0.933, correlation about mean = 0.561, overlap = 5503
steps = 44, shift = 0.016, angle = 0.0107 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#2) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.93613085 -0.35165187 0.00003575 66.87067994
0.35165187 0.93613085 0.00000027 -52.40843031
-0.00003357 0.00001232 1.00000000 -7.23105863
Axis 0.00001714 0.00009857 0.99999999
Axis point 177.70905327 157.88534746 0.00000000
Rotation angle (degrees) 20.58838415
Shift along axis -7.23507783
> fitmap #2 inMap #3
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 59234 points
correlation = 0.933, correlation about mean = 0.5609, overlap = 5503
steps = 28, shift = 0.00777, angle = 0.0155 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#2) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.93619838 -0.35147197 0.00022637 66.80227817
0.35147198 0.93619840 -0.00000712 -52.38912881
-0.00020943 0.00008623 0.99999998 -7.21919020
Axis 0.00013281 0.00061997 0.99999980
Axis point 177.69057937 157.81142666 0.00000000
Rotation angle (degrees) 20.57737844
Shift along axis -7.24279676
> show #!1 models
> hide #!3 models
> volume sdLevel 7
> volume sdLevel 8
> select clear
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!5 models
> select add #6
2 models selected
> view matrix models #6,1,0,0,-61.36,0,1,0,-53.004,0,0,1,-86.824
> view matrix models #6,1,0,0,-52.483,0,1,0,-64.661,0,0,1,-83.982
> view matrix models #6,1,0,0,-63.491,0,1,0,-57.837,0,0,1,-61.241
> view matrix models #6,1,0,0,-58.15,0,1,0,-53.383,0,0,1,-64.258
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.97079,-0.20495,0.12477,-39.258,0.20662,0.97842,-0.00048102,-84.022,-0.12198,0.026247,0.99219,-47.115
> view matrix models
> #6,0.95011,-0.30717,-0.054254,9.8104,0.31056,0.94778,0.072594,-107.89,0.029122,-0.085821,0.99588,-54.187
> view matrix models
> #6,0.8908,-0.45359,0.026975,30.955,0.45147,0.89023,0.060605,-119.81,-0.051504,-0.041809,0.9978,-48.416
> fitmap #6 inMap #5
Fit map N55H_CBX_P52_J650_003_volume_map_sharp.mrc in map
N55H_CBX_P52_J650_003_volume_map.mrc using 82839 points
correlation = 0.9776, correlation about mean = 0.7765, overlap = 3191
steps = 76, shift = 4.21, angle = 3.81 degrees
Position of N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) relative to
N55H_CBX_P52_J650_003_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
0.99999999 -0.00012221 0.00003174 0.01872053
0.00012221 0.99999999 0.00001278 -0.01699945
-0.00003175 -0.00001277 1.00000000 -0.01106755
Axis -0.10065730 0.25013285 0.96296504
Axis point 104.73426777 139.34183493 0.00000000
Rotation angle (degrees) 0.00727152
Shift along axis -0.01679415
> select clear
> hide #!6 models
> hide #!5 models
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!3 models
> select clear
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/230903_All_Align.cxs"
> show #!7 models
> hide #!7 models
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/cryosparc_P58_cryosparc_P58_J139_004_volume_map.mrc"
Opened cryosparc_P58_cryosparc_P58_J139_004_volume_map.mrc as #8, grid size
256,256,256, pixel 1.1, shown at level 0.213, step 1, values float32
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/cryosparc_P58_cryosparc_P58_J139_004_volume_map_sharp.mrc"
Opened cryosparc_P58_cryosparc_P58_J139_004_volume_map_sharp.mrc as #9, grid
size 256,256,256, pixel 1.1, shown at level 0.251, step 1, values float32
> volume #9 level 1.218
> volume #8 level 0.6713
> volume #9 level 0.6751
> color #8 #ffaaffff models
> select add #8
2 models selected
> view matrix models
> #8,0.96553,-0.18609,0.18199,6.3063,0.21509,0.96418,-0.15525,-4.1292,-0.14658,0.18904,0.97097,-2.0301
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.96553,-0.18609,0.18199,-15.163,0.21509,0.96418,-0.15525,-44.599,-0.14658,0.18904,0.97097,-40.253
> close #8-9
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/POPE_C6_P58_J139_004_volume_map.mrc"
Opened POPE_C6_P58_J139_004_volume_map.mrc as #8, grid size 256,256,256, pixel
1.1, shown at level 0.213, step 1, values float32
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/POPE_C6_P58_J139_004_volume_map_sharp.mrc"
Opened POPE_C6_P58_J139_004_volume_map_sharp.mrc as #9, grid size 256,256,256,
pixel 1.1, shown at level 0.251, step 1, values float32
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/MBCD_P41_J50_013_volume_map_sharp.mrc"
Opened MBCD_P41_J50_013_volume_map_sharp.mrc as #10, grid size 256,256,256,
pixel 0.848, shown at level 0.101, step 1, values float32
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/MBCD_P41_J50_013_volume_map.mrc"
Opened MBCD_P41_J50_013_volume_map.mrc as #11, grid size 256,256,256, pixel
0.848, shown at level 0.0557, step 1, values float32
> close #7
> color #9 #ffaaffff models
> color #8 #ffaaffff models
> color #10 #55ff7fff models
> color #10 #ffff7fff models
> color #11 #ffff7fff models
> rename #8 id #13
> rename #9 id #21
> rename #10 id #8
> rename #11 id #7
> rename #13 id #9
> rename #21 id #10
> hide #!10 models
> hide #!9 models
> hide #!8 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!7 models
> show #!3 models
> hide #!3 models
> show #!2 models
> fitmap #2 inMap #1
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 99815 points
correlation = 0.971, correlation about mean = 0.8369, overlap = 7482
steps = 36, shift = 0.0243, angle = 0.112 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#2) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.49970799 0.86619393 -0.00002337 -62.05407727
-0.86619393 0.49970799 0.00007907 231.75074858
0.00008016 -0.00001926 1.00000000 -0.01079889
Axis -0.00005676 -0.00005976 -1.00000000
Axis point 169.59688604 169.59486668 0.00000000
Rotation angle (degrees) 60.01931727
Shift along axis 0.00047163
> fitmap #2 inMap #1
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 99815 points
correlation = 0.971, correlation about mean = 0.8369, overlap = 7481
steps = 24, shift = 0.00291, angle = 0.0063 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#2) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.49980261 0.86613934 -0.00001065 -62.06167817
-0.86613934 0.49980262 0.00008105 231.72651458
0.00007552 -0.00003128 1.00000000 -0.01013927
Axis -0.00006485 -0.00004974 -1.00000000
Axis point 169.59740860 169.59610594 0.00000000
Rotation angle (degrees) 60.01305814
Shift along axis 0.00263747
> fitmap #2 inMap #1
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 99815 points
correlation = 0.971, correlation about mean = 0.8369, overlap = 7481
steps = 24, shift = 0.000954, angle = 0.00229 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#2) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.49982438 0.86612678 -0.00000503 -62.06333623
-0.86612678 0.49982438 0.00011166 231.71578740
0.00009922 -0.00005145 1.00000000 -0.01109958
Axis -0.00009416 -0.00006018 -0.99999999
Axis point 169.59311194 169.59373665 0.00000000
Rotation angle (degrees) 60.01161872
Shift along axis 0.00299809
> fitmap #2 inMap #1
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 99815 points
correlation = 0.971, correlation about mean = 0.8368, overlap = 7480
steps = 24, shift = 0.000894, angle = 0.00187 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#2) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.49983338 0.86612158 0.00000375 -62.06467769
-0.86612158 0.49983338 0.00014133 231.70881549
0.00012053 -0.00007388 1.00000000 -0.01094781
Axis -0.00012424 -0.00006742 -0.99999999
Axis point 169.58881342 169.59205723 0.00000000
Rotation angle (degrees) 60.01102315
Shift along axis 0.00303711
> hide #!2 models
> show #!3 models
> fitmap #3 inMap #1
Fit map N55H_CBX_P52_J575_011_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 139334 points
correlation = 0.9577, correlation about mean = 0.7565, overlap = 4265
steps = 28, shift = 0.0122, angle = 0.0223 degrees
Position of N55H_CBX_P52_J575_011_volume_map.mrc (#3) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.16490323 0.98630975 -0.00006520 -21.50055957
-0.98630975 0.16490323 -0.00004310 305.95546684
-0.00003176 0.00007142 1.00000000 7.24393104
Axis 0.00005806 -0.00001695 -1.00000000
Axis point 169.92763744 165.67428224 0.00000000
Rotation angle (degrees) 80.50838717
Shift along axis -7.25036597
> fitmap #3 inMap #1
Fit map N55H_CBX_P52_J575_011_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 139334 points
correlation = 0.9577, correlation about mean = 0.7566, overlap = 4265
steps = 28, shift = 0.0187, angle = 0.0127 degrees
Position of N55H_CBX_P52_J575_011_volume_map.mrc (#3) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.16490975 0.98630865 0.00012942 -21.51548252
-0.98630866 0.16490975 0.00006150 305.94485424
0.00003931 -0.00013778 0.99999999 7.26611301
Axis -0.00010102 0.00004568 -0.99999999
Axis point 169.91481172 165.67878216 0.00000000
Rotation angle (degrees) 80.50800831
Shift along axis -7.24996443
> fitmap #3 inMap #1
Fit map N55H_CBX_P52_J575_011_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 139334 points
correlation = 0.9577, correlation about mean = 0.7565, overlap = 4265
steps = 28, shift = 0.0187, angle = 0.013 degrees
Position of N55H_CBX_P52_J575_011_volume_map.mrc (#3) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.16495336 0.98630137 -0.00007805 -21.50658770
-0.98630137 0.16495337 -0.00001912 305.94552559
-0.00000599 0.00008014 1.00000000 7.23736421
Axis 0.00005032 -0.00003653 -1.00000000
Axis point 169.92795262 165.67348837 0.00000000
Rotation angle (degrees) 80.50547464
Shift along axis -7.24962309
> fitmap #3 inMap #1
Fit map N55H_CBX_P52_J575_011_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 139334 points
correlation = 0.9577, correlation about mean = 0.7565, overlap = 4265
steps = 28, shift = 0.0204, angle = 0.0134 degrees
Position of N55H_CBX_P52_J575_011_volume_map.mrc (#3) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.16491917 0.98630707 0.00015157 -21.51828254
-0.98630709 0.16491918 0.00000606 305.94862304
-0.00001902 -0.00015049 0.99999999 7.27787332
Axis -0.00007936 0.00008648 -0.99999999
Axis point 169.91764035 165.68249919 0.00000000
Rotation angle (degrees) 80.50746096
Shift along axis -7.24970720
> fitmap #3 inMap #1
Fit map N55H_CBX_P52_J575_011_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 139334 points
correlation = 0.9577, correlation about mean = 0.7565, overlap = 4265
steps = 28, shift = 0.0195, angle = 0.0144 degrees
Position of N55H_CBX_P52_J575_011_volume_map.mrc (#3) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.16495211 0.98630157 -0.00009786 -21.50191728
-0.98630158 0.16495211 0.00001929 305.94399383
0.00003517 0.00009334 1.00000000 7.22823081
Axis 0.00003754 -0.00006744 -1.00000000
Axis point 169.92897121 165.66989108 0.00000000
Rotation angle (degrees) 80.50554765
Shift along axis -7.24967081
> show #!4 models
> hide #!3 models
> fitmap #4 inMap #1
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 12433 points
correlation = 0.9371, correlation about mean = 0.6672, overlap = 951.8
steps = 40, shift = 0.0283, angle = 0.114 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.16282305 0.98665528 0.00016666 -21.23307101
-0.98665529 0.16282305 0.00005543 306.34837222
0.00002755 -0.00017346 0.99999999 7.23320926
Axis -0.00011599 0.00007050 -0.99999999
Axis point 169.90685351 165.68705673 0.00000000
Rotation angle (degrees) 80.62920615
Shift along axis -7.20914960
> fitmap #4 inMap #1
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 12433 points
correlation = 0.9371, correlation about mean = 0.6672, overlap = 951.8
steps = 40, shift = 0.00272, angle = 0.00921 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.16289152 0.98664399 0.00002693 -21.22266299
-0.98664399 0.16289153 0.00001690 306.34241284
0.00001228 -0.00002932 1.00000001 7.21105055
Axis -0.00002342 0.00000743 -1.00000000
Axis point 169.92131143 165.67820214 0.00000000
Rotation angle (degrees) 80.62522917
Shift along axis -7.20827818
> show #!5 models
> hide #!4 models
> fitmap #5 inMap #1
Fit map N55H_CBX_P52_J650_003_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 116859 points
correlation = 0.8744, correlation about mean = 0.4317, overlap = 2545
steps = 48, shift = 0.15, angle = 0.0923 degrees
Position of N55H_CBX_P52_J650_003_volume_map.mrc (#5) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.71988999 0.69408819 0.00000726 -65.12809921
-0.69408818 0.71988999 0.00006294 165.32008265
0.00003846 -0.00005034 1.00000000 8.55622016
Axis -0.00008161 -0.00002248 -1.00000000
Axis point 172.25973786 163.35168559 0.00000000
Rotation angle (degrees) 43.95460158
Shift along axis -8.55462179
> fitmap #5 inMap #1
Fit map N55H_CBX_P52_J650_003_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 116859 points
correlation = 0.8744, correlation about mean = 0.4317, overlap = 2545
steps = 48, shift = 0.00743, angle = 0.00213 degrees
Position of N55H_CBX_P52_J650_003_volume_map.mrc (#5) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.71988501 0.69409335 -0.00000052 -65.12459227
-0.69409335 0.71988501 0.00002726 165.32038076
0.00001929 -0.00001926 1.00000001 8.55537407
Axis -0.00003351 -0.00001427 -1.00000000
Axis point 172.26003558 163.34618080 0.00000000
Rotation angle (degrees) 43.95501268
Shift along axis -8.55555054
> fitmap #5 inMap #1
Fit map N55H_CBX_P52_J650_003_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 116859 points
correlation = 0.8744, correlation about mean = 0.4317, overlap = 2545
steps = 48, shift = 0.00326, angle = 0.00104 degrees
Position of N55H_CBX_P52_J650_003_volume_map.mrc (#5) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.71988836 0.69408988 -0.00000766 -65.12643914
-0.69408988 0.71988836 0.00004326 165.31803823
0.00003554 -0.00002582 1.00000001 8.55355064
Axis -0.00004976 -0.00003112 -1.00000000
Axis point 172.25738485 163.34795855 0.00000000
Rotation angle (degrees) 43.95473640
Shift along axis -8.55545505
> show #!6 models
> hide #!5 models
> fitmap #6 inMap #1
Fit map N55H_CBX_P52_J650_003_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 82839 points
correlation = 0.88, correlation about mean = 0.3985, overlap = 3044
steps = 52, shift = 0.114, angle = 0.28 degrees
Position of N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.71770198 0.69635040 0.00000560 -65.13465901
-0.69635040 0.71770198 0.00002120 166.04700402
0.00001074 -0.00001911 1.00000001 8.27526673
Axis -0.00002894 -0.00000369 -1.00000000
Axis point 172.22830898 163.35828983 0.00000000
Rotation angle (degrees) 44.13492420
Shift along axis -8.27399520
> fitmap #6 inMap #1
Fit map N55H_CBX_P52_J650_003_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 82839 points
correlation = 0.88, correlation about mean = 0.3986, overlap = 3044
steps = 40, shift = 0.00294, angle = 0.00988 degrees
Position of N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.71758783 0.69646803 -0.00000267 -65.13310955
-0.69646803 0.71758783 -0.00003169 166.09096717
-0.00002016 0.00002460 1.00000001 8.27286225
Axis 0.00004041 0.00001256 -1.00000000
Axis point 172.23554913 163.35881439 0.00000000
Rotation angle (degrees) 44.14431575
Shift along axis -8.27340909
> fitmap #6 inMap #1
Fit map N55H_CBX_P52_J650_003_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 82839 points
correlation = 0.88, correlation about mean = 0.3985, overlap = 3044
steps = 48, shift = 0.0171, angle = 0.00665 degrees
Position of N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.71766792 0.69638550 -0.00000630 -65.13144470
-0.69638550 0.71766792 -0.00004753 166.08357574
-0.00002858 0.00003851 1.00000001 8.27233148
Axis 0.00006178 0.00001600 -1.00000000
Axis point 172.26121192 163.36612522 0.00000000
Rotation angle (degrees) 44.13772657
Shift along axis -8.27369831
> fitmap #6 inMap #1
Fit map N55H_CBX_P52_J650_003_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 82839 points
correlation = 0.88, correlation about mean = 0.3985, overlap = 3044
steps = 48, shift = 0.0152, angle = 0.00794 degrees
Position of N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.71766499 0.69638852 0.00001217 -65.13511717
-0.69638851 0.71766499 0.00008974 166.04786548
0.00005376 -0.00007287 1.00000000 8.27704554
Axis -0.00011675 -0.00002986 -0.99999999
Axis point 172.21289400 163.35394701 0.00000000
Rotation angle (degrees) 44.13796732
Shift along axis -8.27439850
> fitmap #6 inMap #1
Fit map N55H_CBX_P52_J650_003_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 82839 points
correlation = 0.88, correlation about mean = 0.3985, overlap = 3044
steps = 48, shift = 0.00192, angle = 0.00958 degrees
Position of N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.71771821 0.69633367 -0.00001066 -65.13182834
-0.69633367 0.71771821 -0.00005727 166.05114458
-0.00003223 0.00004853 1.00000000 8.27117106
Axis 0.00007597 0.00001549 -1.00000000
Axis point 172.24231644 163.35856663 0.00000000
Rotation angle (degrees) 44.13358878
Shift along axis -8.27354713
> fitmap #6 inMap #1
Fit map N55H_CBX_P52_J650_003_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 82839 points
correlation = 0.88, correlation about mean = 0.3986, overlap = 3044
steps = 44, shift = 0.00219, angle = 0.0108 degrees
Position of N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.71758843 0.69646741 -0.00000847 -65.13389340
-0.69646741 0.71758843 -0.00003032 166.08879279
-0.00001504 0.00002767 1.00000001 8.27139183
Axis 0.00004163 0.00000471 -1.00000000
Axis point 172.23265647 163.35874905 0.00000000
Rotation angle (degrees) 44.14426599
Shift along axis -8.27332044
> fitmap #6 inMap #1
Fit map N55H_CBX_P52_J650_003_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 82839 points
correlation = 0.88, correlation about mean = 0.3985, overlap = 3044
steps = 48, shift = 0.0204, angle = 0.00665 degrees
Position of N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.71766909 0.69638430 -0.00000740 -65.12906304
-0.69638430 0.71766909 -0.00002289 166.08033313
-0.00001063 0.00002159 1.00000001 8.27223681
Axis 0.00003193 0.00000232 -1.00000000
Axis point 172.25863420 163.36200812 0.00000000
Rotation angle (degrees) 44.13763038
Shift along axis -8.27393186
> hide #!6 models
> show #!7 models
> fitmap #7 inMap #1
Fit map MBCD_P41_J50_013_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 167626 points
correlation = 0.9767, correlation about mean = 0.8828, overlap = 3340
steps = 28, shift = 0.00527, angle = 0.0187 degrees
Position of MBCD_P41_J50_013_volume_map.mrc (#7) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.32648733 0.94520158 0.00001033 31.56422650
-0.94520158 0.32648733 0.00000032 236.75791677
-0.00000307 -0.00000986 1.00000001 71.17442525
Axis -0.00000539 0.00000709 -1.00000000
Axis point 181.91423293 96.23100481 0.00000000
Rotation angle (degrees) 70.94429120
Shift along axis -71.17291778
> fitmap #7 inMap #1
Fit map MBCD_P41_J50_013_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 167626 points
correlation = 0.9767, correlation about mean = 0.8826, overlap = 3334
steps = 28, shift = 0.0198, angle = 0.00294 degrees
Position of MBCD_P41_J50_013_volume_map.mrc (#7) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.32644020 0.94521786 0.00001983 31.56764800
-0.94521786 0.32644020 -0.00000755 236.76495497
-0.00001361 -0.00001627 1.00000001 71.15653659
Axis -0.00000461 0.00001769 -1.00000000
Axis point 181.91267583 96.23362999 0.00000000
Rotation angle (degrees) 70.94714789
Shift along axis -71.15249435
> fitmap #7 inMap #1
Fit map MBCD_P41_J50_013_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 167626 points
correlation = 0.9767, correlation about mean = 0.8826, overlap = 3333
steps = 28, shift = 0.00154, angle = 0.0145 degrees
Position of MBCD_P41_J50_013_volume_map.mrc (#7) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.32667814 0.94513565 -0.00000190 31.55230431
-0.94513565 0.32667815 0.00000106 236.72981241
0.00000162 0.00000146 1.00000001 71.15159919
Axis 0.00000021 -0.00000186 -1.00000000
Axis point 181.92378863 96.21999083 0.00000000
Rotation angle (degrees) 70.93272392
Shift along axis -71.15203364
> fitmap #7 inMap #1
Fit map MBCD_P41_J50_013_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 167626 points
correlation = 0.9767, correlation about mean = 0.8826, overlap = 3333
steps = 24, shift = 0.00242, angle = 0.0161 degrees
Position of MBCD_P41_J50_013_volume_map.mrc (#7) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.32641600 0.94522622 0.00002847 31.56904040
-0.94522622 0.32641601 -0.00002670 236.76923540
-0.00003454 -0.00001819 1.00000001 71.15619172
Axis 0.00000450 0.00003333 -1.00000000
Axis point 181.91298101 96.23549463 0.00000000
Rotation angle (degrees) 70.94861472
Shift along axis -71.14815814
> fitmap #7 inMap #1
Fit map MBCD_P41_J50_013_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 167626 points
correlation = 0.9767, correlation about mean = 0.8826, overlap = 3332
steps = 28, shift = 0.00289, angle = 0.0104 degrees
Position of MBCD_P41_J50_013_volume_map.mrc (#7) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.32658305 0.94516851 0.00000036 31.55896388
-0.94516851 0.32658305 -0.00000033 236.74379018
-0.00000043 -0.00000023 1.00000001 71.14830149
Axis 0.00000005 0.00000042 -1.00000000
Axis point 181.91935044 96.22475271 0.00000000
Rotation angle (degrees) 70.93848851
Shift along axis -71.14820052
> fitmap #7 inMap #1
Fit map MBCD_P41_J50_013_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 167626 points
correlation = 0.9767, correlation about mean = 0.8826, overlap = 3332
steps = 24, shift = 0.00369, angle = 0.00704 degrees
Position of MBCD_P41_J50_013_volume_map.mrc (#7) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.32646836 0.94520813 -0.00000900 31.56552567
-0.94520813 0.32646836 -0.00001683 236.75945548
-0.00001298 0.00001400 1.00000001 71.14833813
Axis 0.00001631 0.00000211 -1.00000000
Axis point 181.91295869 96.23007220 0.00000000
Rotation angle (degrees) 70.94544087
Shift along axis -71.14732480
> show #!8 models
> hide #!7 models
> fitmap #8 inMap #1
Fit map MBCD_P41_J50_013_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 167414 points
correlation = 0.9352, correlation about mean = 0.7931, overlap = 8319
steps = 28, shift = 0.0261, angle = 0.0032 degrees
Position of MBCD_P41_J50_013_volume_map_sharp.mrc (#8) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.32677736 0.94510135 0.00000555 31.54471428
-0.94510135 0.32677736 -0.00000202 236.71542500
-0.00000373 -0.00000458 1.00000001 71.14255560
Axis -0.00000136 0.00000491 -1.00000000
Axis point 181.92863236 96.21598414 0.00000000
Rotation angle (degrees) 70.92670931
Shift along axis -71.14143624
> fitmap #8 inMap #1
Fit map MBCD_P41_J50_013_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 167414 points
correlation = 0.9352, correlation about mean = 0.7931, overlap = 8320
steps = 28, shift = 0.00484, angle = 0.00355 degrees
Position of MBCD_P41_J50_013_volume_map_sharp.mrc (#8) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.32680534 0.94509168 0.00003413 31.54151840
-0.94509168 0.32680534 0.00004432 236.71127882
0.00003073 -0.00004673 1.00000000 71.14391021
Axis -0.00004817 0.00000179 -1.00000000
Axis point 181.92750787 96.21768794 0.00000000
Rotation angle (degrees) 70.92501320
Shift along axis -71.14500470
> fitmap #8 inMap #1
Fit map MBCD_P41_J50_013_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 167414 points
correlation = 0.9352, correlation about mean = 0.7931, overlap = 8320
steps = 24, shift = 0.00245, angle = 0.000842 degrees
Position of MBCD_P41_J50_013_volume_map_sharp.mrc (#8) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.32679412 0.94509556 0.00003125 31.54467707
-0.94509556 0.32679412 0.00003614 236.71242835
0.00002394 -0.00004134 1.00000001 71.14392048
Axis -0.00004099 0.00000386 -1.00000000
Axis point 181.92816603 96.21603847 0.00000000
Rotation angle (degrees) 70.92569330
Shift along axis -71.14429871
> fitmap #8 inMap #1
Fit map MBCD_P41_J50_013_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 167414 points
correlation = 0.9352, correlation about mean = 0.7931, overlap = 8319
steps = 24, shift = 0.00309, angle = 0.00163 degrees
Position of MBCD_P41_J50_013_volume_map_sharp.mrc (#8) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.32679249 0.94509612 0.00004485 31.54479877
-0.94509612 0.32679249 0.00001118 236.71238877
-0.00000409 -0.00004603 1.00000001 71.14707166
Axis -0.00003027 0.00002589 -1.00000000
Axis point 181.92937705 96.21622192 0.00000000
Rotation angle (degrees) 70.92579216
Shift along axis -71.14189726
> hide #!8 models
> show #!9 models
> volume #9 level 0.4302
> ui mousemode right "translate selected models"
> select add #9
2 models selected
> view matrix models #9,1,0,0,-31.584,0,1,0,-27.038,0,0,1,-47.529
> view matrix models #9,1,0,0,-31.968,0,1,0,-32.32,0,0,1,-47.955
> view matrix models #9,1,0,0,-32.181,0,1,0,-33.826,0,0,1,-41.86
> fitmap #9 inMap #1
Fit map POPE_C6_P58_J139_004_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 54576 points
correlation = 0.8879, correlation about mean = 0.477, overlap = 6261
steps = 72, shift = 1.8, angle = 5.02 degrees
Position of POPE_C6_P58_J139_004_volume_map.mrc (#9) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40824369 0.91287298 -0.00010655 -16.39712695
-0.91287299 0.40824369 -0.00002177 240.65586812
0.00002363 0.00010616 1.00000000 30.17233731
Axis 0.00007007 -0.00007130 -1.00000000
Axis point 177.42474525 132.97274228 0.00000000
Rotation angle (degrees) 65.90544611
Shift along axis -30.19064566
> fitmap #9 inMap #1
Fit map POPE_C6_P58_J139_004_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 54576 points
correlation = 0.8879, correlation about mean = 0.477, overlap = 6261
steps = 40, shift = 0.0107, angle = 0.00365 degrees
Position of POPE_C6_P58_J139_004_volume_map.mrc (#9) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40824794 0.91287109 -0.00004335 -16.41297815
-0.91287109 0.40824794 -0.00002746 240.64763680
-0.00000737 0.00005079 1.00000001 30.18383454
Axis 0.00004286 -0.00001970 -1.00000000
Axis point 177.41220752 132.98232956 0.00000000
Rotation angle (degrees) 65.90517947
Shift along axis -30.18927959
> fitmap #9 inMap #1
Fit map POPE_C6_P58_J139_004_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 54576 points
correlation = 0.8879, correlation about mean = 0.477, overlap = 6261
steps = 40, shift = 0.0169, angle = 0.00997 degrees
Position of POPE_C6_P58_J139_004_volume_map.mrc (#9) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40837230 0.91281547 0.00004546 -16.42525594
-0.91281547 0.40837230 0.00003457 240.62771733
0.00001299 -0.00005561 1.00000000 30.19789465
Axis -0.00004940 0.00001779 -1.00000000
Axis point 177.41788563 132.98644552 0.00000000
Rotation angle (degrees) 65.89737404
Shift along axis -30.19280293
> select clear
> volume #9 level 0.5816
> hide #!9 models
> show #!9 models
> hide #!1 models
> show #!10 models
> hide #!9 models
> show #!9 models
> select add #10
2 models selected
> view matrix models #10,1,0,0,-20.023,0,1,0,-1.9994,0,0,1,-35.737
> view matrix models #10,1,0,0,-29.305,0,1,0,-27.566,0,0,1,-36.121
> view matrix models #10,1,0,0,-31.04,0,1,0,-30.919,0,0,1,-36.842
> fitmap #10 inMap #1
Fit map POPE_C6_P58_J139_004_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 167755 points
correlation = 0.8519, correlation about mean = 0.6055, overlap = 1.435e+04
steps = 96, shift = 4.4, angle = 4.96 degrees
Position of POPE_C6_P58_J139_004_volume_map_sharp.mrc (#10) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40724988 0.91331678 -0.00006463 -16.33373300
-0.91331677 0.40724988 0.00012957 240.84693588
0.00014466 0.00000627 1.00000000 30.29928277
Axis -0.00006750 -0.00011458 -0.99999999
Axis point 177.37941548 133.00691898 0.00000000
Rotation angle (degrees) 65.96780711
Shift along axis -30.32577607
> fitmap #10 inMap #1
Fit map POPE_C6_P58_J139_004_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 167755 points
correlation = 0.8519, correlation about mean = 0.6055, overlap = 1.435e+04
steps = 24, shift = 0.000953, angle = 0.000902 degrees
Position of POPE_C6_P58_J139_004_volume_map_sharp.mrc (#10) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40724981 0.91331681 -0.00007833 -16.33268604
-0.91331680 0.40724981 0.00012179 240.84781521
0.00014313 0.00002194 1.00000000 30.29759993
Axis -0.00005466 -0.00012124 -0.99999999
Axis point 177.38064010 133.00615026 0.00000000
Rotation angle (degrees) 65.96781144
Shift along axis -30.32590659
> fitmap #10 inMap #1
Fit map POPE_C6_P58_J139_004_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 167755 points
correlation = 0.8519, correlation about mean = 0.6055, overlap = 1.435e+04
steps = 28, shift = 0.0256, angle = 0.0123 degrees
Position of POPE_C6_P58_J139_004_volume_map_sharp.mrc (#10) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40724998 0.91331674 0.00004186 -16.33362864
-0.91331673 0.40724999 -0.00005652 240.85258712
-0.00006867 -0.00001521 1.00000000 30.33231112
Axis 0.00002262 0.00006051 -1.00000000
Axis point 177.38930036 133.01021389 0.00000000
Rotation angle (degrees) 65.96780026
Shift along axis -30.31810719
> fitmap #10 inMap #1
Fit map POPE_C6_P58_J139_004_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 167755 points
correlation = 0.8519, correlation about mean = 0.6055, overlap = 1.435e+04
steps = 24, shift = 0.000526, angle = 5.42e-05 degrees
Position of POPE_C6_P58_J139_004_volume_map_sharp.mrc (#10) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40725023 0.91331663 0.00004113 -16.33323622
-0.91331663 0.40725023 -0.00005707 240.85258075
-0.00006887 -0.00001432 1.00000000 30.33263857
Axis 0.00002340 0.00006022 -1.00000000
Axis point 177.38955117 133.00988947 0.00000000
Rotation angle (degrees) 65.96778497
Shift along axis -30.31851570
> fitmap #10 inMap #1
Fit map POPE_C6_P58_J139_004_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 167755 points
correlation = 0.8519, correlation about mean = 0.6055, overlap = 1.435e+04
steps = 28, shift = 0.0255, angle = 0.0124 degrees
Position of POPE_C6_P58_J139_004_volume_map_sharp.mrc (#10) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40725004 0.91331671 -0.00010544 -16.33088750
-0.91331670 0.40725005 0.00010111 240.84833378
0.00013528 0.00005512 1.00000000 30.29372574
Axis -0.00002518 -0.00013178 -0.99999999
Axis point 177.38219105 133.00417905 0.00000000
Rotation angle (degrees) 65.96779684
Shift along axis -30.32505420
> select clear
> hide #!10 models
> hide #!9 models
> show #!9 models
> show #!10 models
> volume #10 level 0.9296
> hide #!10 models
> rename #14 id #13
> rename #15 id #15
> select clear
> hide #!9 models
> show #!9 models
> show #!10 models
> hide #!9 models
> volume #10 level 0.6164
> hide #!10 models
> show #!13 models
> volume #13 level 0.1911
> show #!15 models
> hide #!13 models
> volume #15 level 0.2058
> rename #13 id #40
> rename #15 id 41
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/M257_POPE_C6_P38_J358_sharp.mrc"
Opened M257_POPE_C6_P38_J358_sharp.mrc as #11, grid size 360,360,360, pixel
0.842, shown at level 0.058, step 2, values float32
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/M257_POPE_C2_P38_J250_sharp.mrc"
Opened M257_POPE_C2_P38_J250_sharp.mrc as #12, grid size 360,360,360, pixel
0.842, shown at level 0.143, step 2, values float32
> rename #11 id #14
> rename #40 id #13
> color #12 #ffaa00ff models
> close #13
> close #41
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/M257_POPE_C6_P38_J358.mrc"
Opened M257_POPE_C6_P38_J358.mrc as #11, grid size 360,360,360, pixel 0.842,
shown at level 0.0553, step 2, values float32
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/M257_POPE_C2_P38_J250.mrc"
Opened M257_POPE_C2_P38_J250.mrc as #13, grid size 360,360,360, pixel 0.842,
shown at level 0.129, step 2, values float32
> rename #13 id #15
> rename #14 id #16
> color #15 #aaff7fff models
> color #16 #aaff7fff models
> volume #15 level 0.1735
> volume #16 level 0.1266
> fitmap #15 inMap #1
Fit map M257_POPE_C2_P38_J250.mrc in map WT_PIP2_P68_J150_009_volume_map.mrc
using 26700 points
correlation = 0.6703, correlation about mean = 0.1306, overlap = 466.9
steps = 400, shift = 58.1, angle = 7.22 degrees
Position of M257_POPE_C2_P38_J250.mrc (#15) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.28988954 0.95011652 -0.11507676 19.15503782
-0.95455232 0.29573099 0.03705497 259.22658207
0.06923830 0.09910494 0.99266524 5.03668678
Axis 0.03240932 -0.09626959 -0.99482752
Axis point 183.20058378 115.76111380 0.00000000
Rotation angle (degrees) 73.19335142
Shift along axis -29.34546976
> show #!1 models
> hide #!12 models
> hide #!11 models
> hide #!16 models
> ui mousemode right "translate selected models"
> select add #15
2 models selected
> view matrix models
> #15,0.99688,0.030996,-0.072617,-33.381,-0.037962,0.9946,-0.096602,-23.347,0.06923,0.099057,0.99267,-66.479
> fitmap #15 inMap #1
Fit map M257_POPE_C2_P38_J250.mrc in map WT_PIP2_P68_J150_009_volume_map.mrc
using 26700 points
correlation = 0.8496, correlation about mean = 0.4508, overlap = 891.5
steps = 212, shift = 5.77, angle = 19.9 degrees
Position of M257_POPE_C2_P38_J250.mrc (#15) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.02787624 0.99961136 0.00023720 22.38512496
-0.99961137 -0.02787620 -0.00017883 325.25294858
-0.00017216 -0.00024209 0.99999996 24.44944515
Axis -0.00003164 0.00020476 -0.99999998
Axis point 169.34912853 151.74456635 0.00000000
Rotation angle (degrees) 91.59739769
Shift along axis -24.38355454
> show #!16 models
> hide #!15 models
> show #!15 models
> select add #16
4 models selected
> select subtract #15
2 models selected
> view matrix models #16,1,0,0,-61.472,0,1,0,17.627,0,0,1,3.8232
> view matrix models #16,1,0,0,-43.151,0,1,0,9.9238,0,0,1,-45.465
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.8025,0.5874,0.1047,125.18,0.59457,0.80194,0.05808,-58.854,-0.049848,0.10886,-0.99281,244.74
> view matrix models
> #16,-0.89785,-0.40706,-0.16782,331.17,-0.39891,0.91338,-0.081244,95.663,0.18635,-0.0060006,-0.98246,224.8
> view matrix models
> #16,-0.86924,-0.47691,0.13032,292.66,-0.4762,0.87849,0.038562,94.67,-0.13287,-0.028538,-0.99072,277.81
> view matrix models
> #16,-0.86998,-0.28295,-0.40382,343.57,-0.47983,0.67444,0.56116,47.68,0.11357,0.68196,-0.72252,92.603
> view matrix models
> #16,-0.99975,-0.0045195,0.021975,257.14,0.01204,0.7184,0.69553,-53.651,-0.01893,0.69562,-0.71817,109.95
> view matrix models
> #16,-0.99712,0.069303,0.030949,244.21,0.065784,0.9925,-0.10303,16.561,-0.037857,-0.10069,-0.9942,274.87
> view matrix models
> #16,-0.99286,0.078246,-0.090086,260.38,0.061469,0.98249,0.17589,-23.138,0.10227,0.1691,-0.98028,210.69
> view matrix models
> #16,-0.97409,0.11976,-0.19183,266.52,0.073706,0.97007,0.23137,-31.437,0.2138,0.21123,-0.95377,183.43
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.97409,0.11976,-0.19183,266.33,0.073706,0.97007,0.23137,-88.807,0.2138,0.21123,-0.95377,197.54
> fitmap #15 inMap #1
Fit map M257_POPE_C2_P38_J250.mrc in map WT_PIP2_P68_J150_009_volume_map.mrc
using 26700 points
correlation = 0.8496, correlation about mean = 0.4508, overlap = 891.5
steps = 40, shift = 0.0151, angle = 0.0354 degrees
Position of M257_POPE_C2_P38_J250.mrc (#15) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.02787659 0.99961133 -0.00031896 22.45324025
-0.99961137 -0.02787656 0.00009055 325.22044868
0.00008162 0.00032137 0.99999995 24.32566065
Axis 0.00011546 -0.00020037 -0.99999997
Axis point 169.36431373 151.68851472 0.00000000
Rotation angle (degrees) 91.59741848
Shift along axis -24.38823136
> volume #16 level 0.2367
> volume #15 level 0.2434
> select clear
> color #16 #ffaa00ff models
> color #12 #55ff7fff models
> color #12 #aaff7fff models
> hide #!15 models
> select add #16
2 models selected
> select subtract #16
Nothing selected
> rename #11 id #13
> rename #16 id #14
> color #13 #ffaa00ff models
> rename #12 id #16
> hide #!14 models
> show #!13 models
> volume #13 level 0.1701
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select add #13
2 models selected
> view matrix models
> #13,0.75398,-0.65649,0.023084,133.21,-0.62269,-0.70308,0.34341,300.32,-0.20922,-0.2733,-0.9389,366.51
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.75398,-0.65649,0.023084,109.17,-0.62269,-0.70308,0.34341,286.81,-0.20922,-0.2733,-0.9389,300.44
> view matrix models
> #13,0.75398,-0.65649,0.023084,90.458,-0.62269,-0.70308,0.34341,250.69,-0.20922,-0.2733,-0.9389,297.65
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.97303,-0.22936,0.024715,-7.6663,-0.23068,-0.96784,0.10034,268.2,0.00090721,-0.10333,-0.99465,248.52
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.97303,-0.22936,0.024715,-5.5313,-0.23068,-0.96784,0.10034,269.59,0.00090721,-0.10333,-0.99465,265.75
> view matrix models
> #13,0.97303,-0.22936,0.024715,-8.676,-0.23068,-0.96784,0.10034,272.95,0.00090721,-0.10333,-0.99465,266.23
> fitmap #13 inMap #1
Fit map M257_POPE_C6_P38_J358.mrc in map WT_PIP2_P68_J150_009_volume_map.mrc
using 20237 points
correlation = 0.8865, correlation about mean = 0.5322, overlap = 771.4
steps = 84, shift = 2.03, angle = 8.19 degrees
Position of M257_POPE_C6_P38_J358.mrc (#13) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.19754912 -0.98029299 -0.00001922 288.16928350
-0.98029299 -0.19754913 0.00010596 347.98513192
-0.00010768 -0.00000210 -1.00000000 323.42067267
Axis -0.77380399 0.63342512 0.00003299
Axis point 0.00000000 291.94553300 161.70859199
Rotation angle (degrees) 179.99599929
Shift along axis -2.55335028
> fitmap #13 inMap #1
Fit map M257_POPE_C6_P38_J358.mrc in map WT_PIP2_P68_J150_009_volume_map.mrc
using 20237 points
correlation = 0.8865, correlation about mean = 0.5322, overlap = 771.4
steps = 28, shift = 0.015, angle = 0.0136 degrees
Position of M257_POPE_C6_P38_J358.mrc (#13) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.19751744 -0.98029937 0.00008365 288.14830986
-0.98029937 -0.19751746 -0.00010525 348.02394264
0.00011970 -0.00006122 -0.99999999 323.39543721
Axis 0.77379809 -0.63343233 0.00004606
Axis point 0.00000000 291.94832787 161.69235608
Rotation angle (degrees) 179.99836980
Shift along axis 2.53389110
> select clear
> hide #!13 models
> show #!14 models
> ui mousemode right "translate selected models"
> select add #14
2 models selected
> view matrix models
> #14,-0.97409,0.11976,-0.19183,273.04,0.073706,0.97007,0.23137,-87.933,0.2138,0.21123,-0.95377,170.1
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.96857,-0.23903,0.068866,286.42,-0.22226,0.9559,0.19197,-34.895,-0.11172,0.17063,-0.97898,229.44
> view matrix models
> #14,-0.92822,-0.37102,-0.02739,315.12,-0.36956,0.92803,-0.04677,28.384,0.042771,-0.03329,-0.99853,239.93
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.92822,-0.37102,-0.02739,307.68,-0.36956,0.92803,-0.04677,35.167,0.042771,-0.03329,-0.99853,246.88
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.97786,0.10238,-0.1825,267.37,0.10412,0.99456,4.6048e-05,-53.866,0.18152,-0.018958,-0.9832,221.34
> view matrix models
> #14,-0.98765,0.15258,-0.035492,238.62,0.15589,0.97962,-0.12668,-39.938,0.01544,-0.13065,-0.99131,264.66
> fitmap #13 inMap #1
Fit map M257_POPE_C6_P38_J358.mrc in map WT_PIP2_P68_J150_009_volume_map.mrc
using 20237 points
correlation = 0.8865, correlation about mean = 0.5321, overlap = 771.4
steps = 28, shift = 0.0161, angle = 0.016 degrees
Position of M257_POPE_C6_P38_J358.mrc (#13) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.19764340 -0.98027398 -0.00010503 288.16975596
-0.98027399 -0.19764340 0.00005489 348.00977141
-0.00007457 0.00009210 -1.00000000 323.40169742
Axis 0.77383935 -0.63338192 -0.00008128
Axis point 0.00000000 291.93480665 161.71869809
Rotation angle (degrees) 179.99862237
Shift along axis 2.54771226
> fitmap #14 inMap #1
Fit map M257_POPE_C6_P38_J358_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 14513 points
correlation = 0.9138, correlation about mean = 0.5534, overlap = 924.7
steps = 84, shift = 5.53, angle = 7.65 degrees
Position of M257_POPE_C6_P38_J358_sharp.mrc (#14) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.19704167 0.98039513 0.00002225 50.94052243
0.98039513 0.19704167 0.00005015 -8.75807320
0.00004479 0.00003170 -1.00000001 323.22621751
Axis -0.63351529 -0.77373017 -0.00006385
Axis point 29.05421019 0.00000000 161.61363379
Rotation angle (degrees) 179.99916532
Shift along axis -25.51585069
> select clear
> show #!13 models
> hide #!13 models
> hide #!14 models
> show #!15 models
> fitmap #15 inMap #1
Fit map M257_POPE_C2_P38_J250.mrc in map WT_PIP2_P68_J150_009_volume_map.mrc
using 12078 points
correlation = 0.8441, correlation about mean = 0.3777, overlap = 657.2
steps = 44, shift = 0.021, angle = 0.0332 degrees
Position of M257_POPE_C2_P38_J250.mrc (#15) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.02757911 0.99961962 0.00016019 22.35205544
-0.99961963 -0.02757911 -0.00003857 325.19101448
-0.00003414 -0.00016118 0.99999999 24.43275705
Axis -0.00006133 0.00009720 -0.99999999
Axis point 169.34786532 151.72548434 0.00000000
Rotation angle (degrees) 91.58036713
Shift along axis -24.40251912
> fitmap #15 inMap #1
Fit map M257_POPE_C2_P38_J250.mrc in map WT_PIP2_P68_J150_009_volume_map.mrc
using 12078 points
correlation = 0.8441, correlation about mean = 0.3777, overlap = 657.2
steps = 48, shift = 0.00239, angle = 0.0155 degrees
Position of M257_POPE_C2_P38_J250.mrc (#15) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.02761648 0.99961859 -0.00008572 22.39020609
-0.99961860 -0.02761647 0.00006611 325.18094660
0.00006372 0.00008752 1.00000000 24.38059754
Axis 0.00001071 -0.00007475 -1.00000000
Axis point 169.35496789 151.69934766 0.00000000
Rotation angle (degrees) 91.58250870
Shift along axis -24.40466425
> fitmap #15 inMap #1
Fit map M257_POPE_C2_P38_J250.mrc in map WT_PIP2_P68_J150_009_volume_map.mrc
using 12078 points
correlation = 0.8441, correlation about mean = 0.3777, overlap = 657.2
steps = 48, shift = 0.0155, angle = 0.0106 degrees
Position of M257_POPE_C2_P38_J250.mrc (#15) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.02761734 0.99961857 0.00008108 22.35558760
-0.99961857 -0.02761734 -0.00001450 325.20292140
-0.00001226 -0.00008145 1.00000000 24.41756722
Axis -0.00003349 0.00004669 -1.00000000
Axis point 169.34911232 151.72918786 0.00000000
Rotation angle (degrees) 91.58255802
Shift along axis -24.40313236
> show #!16 models
> hide #!15 models
> volume #16 level 0.3693
> volume #16 step 1
> volume #13 step 1
> volume #15 step 1
> volume #14 step 1
> ui mousemode right "translate selected models"
> select add #16
2 models selected
> view matrix models #16,1,0,0,-56.595,0,1,0,-71.964,0,0,1,-51.988
> view matrix models #16,1,0,0,-38.296,0,1,0,-43.509,0,0,1,-54.146
> show #!15 models
> hide #!16 models
> hide #!1 models
> show #!16 models
> hide #!15 models
> ui mousemode right "rotate selected models"
> show #!1 models
> view matrix models
> #16,0.99746,0.014917,-0.06972,-30.19,0.00098553,0.97489,0.22268,-71.728,0.071291,-0.22218,0.97239,-27.339
> view matrix models
> #16,0.96319,0.26875,0.0062593,-74.323,-0.26314,0.9378,0.22648,-26.646,0.054996,-0.21979,0.974,-25.463
> view matrix models
> #16,0.95851,0.2539,0.12956,-89.014,-0.24533,0.96625,-0.078561,10.008,-0.14514,0.043517,0.98845,-37.101
> view matrix models
> #16,0.9422,0.30956,0.12816,-94.774,-0.30024,0.94988,-0.087065,22.022,-0.14869,0.043554,0.98792,-36.493
> fitmap #16 inMap #1
Fit map M257_POPE_C2_P38_J250_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 97390 points
correlation = 0.8266, correlation about mean = 0.4255, overlap = 9653
steps = 128, shift = 8.44, angle = 9.38 degrees
Position of M257_POPE_C2_P38_J250_sharp.mrc (#16) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.02937989 0.99956832 -0.00004198 22.64451997
-0.99956832 -0.02937988 0.00009607 325.44925760
0.00009479 0.00004479 1.00000000 24.31347886
Axis -0.00002565 -0.00006841 -1.00000000
Axis point 169.33314922 151.72974080 0.00000000
Rotation angle (degrees) 91.68358562
Shift along axis -24.33632496
> fitmap #16 inMap #1
Fit map M257_POPE_C2_P38_J250_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 97390 points
correlation = 0.8266, correlation about mean = 0.4255, overlap = 9653
steps = 44, shift = 0.00244, angle = 0.00363 degrees
Position of M257_POPE_C2_P38_J250_sharp.mrc (#16) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.02939108 0.99956799 -0.00008000 22.65073339
-0.99956799 -0.02939107 0.00004669 325.45628025
0.00004431 0.00008134 1.00000000 24.31726615
Axis 0.00001733 -0.00006218 -1.00000000
Axis point 169.33849179 151.72992629 0.00000000
Rotation angle (degrees) 91.68422710
Shift along axis -24.33711119
> fitmap #16 inMap #1
Fit map M257_POPE_C2_P38_J250_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 97390 points
correlation = 0.8266, correlation about mean = 0.4255, overlap = 9653
steps = 40, shift = 0.00757, angle = 0.0192 degrees
Position of M257_POPE_C2_P38_J250_sharp.mrc (#16) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.02940695 0.99956751 0.00020425 22.61918385
-0.99956752 -0.02940692 -0.00012852 325.47853288
-0.00012246 -0.00020794 0.99999998 24.38492306
Axis -0.00003973 0.00016343 -0.99999999
Axis point 169.33298329 151.75996741 0.00000000
Rotation angle (degrees) 91.68513674
Shift along axis -24.33262966
> select clear
> hide #!16 models
> show #!2 models
> fitmap #2 inMap #1
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 99815 points
correlation = 0.971, correlation about mean = 0.8368, overlap = 7480
steps = 24, shift = 0.000714, angle = 0.00187 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#2) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.49984045 0.86611751 0.00001377 -62.06623734
-0.86611750 0.49984044 0.00017121 231.70221565
0.00014140 -0.00009750 0.99999999 -0.01055102
Axis -0.00015512 -0.00007368 -0.99999999
Axis point 169.58420822 169.59061359 0.00000000
Rotation angle (degrees) 60.01055616
Shift along axis 0.00310696
> fitmap #2 inMap #1
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 99815 points
correlation = 0.971, correlation about mean = 0.8368, overlap = 7479
steps = 24, shift = 0.000569, angle = 0.00185 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#2) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.49984269 0.86611621 0.00002298 -62.06746585
-0.86611620 0.49984268 0.00020203 231.69672752
0.00016349 -0.00012088 0.99999999 -0.01035222
Axis -0.00018641 -0.00008111 -0.99999998
Axis point 169.57944127 169.58909363 0.00000000
Rotation angle (degrees) 60.01040829
Shift along axis 0.00312904
> fitmap #2 inMap #1
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 99815 points
correlation = 0.971, correlation about mean = 0.8368, overlap = 7479
steps = 24, shift = 0.000571, angle = 0.00227 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#2) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.49983636 0.86611986 0.00003776 -62.06897327
-0.86611984 0.49983634 0.00023802 231.69257404
0.00018727 -0.00015167 0.99999998 -0.00922210
Axis -0.00022496 -0.00008631 -0.99999997
Axis point 169.57339967 169.58786874 0.00000000
Rotation angle (degrees) 60.01082718
Shift along axis 0.00318786
> hide #!2 models
> hide #!1 models
> show #!3 models
> show #!4 models
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12433 points
correlation = 0.9589, correlation about mean = 0.7487, overlap = 1063
steps = 40, shift = 0.0318, angle = 0.0883 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999985 0.00055119 0.00000194 -0.09240209
-0.00055119 0.99999985 0.00001029 0.08196583
-0.00000193 -0.00001030 1.00000000 -0.01614407
Axis -0.01867502 0.00351206 -0.99981944
Axis point 148.54625996 167.06801976 0.00000000
Rotation angle (degrees) 0.03158636
Shift along axis 0.01815463
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12433 points
correlation = 0.9589, correlation about mean = 0.7487, overlap = 1063
steps = 24, shift = 0.000825, angle = 0.00129 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999986 0.00054230 0.00000090 -0.09036619
-0.00054230 0.99999986 -0.00001041 0.08349549
-0.00000091 0.00001041 1.00000000 -0.02041424
Axis 0.01919107 0.00166384 -0.99981445
Axis point 153.86180876 167.34197317 0.00000000
Rotation angle (degrees) 0.03107739
Shift along axis 0.01881515
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12433 points
correlation = 0.9589, correlation about mean = 0.7487, overlap = 1063
steps = 24, shift = 0.000975, angle = 0.00108 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999986 0.00053936 0.00000209 -0.09020968
-0.00053936 0.99999986 -0.00002903 0.08503506
-0.00000211 0.00002903 1.00000000 -0.02353809
Axis 0.05374507 0.00389170 -0.99854711
Axis point 157.47686114 169.18801060 0.00000000
Rotation angle (degrees) 0.03094794
Shift along axis 0.01898650
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12433 points
correlation = 0.9588, correlation about mean = 0.7486, overlap = 1063
steps = 24, shift = 0.00106, angle = 0.00104 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999986 0.00053736 0.00000315 -0.09010829
-0.00053736 0.99999986 -0.00004696 0.08652138
-0.00000317 0.00004696 1.00000000 -0.02656146
Axis 0.08705806 0.00586040 -0.99618600
Axis point 160.75791326 170.82903542 0.00000000
Rotation angle (degrees) 0.03090619
Shift along axis 0.01912255
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12433 points
correlation = 0.9588, correlation about mean = 0.7485, overlap = 1063
steps = 24, shift = 0.0014, angle = 0.000995 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999986 0.00053691 0.00000234 -0.09025616
-0.00053690 0.99999986 -0.00006430 0.08825050
-0.00000238 0.00006430 1.00000000 -0.03053340
Axis 0.11891351 0.00435981 -0.99289504
Axis point 164.15968367 172.57106631 0.00000000
Rotation angle (degrees) 0.03098255
Shift along axis 0.01996854
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12433 points
correlation = 0.9588, correlation about mean = 0.7486, overlap = 1063
steps = 28, shift = 0.0236, angle = 0.0132 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999989 0.00046570 -0.00001470 -0.07453313
-0.00046570 0.99999988 0.00015418 0.06520726
0.00001477 -0.00015417 0.99999999 0.00227487
Axis -0.31413567 -0.03002360 -0.94890324
Axis point 141.22543473 147.06022233 0.00000000
Rotation angle (degrees) 0.02811964
Shift along axis 0.01929713
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12433 points
correlation = 0.9589, correlation about mean = 0.7487, overlap = 1063
steps = 28, shift = 0.0235, angle = 0.0233 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999989 0.00047905 0.00002003 -0.08305500
-0.00047905 0.99999986 -0.00025013 0.10836878
-0.00002016 0.00025012 0.99999997 -0.05793683
Axis 0.46251908 0.03715812 -0.88583033
Axis point 224.84576409 189.77740570 0.00000000
Rotation angle (degrees) 0.03098511
Shift along axis 0.01693446
> hide #!4 models
> hide #!3 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!6 models
> fitmap #6 inMap #5
Fit map N55H_CBX_P52_J650_003_volume_map_sharp.mrc in map
N55H_CBX_P52_J650_003_volume_map.mrc using 82839 points
correlation = 0.9775, correlation about mean = 0.7763, overlap = 3190
steps = 60, shift = 0.262, angle = 0.175 degrees
Position of N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) relative to
N55H_CBX_P52_J650_003_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
0.99999999 0.00013389 0.00000625 -0.01917133
-0.00013389 0.99999999 0.00000271 0.02873917
-0.00000625 -0.00000271 1.00000000 -0.01741979
Axis -0.02022973 0.04661059 -0.99870827
Axis point 207.98263717 140.31306037 0.00000000
Rotation angle (degrees) 0.00768117
Shift along axis 0.01912467
> fitmap #6 inMap #5
Fit map N55H_CBX_P52_J650_003_volume_map_sharp.mrc in map
N55H_CBX_P52_J650_003_volume_map.mrc using 82839 points
correlation = 0.9776, correlation about mean = 0.7766, overlap = 3191
steps = 44, shift = 0.0148, angle = 0.00826 degrees
Position of N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) relative to
N55H_CBX_P52_J650_003_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
1.00000000 -0.00000858 -0.00001115 0.00192696
0.00000858 1.00000000 -0.00001145 -0.00647080
0.00001115 0.00001145 1.00000000 -0.02181622
Axis 0.63132344 -0.61450785 0.47308649
Axis point -0.00000000 1692.86492808 -840.06636952
Rotation angle (degrees) 0.00103951
Shift along axis -0.00512806
> fitmap #6 inMap #5
Fit map N55H_CBX_P52_J650_003_volume_map_sharp.mrc in map
N55H_CBX_P52_J650_003_volume_map.mrc using 82839 points
correlation = 0.9775, correlation about mean = 0.7758, overlap = 3188
steps = 28, shift = 0.0214, angle = 0.0106 degrees
Position of N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) relative to
N55H_CBX_P52_J650_003_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
0.99999999 0.00017015 0.00001754 -0.03173266
-0.00017015 0.99999999 0.00002805 0.03841492
-0.00001753 -0.00002806 1.00000000 -0.01165769
Axis -0.16185045 0.10117054 -0.98161548
Axis point 213.58301363 167.04604809 0.00000000
Rotation angle (degrees) 0.00993165
Shift along axis 0.02046577
> fitmap #6 inMap #5
Fit map N55H_CBX_P52_J650_003_volume_map_sharp.mrc in map
N55H_CBX_P52_J650_003_volume_map.mrc using 82839 points
correlation = 0.9775, correlation about mean = 0.7763, overlap = 3190
steps = 40, shift = 0.0225, angle = 0.00516 degrees
Position of N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) relative to
N55H_CBX_P52_J650_003_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
0.99999997 0.00022898 -0.00002173 -0.03518817
-0.00022898 0.99999997 -0.00002756 0.03441227
0.00002173 0.00002757 1.00000000 -0.02690326
Axis 0.11899632 -0.09379608 -0.98845444
Axis point 158.12166382 163.65845403 0.00000000
Rotation angle (degrees) 0.01327282
Shift along axis 0.01917765
> fitmap #6 inMap #5
Fit map N55H_CBX_P52_J650_003_volume_map_sharp.mrc in map
N55H_CBX_P52_J650_003_volume_map.mrc using 82839 points
correlation = 0.9775, correlation about mean = 0.7761, overlap = 3189
steps = 28, shift = 0.0219, angle = 0.0127 degrees
Position of N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) relative to
N55H_CBX_P52_J650_003_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
1.00000000 0.00001507 0.00001440 -0.00479665
-0.00001507 1.00000000 0.00002131 0.01303426
-0.00001440 -0.00002131 1.00000000 -0.01115593
Axis -0.71497916 0.48301444 -0.50547191
Axis point 0.00000000 -159.06759722 -263.41424560
Rotation angle (degrees) 0.00170765
Shift along axis 0.01536425
> fitmap #6 inMap #5
Fit map N55H_CBX_P52_J650_003_volume_map_sharp.mrc in map
N55H_CBX_P52_J650_003_volume_map.mrc using 82839 points
correlation = 0.9776, correlation about mean = 0.7764, overlap = 3190
steps = 40, shift = 0.0213, angle = 0.00855 degrees
Position of N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) relative to
N55H_CBX_P52_J650_003_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
0.99999999 0.00015851 -0.00000937 -0.02502099
-0.00015851 0.99999999 -0.00001263 0.02095367
0.00000937 0.00001263 1.00000000 -0.02243841
Axis 0.07929327 -0.05881619 -0.99511468
Axis point 139.27027763 167.42364491 0.00000000
Rotation angle (degrees) 0.00912651
Shift along axis 0.01911238
> fitmap #6 inMap #5
Fit map N55H_CBX_P52_J650_003_volume_map_sharp.mrc in map
N55H_CBX_P52_J650_003_volume_map.mrc using 82839 points
correlation = 0.9776, correlation about mean = 0.7764, overlap = 3190
steps = 28, shift = 0.0177, angle = 0.00819 degrees
Position of N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) relative to
N55H_CBX_P52_J650_003_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
1.00000000 0.00001859 0.00000813 -0.00392441
-0.00001859 1.00000000 0.00001118 0.01165082
-0.00000813 -0.00001118 1.00000000 -0.01443627
Axis -0.48247479 0.35096052 -0.80252402
Axis point 294.99137908 -244.78073583 0.00000000
Rotation angle (degrees) 0.00132755
Shift along axis 0.01756785
> fitmap #6 inMap #5
Fit map N55H_CBX_P52_J650_003_volume_map_sharp.mrc in map
N55H_CBX_P52_J650_003_volume_map.mrc using 82839 points
correlation = 0.9776, correlation about mean = 0.7766, overlap = 3191
steps = 40, shift = 0.0151, angle = 0.00797 degrees
Position of N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) relative to
N55H_CBX_P52_J650_003_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
0.99999999 0.00015625 -0.00000385 -0.02537294
-0.00015625 0.99999999 -0.00000521 0.02198442
0.00000385 0.00000521 1.00000000 -0.02006773
Axis 0.03329683 -0.02461891 -0.99914225
Axis point 143.62414402 166.37091649 0.00000000
Rotation angle (degrees) 0.00896040
Shift along axis 0.01866445
> fitmap #6 inMap #5
Fit map N55H_CBX_P52_J650_003_volume_map_sharp.mrc in map
N55H_CBX_P52_J650_003_volume_map.mrc using 82839 points
correlation = 0.9775, correlation about mean = 0.7762, overlap = 3190
steps = 28, shift = 0.0156, angle = 0.00993 degrees
Position of N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) relative to
N55H_CBX_P52_J650_003_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
1.00000000 -0.00001419 0.00001688 0.00141571
0.00001419 1.00000000 0.00001789 0.00557351
-0.00001688 -0.00001789 1.00000000 -0.01310405
Axis -0.62991864 0.59444727 0.49983492
Axis point 0.00000000 -617.17708422 -448.76557029
Rotation angle (degrees) 0.00162710
Shift along axis -0.00412848
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!8 models
> show #!7 models
> hide #!8 models
> hide #!7 models
> show #!8 models
> fitmap #8 inMap #7
Fit map MBCD_P41_J50_013_volume_map_sharp.mrc in map
MBCD_P41_J50_013_volume_map.mrc using 167414 points
correlation = 0.9592, correlation about mean = 0.8729, overlap = 6878
steps = 28, shift = 0.0112, angle = 0.0226 degrees
Position of MBCD_P41_J50_013_volume_map_sharp.mrc (#8) relative to
MBCD_P41_J50_013_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
1.00000000 0.00004752 -0.00000058 -0.00508582
-0.00004752 1.00000000 -0.00000002 0.00516433
0.00000058 0.00000002 1.00000000 0.00077921
Axis 0.00042198 -0.01223589 -0.99992505
Axis point 108.45586571 107.01873636 0.00000000
Rotation angle (degrees) 0.00272293
Shift along axis -0.00084449
> fitmap #8 inMap #7
Fit map MBCD_P41_J50_013_volume_map_sharp.mrc in map
MBCD_P41_J50_013_volume_map.mrc using 167414 points
correlation = 0.9591, correlation about mean = 0.8727, overlap = 6872
steps = 24, shift = 0.00284, angle = 0.00995 degrees
Position of MBCD_P41_J50_013_volume_map_sharp.mrc (#8) relative to
MBCD_P41_J50_013_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.99999999 -0.00012620 0.00000067 0.01376194
0.00012620 0.99999999 0.00000089 -0.01369917
-0.00000068 -0.00000089 1.00000000 0.00384887
Axis -0.00706566 0.00534856 0.99996073
Axis point 108.71746430 109.25109556 0.00000000
Rotation angle (degrees) 0.00723079
Shift along axis 0.00367821
> fitmap #8 inMap #7
Fit map MBCD_P41_J50_013_volume_map_sharp.mrc in map
MBCD_P41_J50_013_volume_map.mrc using 167414 points
correlation = 0.9591, correlation about mean = 0.8725, overlap = 6866
steps = 24, shift = 0.00344, angle = 0.00354 degrees
Position of MBCD_P41_J50_013_volume_map_sharp.mrc (#8) relative to
MBCD_P41_J50_013_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.99999998 -0.00018790 0.00000038 0.02060857
0.00018790 0.99999998 0.00000079 -0.02029832
-0.00000038 -0.00000079 1.00000000 0.00724350
Axis -0.00423058 0.00203756 0.99998898
Axis point 108.11568794 109.82940882 0.00000000
Rotation angle (degrees) 0.01076590
Shift along axis 0.00711487
> fitmap #8 inMap #7
Fit map MBCD_P41_J50_013_volume_map_sharp.mrc in map
MBCD_P41_J50_013_volume_map.mrc using 167414 points
correlation = 0.959, correlation about mean = 0.8723, overlap = 6858
steps = 28, shift = 0.0248, angle = 0.0164 degrees
Position of MBCD_P41_J50_013_volume_map_sharp.mrc (#8) relative to
MBCD_P41_J50_013_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
1.00000000 0.00009869 -0.00000252 -0.01057560
-0.00009869 1.00000000 -0.00000236 0.01088564
0.00000252 0.00000236 1.00000000 -0.01818008
Axis 0.02391665 -0.02549781 -0.99938874
Axis point 114.85175271 111.43883942 0.00000000
Rotation angle (degrees) 0.00565804
Shift along axis 0.01763848
> fitmap #8 inMap #7
Fit map MBCD_P41_J50_013_volume_map_sharp.mrc in map
MBCD_P41_J50_013_volume_map.mrc using 167414 points
correlation = 0.959, correlation about mean = 0.8723, overlap = 6858
steps = 24, shift = 0.000193, angle = 0.000916 degrees
Position of MBCD_P41_J50_013_volume_map_sharp.mrc (#8) relative to
MBCD_P41_J50_013_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.99999999 0.00010106 -0.00001826 -0.00936267
-0.00010106 0.99999999 -0.00000090 0.01112222
0.00001826 0.00000091 1.00000000 -0.01984722
Axis 0.00880526 -0.17778757 -0.98402949
Axis point 140.78936883 94.17692744 0.00000000
Rotation angle (degrees) 0.00588412
Shift along axis 0.01747042
> fitmap #8 inMap #7
Fit map MBCD_P41_J50_013_volume_map_sharp.mrc in map
MBCD_P41_J50_013_volume_map.mrc using 167414 points
correlation = 0.959, correlation about mean = 0.8723, overlap = 6858
steps = 24, shift = 0.00062, angle = 0.00205 degrees
Position of MBCD_P41_J50_013_volume_map_sharp.mrc (#8) relative to
MBCD_P41_J50_013_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
1.00000000 0.00008611 -0.00003194 -0.00654472
-0.00008611 1.00000000 0.00002854 0.00713335
0.00003194 -0.00002854 1.00000000 -0.01837319
Axis -0.29671287 -0.33211949 -0.89535363
Axis point 144.63529658 20.79829810 0.00000000
Rotation angle (degrees) 0.00551057
Shift along axis 0.01602328
> fitmap #8 inMap #7
Fit map MBCD_P41_J50_013_volume_map_sharp.mrc in map
MBCD_P41_J50_013_volume_map.mrc using 167414 points
correlation = 0.9591, correlation about mean = 0.8725, overlap = 6867
steps = 28, shift = 0.0241, angle = 0.0162 degrees
Position of MBCD_P41_J50_013_volume_map_sharp.mrc (#8) relative to
MBCD_P41_J50_013_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.99999998 -0.00019310 -0.00000053 0.02097956
0.00019310 0.99999998 0.00000086 -0.02098391
0.00000053 -0.00000086 1.00000000 0.00611843
Axis -0.00444030 -0.00276080 0.99998633
Axis point 108.59376973 108.77711118 0.00000000
Rotation angle (degrees) 0.01106380
Shift along axis 0.00608313
> hide #!8 models
> show #!10 models
> fitmap #10 inMap #9
Fit map POPE_C6_P58_J139_004_volume_map_sharp.mrc in map
POPE_C6_P58_J139_004_volume_map.mrc using 54922 points
correlation = 0.9074, correlation about mean = 0.5736, overlap = 5.28e+04
steps = 48, shift = 0.193, angle = 0.0568 degrees
Position of POPE_C6_P58_J139_004_volume_map_sharp.mrc (#10) relative to
POPE_C6_P58_J139_004_volume_map.mrc (#9) coordinates:
Matrix rotation and translation
0.99999997 0.00024058 -0.00004451 -0.03115888
-0.00024058 0.99999997 -0.00009998 0.03042301
0.00004448 0.00009999 0.99999999 -0.08485667
Axis 0.37830695 -0.16835513 -0.91024195
Axis point 168.64409246 224.40956528 0.00000000
Rotation angle (degrees) 0.01514332
Shift along axis 0.06033061
> fitmap #10 inMap #9
Fit map POPE_C6_P58_J139_004_volume_map_sharp.mrc in map
POPE_C6_P58_J139_004_volume_map.mrc using 54922 points
correlation = 0.9076, correlation about mean = 0.5744, overlap = 5.286e+04
steps = 40, shift = 0.019, angle = 0.00521 degrees
Position of POPE_C6_P58_J139_004_volume_map_sharp.mrc (#10) relative to
POPE_C6_P58_J139_004_volume_map.mrc (#9) coordinates:
Matrix rotation and translation
0.99999995 0.00032817 -0.00002148 -0.04324035
-0.00032817 0.99999994 -0.00009201 0.06040807
0.00002145 0.00009202 1.00000000 -0.08075426
Axis 0.26945093 -0.06285834 -0.96096047
Axis point 195.94773520 182.82735064 0.00000000
Rotation angle (degrees) 0.01956661
Shift along axis 0.06215335
> fitmap #10 inMap #9
Fit map POPE_C6_P58_J139_004_volume_map_sharp.mrc in map
POPE_C6_P58_J139_004_volume_map.mrc using 54922 points
correlation = 0.9076, correlation about mean = 0.5742, overlap = 5.284e+04
steps = 44, shift = 0.00433, angle = 0.0132 degrees
Position of POPE_C6_P58_J139_004_volume_map_sharp.mrc (#10) relative to
POPE_C6_P58_J139_004_volume_map.mrc (#9) coordinates:
Matrix rotation and translation
0.99999991 0.00041245 0.00000886 -0.05898719
-0.00041245 0.99999991 0.00012093 0.03987755
-0.00000881 -0.00012093 0.99999999 -0.04898751
Axis -0.28129795 0.02055495 -0.95940031
Axis point 93.45177575 99.10591578 0.00000000
Rotation angle (degrees) 0.02463180
Shift along axis 0.06441129
> fitmap #10 inMap #9
Fit map POPE_C6_P58_J139_004_volume_map_sharp.mrc in map
POPE_C6_P58_J139_004_volume_map.mrc using 54922 points
correlation = 0.9075, correlation about mean = 0.5741, overlap = 5.283e+04
steps = 44, shift = 0.00611, angle = 0.0115 degrees
Position of POPE_C6_P58_J139_004_volume_map_sharp.mrc (#10) relative to
POPE_C6_P58_J139_004_volume_map.mrc (#9) coordinates:
Matrix rotation and translation
0.99999992 0.00041157 -0.00002130 -0.05486735
-0.00041157 0.99999991 -0.00007805 0.07233298
0.00002127 0.00007806 1.00000000 -0.08363278
Axis 0.18608570 -0.05074224 -0.98122237
Axis point 184.11881900 164.17744867 0.00000000
Rotation angle (degrees) 0.02403261
Shift along axis 0.06818199
> fitmap #10 inMap #9
Fit map POPE_C6_P58_J139_004_volume_map_sharp.mrc in map
POPE_C6_P58_J139_004_volume_map.mrc using 54922 points
correlation = 0.9074, correlation about mean = 0.5737, overlap = 5.28e+04
steps = 40, shift = 0.0164, angle = 0.00486 degrees
Position of POPE_C6_P58_J139_004_volume_map_sharp.mrc (#10) relative to
POPE_C6_P58_J139_004_volume_map.mrc (#9) coordinates:
Matrix rotation and translation
0.99999988 0.00049596 -0.00001548 -0.06705826
-0.00049596 0.99999987 -0.00008501 0.06937561
0.00001544 0.00008502 1.00000000 -0.07945702
Axis 0.16887899 -0.03070933 -0.98515827
Axis point 143.85526683 157.31805413 0.00000000
Rotation angle (degrees) 0.02884444
Shift along axis 0.06482253
> fitmap #10 inMap #9
Fit map POPE_C6_P58_J139_004_volume_map_sharp.mrc in map
POPE_C6_P58_J139_004_volume_map.mrc using 54922 points
correlation = 0.9074, correlation about mean = 0.5736, overlap = 5.28e+04
steps = 40, shift = 0.0254, angle = 0.0105 degrees
Position of POPE_C6_P58_J139_004_volume_map_sharp.mrc (#10) relative to
POPE_C6_P58_J139_004_volume_map.mrc (#9) coordinates:
Matrix rotation and translation
0.99999988 0.00049137 0.00003641 -0.07206157
-0.00049137 0.99999988 0.00009060 0.07028528
-0.00003636 -0.00009062 1.00000000 -0.04785929
Axis -0.18086684 0.07262584 -0.98082245
Axis point 133.38971120 122.73362700 0.00000000
Rotation angle (degrees) 0.02870371
Shift along axis 0.06507955
> fitmap #10 inMap #9
Fit map POPE_C6_P58_J139_004_volume_map_sharp.mrc in map
POPE_C6_P58_J139_004_volume_map.mrc using 54922 points
correlation = 0.9076, correlation about mean = 0.5742, overlap = 5.285e+04
steps = 40, shift = 0.00953, angle = 0.0139 degrees
Position of POPE_C6_P58_J139_004_volume_map_sharp.mrc (#10) relative to
POPE_C6_P58_J139_004_volume_map.mrc (#9) coordinates:
Matrix rotation and translation
0.99999996 0.00025772 0.00007491 -0.03844036
-0.00025772 0.99999997 0.00003452 0.03760464
-0.00007490 -0.00003454 1.00000000 -0.04932415
Axis -0.12762121 0.27682525 -0.95240779
Axis point 78.98769853 118.32205363 0.00000000
Rotation angle (degrees) 0.01550392
Shift along axis 0.06229242
> fitmap #10 inMap #9
Fit map POPE_C6_P58_J139_004_volume_map_sharp.mrc in map
POPE_C6_P58_J139_004_volume_map.mrc using 54922 points
correlation = 0.9074, correlation about mean = 0.5736, overlap = 5.28e+04
steps = 44, shift = 0.00614, angle = 0.0144 degrees
Position of POPE_C6_P58_J139_004_volume_map_sharp.mrc (#10) relative to
POPE_C6_P58_J139_004_volume_map.mrc (#9) coordinates:
Matrix rotation and translation
0.99999987 0.00050603 0.00006901 -0.06845080
-0.00050603 0.99999987 -0.00000760 0.07381286
-0.00006901 0.00000756 1.00000000 -0.05681728
Axis 0.01484075 0.13511135 -0.99071927
Axis point 128.41120788 137.21730184 0.00000000
Rotation angle (degrees) 0.02926488
Shift along axis 0.06524707
> show #!9 models
> hide #!10 models
> hide #!9 models
> show #!13 models
> show #!14 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> fitmap #14 inMap #13
Fit map M257_POPE_C6_P38_J358_sharp.mrc in map M257_POPE_C6_P38_J358.mrc using
115765 points
correlation = 0.9892, correlation about mean = 0.8953, overlap = 1.49e+04
steps = 48, shift = 0.14, angle = 0.023 degrees
Position of M257_POPE_C6_P38_J358_sharp.mrc (#14) relative to
M257_POPE_C6_P38_J358.mrc (#13) coordinates:
Matrix rotation and translation
-0.99999998 0.00023449 -0.00000421 302.90638269
-0.00023450 -0.99999999 0.00000134 302.98355713
-0.00000421 0.00000134 1.00000001 0.02737558
Axis 0.00000569 -0.00000258 -1.00000000
Axis point 151.47095350 151.47402098 0.00000000
Rotation angle (degrees) 179.98656439
Shift along axis -0.02643350
> fitmap #14 inMap #13
Fit map M257_POPE_C6_P38_J358_sharp.mrc in map M257_POPE_C6_P38_J358.mrc using
115765 points
correlation = 0.9892, correlation about mean = 0.8953, overlap = 1.49e+04
steps = 44, shift = 0.0183, angle = 0.011 degrees
Position of M257_POPE_C6_P38_J358_sharp.mrc (#14) relative to
M257_POPE_C6_P38_J358.mrc (#13) coordinates:
Matrix rotation and translation
-0.99999998 0.00017357 -0.00017867 302.94242834
-0.00017356 -1.00000000 -0.00004962 302.96397238
-0.00017868 -0.00004958 0.99999999 0.06236017
Axis 0.00009417 0.00002222 -1.00000000
Axis point 151.48436288 151.46884205 0.00000000
Rotation angle (degrees) 179.99005562
Shift along axis -0.02709816
> fitmap #14 inMap #13
Fit map M257_POPE_C6_P38_J358_sharp.mrc in map M257_POPE_C6_P38_J358.mrc using
115765 points
correlation = 0.9892, correlation about mean = 0.8953, overlap = 1.49e+04
steps = 28, shift = 0.0144, angle = 0.016 degrees
Position of M257_POPE_C6_P38_J358_sharp.mrc (#14) relative to
M257_POPE_C6_P38_J358.mrc (#13) coordinates:
Matrix rotation and translation
-0.99999994 0.00037470 0.00000870 302.88137888
-0.00037471 -0.99999994 0.00000271 303.00059820
0.00000870 0.00000271 1.00000001 0.02635525
Axis -0.00000211 -0.00000255 -1.00000000
Axis point 151.46907340 151.47192624 0.00000000
Rotation angle (degrees) 179.97853096
Shift along axis -0.02776532
> fitmap #14 inMap #13
Fit map M257_POPE_C6_P38_J358_sharp.mrc in map M257_POPE_C6_P38_J358.mrc using
115765 points
correlation = 0.9892, correlation about mean = 0.8953, overlap = 1.49e+04
steps = 44, shift = 0.0113, angle = 0.00731 degrees
Position of M257_POPE_C6_P38_J358_sharp.mrc (#14) relative to
M257_POPE_C6_P38_J358.mrc (#13) coordinates:
Matrix rotation and translation
-0.99999998 0.00025000 -0.00001693 302.90553628
-0.00025000 -0.99999998 -0.00000464 302.97160730
-0.00001693 -0.00000463 1.00000001 0.03151126
Axis 0.00001182 0.00000053 -1.00000000
Axis point 151.47170427 151.46687184 0.00000000
Rotation angle (degrees) 179.98567589
Shift along axis -0.02776952
> fitmap #14 inMap #13
Fit map M257_POPE_C6_P38_J358_sharp.mrc in map M257_POPE_C6_P38_J358.mrc using
115765 points
correlation = 0.9892, correlation about mean = 0.8953, overlap = 1.49e+04
steps = 44, shift = 0.0178, angle = 0.0105 degrees
Position of M257_POPE_C6_P38_J358_sharp.mrc (#14) relative to
M257_POPE_C6_P38_J358.mrc (#13) coordinates:
Matrix rotation and translation
-0.99999997 0.00025611 0.00015764 302.87517911
-0.00025611 -0.99999998 0.00005062 302.98164074
0.00015766 0.00005059 1.00000000 -0.00344672
Axis -0.00007555 -0.00002705 -1.00000000
Axis point 151.45698901 151.47142791 0.00000000
Rotation angle (degrees) 179.98532586
Shift along axis -0.02762950
> hide #!14 models
> show #!15 models
> fitmap #16 inMap #15
Fit map M257_POPE_C2_P38_J250_sharp.mrc in map M257_POPE_C2_P38_J250.mrc using
97390 points
correlation = 0.9415, correlation about mean = 0.6841, overlap = 2.819e+04
steps = 40, shift = 0.0433, angle = 0.0715 degrees
Position of M257_POPE_C2_P38_J250_sharp.mrc (#16) relative to
M257_POPE_C2_P38_J250.mrc (#15) coordinates:
Matrix rotation and translation
0.99999985 0.00054916 0.00005761 -0.09516842
-0.00054916 0.99999985 0.00001304 0.08084848
-0.00005760 -0.00001307 1.00000000 -0.01521159
Axis -0.02364215 0.10429416 -0.99426545
Axis point 142.27427499 172.22756707 0.00000000
Rotation angle (degrees) 0.03164588
Shift along axis 0.02580637
> fitmap #16 inMap #15
Fit map M257_POPE_C2_P38_J250_sharp.mrc in map M257_POPE_C2_P38_J250.mrc using
97390 points
correlation = 0.9415, correlation about mean = 0.684, overlap = 2.819e+04
steps = 28, shift = 0.0149, angle = 0.00906 degrees
Position of M257_POPE_C2_P38_J250_sharp.mrc (#16) relative to
M257_POPE_C2_P38_J250.mrc (#15) coordinates:
Matrix rotation and translation
0.99999983 0.00054481 0.00020033 -0.09993066
-0.00054480 0.99999985 -0.00005481 0.08676963
-0.00020036 0.00005470 0.99999998 -0.00389516
Axis 0.09391418 0.34362189 -0.93440041
Axis point 144.03613699 187.61786894 0.00000000
Rotation angle (degrees) 0.03340626
Shift along axis 0.02407068
> fitmap #16 inMap #15
Fit map M257_POPE_C2_P38_J250_sharp.mrc in map M257_POPE_C2_P38_J250.mrc using
97390 points
correlation = 0.9415, correlation about mean = 0.684, overlap = 2.819e+04
steps = 28, shift = 0.0221, angle = 0.0264 degrees
Position of M257_POPE_C2_P38_J250_sharp.mrc (#16) relative to
M257_POPE_C2_P38_J250.mrc (#15) coordinates:
Matrix rotation and translation
0.99999982 0.00053769 -0.00024884 -0.05721246
-0.00053768 0.99999985 0.00004964 0.07696221
0.00024887 -0.00004951 0.99999997 -0.05617801
Axis -0.08338454 -0.41856378 -0.90435136
Axis point 161.29717266 102.83428451 0.00000000
Rotation angle (degrees) 0.03406520
Shift along axis 0.02336170
> fitmap #16 inMap #15
Fit map M257_POPE_C2_P38_J250_sharp.mrc in map M257_POPE_C2_P38_J250.mrc using
97390 points
correlation = 0.9415, correlation about mean = 0.684, overlap = 2.819e+04
steps = 28, shift = 0.0196, angle = 0.0257 degrees
Position of M257_POPE_C2_P38_J250_sharp.mrc (#16) relative to
M257_POPE_C2_P38_J250.mrc (#15) coordinates:
Matrix rotation and translation
0.99999983 0.00054469 0.00019226 -0.10096020
-0.00054468 0.99999985 -0.00003505 0.08566738
-0.00019228 0.00003494 0.99999998 -0.00211528
Axis 0.06047140 0.33225337 -0.94124965
Axis point 142.37486021 188.10011365 0.00000000
Rotation angle (degrees) 0.03315622
Shift along axis 0.02434907
> fitmap #16 inMap #15
Fit map M257_POPE_C2_P38_J250_sharp.mrc in map M257_POPE_C2_P38_J250.mrc using
97390 points
correlation = 0.9415, correlation about mean = 0.6841, overlap = 2.819e+04
steps = 28, shift = 0.0169, angle = 0.0253 degrees
Position of M257_POPE_C2_P38_J250_sharp.mrc (#16) relative to
M257_POPE_C2_P38_J250.mrc (#15) coordinates:
Matrix rotation and translation
0.99999982 0.00054803 -0.00023705 -0.05769852
-0.00054802 0.99999985 0.00007142 0.07514864
0.00023709 -0.00007129 0.99999997 -0.05105295
Axis -0.11864943 -0.39422450 -0.91132286
Axis point 154.18244321 100.19177884 0.00000000
Rotation angle (degrees) 0.03445494
Shift along axis 0.02374619
> fitmap #16 inMap #15
Fit map M257_POPE_C2_P38_J250_sharp.mrc in map M257_POPE_C2_P38_J250.mrc using
97390 points
correlation = 0.9415, correlation about mean = 0.6841, overlap = 2.819e+04
steps = 28, shift = 0.0163, angle = 0.0261 degrees
Position of M257_POPE_C2_P38_J250_sharp.mrc (#16) relative to
M257_POPE_C2_P38_J250.mrc (#15) coordinates:
Matrix rotation and translation
0.99999983 0.00054475 0.00020342 -0.10314471
-0.00054474 0.99999985 -0.00004616 0.08705204
-0.00020345 0.00004605 0.99999998 -0.00210500
Axis 0.07903192 0.34875129 -0.93387713
Axis point 144.27426272 192.89362322 0.00000000
Rotation angle (degrees) 0.03342179
Shift along axis 0.02417360
> fitmap #16 inMap #15
Fit map M257_POPE_C2_P38_J250_sharp.mrc in map M257_POPE_C2_P38_J250.mrc using
97390 points
correlation = 0.9415, correlation about mean = 0.6841, overlap = 2.819e+04
steps = 28, shift = 0.0155, angle = 0.0257 degrees
Position of M257_POPE_C2_P38_J250_sharp.mrc (#16) relative to
M257_POPE_C2_P38_J250.mrc (#15) coordinates:
Matrix rotation and translation
0.99999982 0.00054913 -0.00022777 -0.05835874
-0.00054911 0.99999985 0.00007573 0.07454867
0.00022782 -0.00007561 0.99999997 -0.04898544
Axis -0.12626556 -0.38010764 -0.91628336
Axis point 152.28970373 100.82469736 0.00000000
Rotation angle (degrees) 0.03433687
Shift along axis 0.02391673
> fitmap #16 inMap #15
Fit map M257_POPE_C2_P38_J250_sharp.mrc in map M257_POPE_C2_P38_J250.mrc using
97390 points
correlation = 0.9415, correlation about mean = 0.6841, overlap = 2.819e+04
steps = 28, shift = 0.0147, angle = 0.0262 degrees
Position of M257_POPE_C2_P38_J250_sharp.mrc (#16) relative to
M257_POPE_C2_P38_J250.mrc (#15) coordinates:
Matrix rotation and translation
0.99999983 0.00054768 0.00020915 -0.10524708
-0.00054767 0.99999985 -0.00005679 0.08905797
-0.00020919 0.00005667 0.99999998 -0.00282936
Axis 0.09631443 0.35512710 -0.92984315
Axis point 146.91701098 196.45588582 0.00000000
Rotation angle (degrees) 0.03374718
Shift along axis 0.02412094
> select clear
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/230903_All_Align.cxs"
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Models/230809_PIP2_HC_85.pdb"
Chain information for 230809_PIP2_HC_85.pdb #11
---
Chain | Description
A B C D E F | No description available
> color #11 #ff007fff
> color #11 #ff557fff
> rename #11 id #17
> rename #30 id #11
> rename #31 id #12
> hide #!15 models
> show #!2 models
> hide #!2 models
> show #!2 models
> ui mousemode right "translate selected models"
> select add #17
11430 atoms, 11646 bonds, 6 pseudobonds, 1266 residues, 2 models selected
> view matrix models #17,1,0,0,-50.17,0,1,0,-52.751,0,0,1,-90.807
> view matrix models #17,1,0,0,-48.624,0,1,0,-38.335,0,0,1,-74.94
> view matrix models #17,1,0,0,-59.243,0,1,0,-59.771,0,0,1,-71.021
> hide sel atoms
> show sel cartoons
> fitmap #17 inMap #2
Fit molecule 230809_PIP2_HC_85.pdb (#17) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#2) using 11430 atoms
average map value = 0.3626, steps = 96
shifted from previous position = 2.22
rotated from previous position = 10.9 degrees
atoms outside contour = 2620, contour level = 0.1849
Position of 230809_PIP2_HC_85.pdb (#17) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999999 0.00009774 -0.00002671 -0.00161005
-0.00009774 0.99999999 0.00011432 -0.00238563
0.00002672 -0.00011431 0.99999999 0.01669555
Axis -0.74834922 -0.17491593 -0.63982644
Axis point 0.00000000 95.33821482 34.74110510
Rotation angle (degrees) 0.00875226
Shift along axis -0.00906009
> fitmap #17 inMap #2
Fit molecule 230809_PIP2_HC_85.pdb (#17) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#2) using 11430 atoms
average map value = 0.3626, steps = 24
shifted from previous position = 0.00318
rotated from previous position = 0.0136 degrees
atoms outside contour = 2622, contour level = 0.1849
Position of 230809_PIP2_HC_85.pdb (#17) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999998 0.00016648 0.00012701 -0.03941683
-0.00016648 0.99999998 -0.00005340 0.03458696
-0.00012702 0.00005338 0.99999999 0.01422386
Axis 0.24708112 0.58774550 -0.77039350
Axis point 209.03740561 236.23969777 0.00000000
Rotation angle (degrees) 0.01238156
Shift along axis -0.00036879
> fitmap #17 inMap #2
Fit molecule 230809_PIP2_HC_85.pdb (#17) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#2) using 11430 atoms
average map value = 0.3626, steps = 24
shifted from previous position = 0.000327
rotated from previous position = 0.0042 degrees
atoms outside contour = 2626, contour level = 0.1849
Position of 230809_PIP2_HC_85.pdb (#17) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999997 0.00016452 0.00019600 -0.05069753
-0.00016451 0.99999998 -0.00007817 0.03815123
-0.00019601 0.00007814 0.99999998 0.02174730
Axis 0.29210445 0.73254808 -0.61485633
Axis point 110.18777296 0.00000000 258.33025232
Rotation angle (degrees) 0.01533064
Shift along axis -0.00023283
> select clear
> transparency 30
> select clear
> transparency 50
> transparency 80
> transparency 50
> transparency 30
> select clear
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Models/230904_Chol_HC_150.pdb"
Summary of feedback from opening C:/Users/OJS/OneDrive -
korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Models/230904_Chol_HC_150.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
9495 messages similar to the above omitted
Chain information for 230904_Chol_HC_150.pdb #18
---
Chain | Description
A B C D E F | No description available
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Models/230926_CBX_HC_181.pdb"
Chain information for 230926_CBX_HC_181.pdb #19
---
Chain | Description
A B C D E F | No description available
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Models/230926_MBCD_HC_10.pdb"
Chain information for 230926_MBCD_HC_10.pdb #20
---
Chain | Description
A B C D E F | No description available
> hide #!17-20 atoms
> show #!17-20 cartoons
> color #18 #00aaffff
> color #19 #aa55ffff
> color #20 #ffff7fff
> show #!7 models
> hide #!7 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> hide #!17 models
> hide #!19 models
> hide #!20 models
> show #!3 models
> hide #!3 models
> show #!4 models
> ui mousemode right "translate selected models"
> select add #4
2 models selected
> view matrix models
> #4,0.98598,0.16689,-6.2247e-05,-83.237,-0.16689,0.98598,-0.00028856,-28.341,1.3215e-05,0.00029491,1,-66.353
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12433 points
correlation = 0.9587, correlation about mean = 0.7478, overlap = 1061
steps = 60, shift = 2.57, angle = 0.0222 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999970 0.00077202 0.00000277 -0.12842009
-0.00077201 0.99999971 0.00000395 0.12769686
-0.00000277 -0.00000395 1.00000000 -0.02790394
Axis -0.00511477 0.00359104 -0.99998047
Axis point 165.20797882 166.21545399 0.00000000
Rotation angle (degrees) 0.04423410
Shift along axis 0.02901879
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12433 points
correlation = 0.9588, correlation about mean = 0.7484, overlap = 1062
steps = 28, shift = 0.000642, angle = 0.0155 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999988 0.00050111 -0.00000174 -0.08289972
-0.00050111 0.99999988 -0.00000132 0.08337078
0.00000174 0.00000132 1.00000000 -0.03013319
Axis 0.00264134 -0.00347976 -0.99999046
Axis point 166.53748985 165.63111584 0.00000000
Rotation angle (degrees) 0.02871158
Shift along axis 0.02962383
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12433 points
correlation = 0.9588, correlation about mean = 0.7486, overlap = 1063
steps = 28, shift = 0.00529, angle = 0.00875 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999991 0.00041939 0.00009004 -0.07970298
-0.00041939 0.99999991 0.00008936 0.05850703
-0.00009001 -0.00008940 0.99999999 0.00004279
Axis -0.20398850 0.20546374 -0.95716944
Axis point 125.63086367 176.33929505 0.00000000
Rotation angle (degrees) 0.02510451
Shift along axis 0.02823861
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12433 points
correlation = 0.9589, correlation about mean = 0.7487, overlap = 1063
steps = 36, shift = 0.0123, angle = 0.00789 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999986 0.00053877 0.00002407 -0.08970412
-0.00053877 0.99999986 0.00007044 0.08536274
-0.00002404 -0.00007046 1.00000000 -0.00249267
Axis -0.12952993 0.04422948 -0.99058859
Axis point 156.92891605 162.24585982 0.00000000
Rotation angle (degrees) 0.03116251
Shift along axis 0.01786412
> fitmap #4 inMap #3
Fit map N55H_CBX_P52_J575_011_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map.mrc using 12433 points
correlation = 0.9589, correlation about mean = 0.7487, overlap = 1063
steps = 24, shift = 0.00328, angle = 0.00163 degrees
Position of N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999986 0.00052982 -0.00000032 -0.08680692
-0.00052981 0.99999986 0.00008189 0.08407010
0.00000036 -0.00008189 1.00000000 -0.00540741
Axis -0.15275181 -0.00063577 -0.98826438
Axis point 158.65751395 158.53757848 0.00000000
Rotation angle (degrees) 0.03071664
Shift along axis 0.01855042
> select subtract #4
Nothing selected
> select add #18
11400 atoms, 11652 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> view matrix models #18,1,0,0,-33.231,0,1,0,-70.28,0,0,1,-69.119
> view matrix models #18,1,0,0,-56.752,0,1,0,-60.845,0,0,1,-74.385
> fitmap #18 inMap #3
Fit molecule 230904_Chol_HC_150.pdb (#18) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11400 atoms
average map value = 0.06959, steps = 92
shifted from previous position = 3.49
rotated from previous position = 5.08 degrees
atoms outside contour = 8249, contour level = 0.10065
Position of 230904_Chol_HC_150.pdb (#18) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99692341 -0.07838189 0.00005617 13.51889258
0.07838190 0.99692339 -0.00019944 -12.47182784
-0.00004036 0.00020323 0.99999998 -9.94326303
Axis 0.00256859 0.00061575 0.99999651
Axis point 165.56585131 166.30096983 0.00000000
Rotation angle (degrees) 4.49557871
Shift along axis -9.91618345
> fitmap #18 inMap #3
Fit molecule 230904_Chol_HC_150.pdb (#18) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11400 atoms
average map value = 0.06958, steps = 60
shifted from previous position = 0.0139
rotated from previous position = 0.0156 degrees
atoms outside contour = 8243, contour level = 0.10065
Position of 230904_Chol_HC_150.pdb (#18) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99690298 -0.07864127 0.00009551 13.55868484
0.07864128 0.99690297 -0.00012857 -12.52619862
-0.00008511 0.00013569 0.99999999 -9.91106215
Axis 0.00168016 0.00114835 0.99999793
Axis point 165.67939452 166.09866992 0.00000000
Rotation angle (degrees) 4.51047966
Shift along axis -9.90264530
> view matrix models
> #18,0.99609,0.088359,3.2406e-05,-69.57,-0.088359,0.99609,-0.00018126,-41.728,-4.8296e-05,0.00017769,1,-64.242
> fitmap #18 inMap #3
Fit molecule 230904_Chol_HC_150.pdb (#18) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11400 atoms
average map value = 0.166, steps = 64
shifted from previous position = 1.98
rotated from previous position = 4.58 degrees
atoms outside contour = 3063, contour level = 0.10065
Position of 230904_Chol_HC_150.pdb (#18) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999932 0.00116433 -0.00005879 -0.18393871
-0.00116433 0.99999932 -0.00010661 0.20774894
0.00005866 0.00010668 1.00000000 -0.03341080
Axis 0.09109683 -0.05016095 -0.99457792
Axis point 178.59479778 158.55612130 0.00000000
Rotation angle (degrees) 0.06707500
Shift along axis 0.00605253
> select clear
> show #!19 models
> hide #!18 models
> hide #!4 models
> show #!6 models
> select add #19
8634 atoms, 8916 bonds, 6 pseudobonds, 1020 residues, 2 models selected
> view matrix models #19,1,0,0,-19.238,0,1,0,-72.039,0,0,1,-54.961
> view matrix models #19,1,0,0,-47.764,0,1,0,-61.635,0,0,1,-75.729
> view matrix models #19,1,0,0,-57.946,0,1,0,-56.54,0,0,1,-63.989
> fitmap #19 inMap #6
Fit molecule 230926_CBX_HC_181.pdb (#19) to map
N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) using 8634 atoms
average map value = 0.04901, steps = 60
shifted from previous position = 2.44
rotated from previous position = 1.43 degrees
atoms outside contour = 7099, contour level = 0.14616
Position of 230926_CBX_HC_181.pdb (#19) relative to
N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.88376224 0.46791617 0.00433058 -59.30912431
-0.46776742 0.88365418 -0.01867940 103.02713435
-0.01256712 0.01448244 0.99981615 -2.88010978
Axis 0.03541329 0.01804493 -0.99920983
Axis point 177.60162724 171.07019505 0.00000000
Rotation angle (degrees) 27.91828071
Shift along axis 2.63662034
> fitmap #19 inMap #6
Fit molecule 230926_CBX_HC_181.pdb (#19) to map
N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) using 8634 atoms
average map value = 0.04903, steps = 44
shifted from previous position = 0.0548
rotated from previous position = 0.0598 degrees
atoms outside contour = 7104, contour level = 0.14616
Position of 230926_CBX_HC_181.pdb (#19) relative to
N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.88354650 0.46831939 0.00474549 -59.45828237
-0.46815354 0.88343143 -0.01952357 103.25953686
-0.01333559 0.01502837 0.99979813 -2.82487869
Axis 0.03686387 0.01929092 -0.99913408
Axis point 177.78747095 171.37648545 0.00000000
Rotation angle (degrees) 27.94619956
Shift along axis 2.62254127
> fitmap #19 inMap #6
Fit molecule 230926_CBX_HC_181.pdb (#19) to map
N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) using 8634 atoms
average map value = 0.04903, steps = 28
shifted from previous position = 0.0208
rotated from previous position = 0.0176 degrees
atoms outside contour = 7106, contour level = 0.14616
Position of 230926_CBX_HC_181.pdb (#19) relative to
N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.88363025 0.46816235 0.00464760 -59.43249858
-0.46799494 0.88351036 -0.01975277 103.23740309
-0.01335370 0.01527909 0.99979409 -2.87142811
Axis 0.03738783 0.01921193 -0.99911614
Axis point 177.83306922 171.36198035 0.00000000
Rotation angle (degrees) 27.93650074
Shift along axis 2.63022789
> ui mousemode right "rotate selected models"
> view matrix models
> #19,0.92631,0.33563,0.17117,-130.29,-0.34848,0.93594,0.05068,5.364,-0.14319,-0.10659,0.98394,-21.158
> view matrix models
> #19,0.91251,0.40806,0.028453,-116.9,-0.40902,0.91117,0.049703,19.68,-0.0056431,-0.056992,0.99836,-54.555
> fitmap #19 inMap #6
Fit molecule 230926_CBX_HC_181.pdb (#19) to map
N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) using 8634 atoms
average map value = 0.1677, steps = 84
shifted from previous position = 3.91
rotated from previous position = 9.49 degrees
atoms outside contour = 3990, contour level = 0.14616
Position of 230926_CBX_HC_181.pdb (#19) relative to
N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.49989397 0.86608661 -0.00005537 -60.75119150
-0.86608661 0.49989396 -0.00009401 226.77277705
-0.00005374 0.00009495 0.99999999 -0.00444179
Axis 0.00010908 -0.00000094 -0.99999999
Axis point 165.98762893 165.99102646 0.00000000
Rotation angle (degrees) 60.00701503
Shift along axis -0.00239837
> fitmap #19 inMap #6
Fit molecule 230926_CBX_HC_181.pdb (#19) to map
N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) using 8634 atoms
average map value = 0.1677, steps = 28
shifted from previous position = 0.00988
rotated from previous position = 0.0129 degrees
atoms outside contour = 3993, contour level = 0.14616
Position of 230926_CBX_HC_181.pdb (#19) relative to
N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.49982973 0.86612367 -0.00015906 -60.73542500
-0.86612367 0.49982975 0.00009258 226.76859341
0.00015970 0.00009149 0.99999998 -0.03968151
Axis -0.00000063 -0.00018402 -0.99999998
Axis point 165.97507836 165.97078373 0.00000000
Rotation angle (degrees) 60.01126428
Shift along axis -0.00200910
> fitmap #19 inMap #6
Fit molecule 230926_CBX_HC_181.pdb (#19) to map
N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) using 8634 atoms
average map value = 0.1677, steps = 44
shifted from previous position = 0.00974
rotated from previous position = 0.0164 degrees
atoms outside contour = 3991, contour level = 0.14616
Position of 230926_CBX_HC_181.pdb (#19) relative to
N55H_CBX_P52_J650_003_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.50001918 0.86601433 -0.00006888 -60.75834803
-0.86601433 0.50001917 -0.00006889 226.73685814
-0.00002522 0.00009410 1.00000000 -0.00548403
Axis 0.00009410 -0.00002521 -1.00000000
Axis point 165.98572536 165.98804691 0.00000000
Rotation angle (degrees) 59.99873156
Shift along axis -0.00594930
> select clear
> show #!20 models
> hide #!19 models
> show #!7 models
> show #!8 models
> hide #!6 models
> hide #!7 models
> fitmap #20 inMap #8
Fit molecule 230926_MBCD_HC_10.pdb (#20) to map
MBCD_P41_J50_013_volume_map_sharp.mrc (#8) using 11784 atoms
average map value = 0.3701, steps = 36
shifted from previous position = 0.0127
rotated from previous position = 0.00864 degrees
atoms outside contour = 1518, contour level = 0.10146
Position of 230926_MBCD_HC_10.pdb (#20) relative to
MBCD_P41_J50_013_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99999999 -0.00009200 0.00006921 0.00468836
0.00009201 0.99999999 -0.00014029 0.00003958
-0.00006920 0.00014030 0.99999999 -0.00451636
Axis 0.77304295 0.38132757 0.50694565
Axis point 0.00000000 37.06904756 -3.39071167
Rotation angle (degrees) 0.01039808
Shift along axis 0.00134985
> fitmap #20 inMap #8
Fit molecule 230926_MBCD_HC_10.pdb (#20) to map
MBCD_P41_J50_013_volume_map_sharp.mrc (#8) using 11784 atoms
average map value = 0.3701, steps = 28
shifted from previous position = 0.0119
rotated from previous position = 0.0125 degrees
atoms outside contour = 1523, contour level = 0.10146
Position of 230926_MBCD_HC_10.pdb (#20) relative to
MBCD_P41_J50_013_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99999997 -0.00024861 -0.00000241 0.02770855
0.00024861 0.99999997 -0.00000542 -0.02703094
0.00000241 0.00000542 1.00000000 -0.00895565
Axis 0.02177657 -0.00969566 0.99971585
Axis point 109.05784539 112.14894527 0.00000000
Rotation angle (degrees) 0.01424833
Shift along axis -0.00808763
> fitmap #20 inMap #8
Fit molecule 230926_MBCD_HC_10.pdb (#20) to map
MBCD_P41_J50_013_volume_map_sharp.mrc (#8) using 11784 atoms
average map value = 0.3701, steps = 28
shifted from previous position = 0.0112
rotated from previous position = 0.00468 degrees
atoms outside contour = 1520, contour level = 0.10146
Position of 230926_MBCD_HC_10.pdb (#20) relative to
MBCD_P41_J50_013_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99999998 -0.00017470 -0.00000627 0.01918424
0.00017470 0.99999998 -0.00003995 -0.01374892
0.00000627 0.00003994 1.00000000 -0.00206805
Axis 0.22276379 -0.03496507 0.97424522
Axis point 78.16273778 106.31375150 0.00000000
Rotation angle (degrees) 0.01027405
Shift along axis 0.00273950
> fitmap #20 inMap #8
Fit molecule 230926_MBCD_HC_10.pdb (#20) to map
MBCD_P41_J50_013_volume_map_sharp.mrc (#8) using 11784 atoms
average map value = 0.3702, steps = 28
shifted from previous position = 0.00791
rotated from previous position = 0.0166 degrees
atoms outside contour = 1524, contour level = 0.10146
Position of 230926_MBCD_HC_10.pdb (#20) relative to
MBCD_P41_J50_013_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
1.00000000 0.00005267 -0.00003358 -0.00211674
-0.00005267 0.99999999 0.00013733 -0.00827343
0.00003358 -0.00013733 0.99999999 0.00643024
Axis -0.91026108 -0.22257260 -0.34912206
Axis point 0.00000000 50.69204616 57.77979788
Rotation angle (degrees) 0.00864413
Shift along axis 0.00152329
> fitmap #20 inMap #8
Fit molecule 230926_MBCD_HC_10.pdb (#20) to map
MBCD_P41_J50_013_volume_map_sharp.mrc (#8) using 11784 atoms
average map value = 0.3701, steps = 28
shifted from previous position = 0.0156
rotated from previous position = 0.0198 degrees
atoms outside contour = 1520, contour level = 0.10146
Position of 230926_MBCD_HC_10.pdb (#20) relative to
MBCD_P41_J50_013_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99999996 -0.00026850 -0.00004410 0.03292880
0.00026850 0.99999996 0.00001179 -0.02835113
0.00004410 -0.00001180 1.00000000 0.00706121
Axis -0.04331710 -0.16191493 0.98585353
Axis point 99.49998612 124.25795737 0.00000000
Rotation angle (degrees) 0.01560490
Shift along axis 0.01012541
> select clear
[Repeated 1 time(s)]
> select
61858 atoms, 63430 bonds, 36 pseudobonds, 7044 residues, 40 models selected
> style sel stick
Changed 61858 atom styles
> color sel byhetero
> select clear
> select
> ::name="6OU"::name="CBO"::name="CLR"::name="MC3"::name="PTY"::name="Y01"
6060 atoms, 5988 bonds, 198 residues, 4 models selected
> color sel gray
> color sel byhetero
> select clear
> volume sdLevel 8
> select clear
> volume sdLevel 7
> volume sdLevel 6
> show #!5 models
> hide #!5 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/230903_All_Align.cxs"
> volume #8 level 0.1561
> transparency 80
> select clear
> transparency 0
> hide #!20 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!8 models
> hide #!2 models
> show #!2 models
> volume #2 level 0.317
> volume sdLevel 7
> volume sdLevel 7.5
> show #!4 models
> show #!6 models
> show #!8 models
> hide #!8 models
> hide #!6 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> show #!8 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #8 level 0.1591
> show #!2 models
> hide #!2 models
> hide #!8 models
> show #!9 models
> show #!10 models
> hide #!9 models
> show #!2 models
> hide #!2 models
> hide #!10 models
> show #!2 models
> hide #!2 models
> show #!17 models
> show #!18 models
> select
61858 atoms, 63430 bonds, 36 pseudobonds, 7044 residues, 40 models selected
> ui tool show "Selection Inspector"
> setattr =sel p display true
Assigning display attribute to 36 items
> setattr =sel p display false
Assigning display attribute to 36 items
> size =sel stickRadius 0.3
Changed 63430 bond radii
> ribbon style thickness 0.6
> select clear
> select add #17
11430 atoms, 11646 bonds, 6 pseudobonds, 1266 residues, 2 models selected
> select clear
> show #!19 models
> ui mousemode right "rotate selected models"
> select add #19
8634 atoms, 8916 bonds, 6 pseudobonds, 1020 residues, 2 models selected
> view matrix models
> #19,0.59572,0.80024,-0.068844,-112.04,-0.77952,0.55538,-0.28964,192.63,-0.19355,0.22621,0.95466,-60.704
> view matrix models
> #19,0.28175,0.95556,0.086727,-110.92,-0.9571,0.27354,0.095546,206.48,0.067577,-0.10993,0.99164,-54.241
> view matrix models
> #19,0.088046,0.99296,0.0792,-83.757,-0.99172,0.094838,-0.086542,271.39,-0.093444,-0.070924,0.9931,-34.227
> view matrix models
> #19,-0.011227,0.99863,0.051133,-63.675,-0.9996,-0.01253,0.025241,272.41,0.025847,-0.05083,0.99837,-58.215
> fitmap #19 inMap #8
Fit molecule 230926_CBX_HC_181.pdb (#19) to map
MBCD_P41_J50_013_volume_map_sharp.mrc (#8) using 8634 atoms
average map value = 0.2334, steps = 68
shifted from previous position = 0.422
rotated from previous position = 4.31 degrees
atoms outside contour = 4013, contour level = 0.15911
Position of 230926_CBX_HC_181.pdb (#19) relative to
MBCD_P41_J50_013_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
-0.06082116 0.99814868 0.00000076 -47.06398438
-0.99814868 -0.06082116 0.00009026 284.30656281
0.00009014 0.00000473 1.00000000 -62.30576461
Axis -0.00004284 -0.00004478 -1.00000000
Axis point 110.22563249 164.29516133 0.00000000
Rotation angle (degrees) 93.48694778
Shift along axis 62.29505076
> show #!20 models
> select clear
[Repeated 1 time(s)]
> select :200
288 atoms, 252 bonds, 36 residues, 6 models selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 0
Assigning ss_type attribute to 36 items
> undo
> hide #!17 models
> hide #!18 models
> hide #!20 models
> select :196-200
1440 atoms, 1440 bonds, 180 residues, 6 models selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 0
Assigning ss_type attribute to 180 items
> setattr sel r ss_type 2
Assigning ss_type attribute to 180 items
> select clear
> show #!18 models
> hide #!18 models
> show #!18 models
> select #19/D:55
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #18/D:54
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #19/D:54
6 atoms, 5 bonds, 1 residue, 1 model selected
> select :52-55
1332 atoms, 1350 bonds, 144 residues, 6 models selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 0
Assigning ss_type attribute to 144 items
> select :200
288 atoms, 252 bonds, 36 residues, 6 models selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 0
Assigning ss_type attribute to 36 items
> select clear
> morph #18,19
Computed 51 frame morph #21
> coordset #21 1,51
> view orient
> turn x 90
> select /b,c,e,f
46600 atoms, 47820 bonds, 28 pseudobonds, 5344 residues, 14 models selected
> hide sel ribbons
> select clear
[Repeated 1 time(s)]
> select /b,c,e,f
46600 atoms, 47820 bonds, 28 pseudobonds, 5344 residues, 14 models selected
> show sel ribbons
> select clear
> select /b,c,e,f
46600 atoms, 47820 bonds, 28 pseudobonds, 5344 residues, 14 models selected
> hide sel ribbons
> view orient
> turn x 90
> turn y 60
> select add #21
49368 atoms, 50676 bonds, 30 pseudobonds, 5680 residues, 14 models selected
> select add #20
53296 atoms, 54698 bonds, 32 pseudobonds, 6092 residues, 14 models selected
> select add #19
56174 atoms, 57670 bonds, 34 pseudobonds, 6432 residues, 14 models selected
> select add #18
59974 atoms, 61554 bonds, 36 pseudobonds, 6844 residues, 14 models selected
> select add #17
63784 atoms, 65436 bonds, 38 pseudobonds, 7266 residues, 14 models selected
> select subtract #18
52384 atoms, 53784 bonds, 32 pseudobonds, 6030 residues, 12 models selected
> select subtract #20
40600 atoms, 41718 bonds, 26 pseudobonds, 4794 residues, 10 models selected
> select subtract #21
32296 atoms, 33150 bonds, 20 pseudobonds, 3786 residues, 8 models selected
> select subtract #17
20866 atoms, 21504 bonds, 14 pseudobonds, 2520 residues, 6 models selected
> select add #12
24082 atoms, 24812 bonds, 16 pseudobonds, 2916 residues, 6 models selected
> select add #11
27244 atoms, 28066 bonds, 18 pseudobonds, 3306 residues, 6 models selected
> select subtract #11
18282 atoms, 18840 bonds, 12 pseudobonds, 2208 residues, 4 models selected
> select subtract #12
8634 atoms, 8916 bonds, 6 pseudobonds, 1020 residues, 2 models selected
> select subtract #19
Nothing selected
> hide #!21 models
> show #!19 models
> show #!18 models
> hide #!19 models
> hide #!18 models
> show #!21 models
> hide #!21 models
> show #!19 models
> show #!18 models
> show #!3 models
> hide #!3 models
> show #!4 models
> transparency 30
> transparency 50
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> volume #4 level 0.2869
> volume #3 level 0.1222
> hide #!4 models
> transparency 80
> hide #!18 models
> show #!18 models
> hide #!19 models
> select
70162 atoms, 71998 bonds, 42 pseudobonds, 8052 residues, 42 models selected
> show sel ribbons
> select clear
> hide #!18 models
> show #!19 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!6 models
> show #!4 models
> hide #!4 models
> show #!18 models
> hide #!18 models
> hide #!19 models
> hide #!6 models
> show #!19 models
> mlp #!19
Map values for surface "230926_CBX_HC_181.pdb_A SES surface": minimum -27.57,
mean 0.8045, maximum 24.47
Map values for surface "230926_CBX_HC_181.pdb_B SES surface": minimum -26.7,
mean 0.8385, maximum 24.42
Map values for surface "230926_CBX_HC_181.pdb_C SES surface": minimum -28.15,
mean 0.8718, maximum 24.27
Map values for surface "230926_CBX_HC_181.pdb_D SES surface": minimum -27.92,
mean 0.8499, maximum 24.31
Map values for surface "230926_CBX_HC_181.pdb_E SES surface": minimum -27.7,
mean 0.8051, maximum 24.33
Map values for surface "230926_CBX_HC_181.pdb_F SES surface": minimum -28.95,
mean 0.8537, maximum 24.25
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!19 models
> show #!18 models
> mlp #!18
Map values for surface "230904_Chol_HC_150.pdb_A SES surface": minimum -27.81,
mean 0.2399, maximum 23.77
Map values for surface "230904_Chol_HC_150.pdb_B SES surface": minimum -28.02,
mean 0.1571, maximum 25.31
Map values for surface "230904_Chol_HC_150.pdb_C SES surface": minimum -27.97,
mean 0.1452, maximum 24.75
Map values for surface "230904_Chol_HC_150.pdb_D SES surface": minimum -27.84,
mean 0.223, maximum 24.9
Map values for surface "230904_Chol_HC_150.pdb_E SES surface": minimum -27.89,
mean 0.1406, maximum 24.79
Map values for surface "230904_Chol_HC_150.pdb_F SES surface": minimum -27.69,
mean 0.1485, maximum 25.26
To also show corresponding color key, enter the above mlp command and add key
true
> show #!19 models
> hide #!18 models
> hide #!19 models
> show #!19 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!19 models
> transparency 50
> transparency 10
> transparency 0
> select clear
> hide #!18 models
> show #!19 models
> show #!18 models
> hide #!18 models
> hide #!19 models
> show #!19 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> hide #!19 models
> show #!17 models
> show #!18 models
> hide #!17-18 surfaces
> close #21
> morph #17,18
Computed 51 frame morph #21
> coordset #21 1,51
> show #!17 models
> show #!18 models
> close #21
> morph #17,18
Computed 51 frame morph #21
> coordset #21 1,51
> show #!18 models
> hide #!21 models
> show #!4 models
> show #!21 models
> hide #!18 models
> show #!18 models
> hide #!4 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> select #21/b,c,e,f
6388 atoms, 6572 bonds, 4 pseudobonds, 788 residues, 2 models selected
> hide sel ribbons
> select #21/b,c,e,f
6388 atoms, 6572 bonds, 4 pseudobonds, 788 residues, 2 models selected
> show sel ribbons
> select clear
> select #21/b,c,e,f
6388 atoms, 6572 bonds, 4 pseudobonds, 788 residues, 2 models selected
> hide sel ribbons
> select #21/a
1597 atoms, 1643 bonds, 1 pseudobond, 197 residues, 2 models selected
> mlp sel
Map values for surface "Morph - 230809_PIP2_HC_85.pdb_A SES surface": minimum
-28.07, mean 0.1466, maximum 23.33
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "Morph - 230809_PIP2_HC_85.pdb_A SES surface": minimum
-27.21, mean 0.05247, maximum 24.21
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
Morph - 230809_PIP2_HC_85.pdb #21/A ASN 55 OD1
Morph - 230809_PIP2_HC_85.pdb #21/A ASN 55 ND2
Adding H-bond-preserving hydrogens to trajectories not supported.
> mlp sel
Map values for surface "Morph - 230809_PIP2_HC_85.pdb_A SES surface": minimum
-27.38, mean 0.06372, maximum 23.69
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "Morph - 230809_PIP2_HC_85.pdb_A SES surface": minimum
-27.38, mean 0.06372, maximum 23.69
To also show corresponding color key, enter the above mlp command and add key
true
> show #!19 models
> hide #!19 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!18 models
> mlp #!18
Map values for surface "230904_Chol_HC_150.pdb_A SES surface": minimum -27.81,
mean 0.2399, maximum 23.77
Map values for surface "230904_Chol_HC_150.pdb_B SES surface": minimum -28.02,
mean 0.1571, maximum 25.31
Map values for surface "230904_Chol_HC_150.pdb_C SES surface": minimum -27.97,
mean 0.1452, maximum 24.75
Map values for surface "230904_Chol_HC_150.pdb_D SES surface": minimum -27.84,
mean 0.223, maximum 24.9
Map values for surface "230904_Chol_HC_150.pdb_E SES surface": minimum -27.89,
mean 0.1406, maximum 24.79
Map values for surface "230904_Chol_HC_150.pdb_F SES surface": minimum -27.69,
mean 0.1485, maximum 25.26
To also show corresponding color key, enter the above mlp command and add key
true
> show #!17 models
> mlp #!17-18
Map values for surface "230809_PIP2_HC_85.pdb_A SES surface": minimum -27.38,
mean 0.01814, maximum 23.69
Map values for surface "230809_PIP2_HC_85.pdb_B SES surface": minimum -27.3,
mean 0.0472, maximum 25.97
Map values for surface "230809_PIP2_HC_85.pdb_C SES surface": minimum -28.05,
mean 0.03183, maximum 23.54
Map values for surface "230809_PIP2_HC_85.pdb_D SES surface": minimum -28,
mean 0.06321, maximum 26.19
Map values for surface "230809_PIP2_HC_85.pdb_E SES surface": minimum -27.44,
mean 0.08273, maximum 23.98
Map values for surface "230809_PIP2_HC_85.pdb_F SES surface": minimum -27.61,
mean 0.03048, maximum 23.45
Map values for surface "230904_Chol_HC_150.pdb_A SES surface": minimum -27.81,
mean 0.2399, maximum 23.77
Map values for surface "230904_Chol_HC_150.pdb_B SES surface": minimum -28.02,
mean 0.1571, maximum 25.31
Map values for surface "230904_Chol_HC_150.pdb_C SES surface": minimum -27.97,
mean 0.1452, maximum 24.75
Map values for surface "230904_Chol_HC_150.pdb_D SES surface": minimum -27.84,
mean 0.223, maximum 24.9
Map values for surface "230904_Chol_HC_150.pdb_E SES surface": minimum -27.89,
mean 0.1406, maximum 24.79
Map values for surface "230904_Chol_HC_150.pdb_F SES surface": minimum -27.69,
mean 0.1485, maximum 25.26
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #!17 models
> morph #17,18,19
Computed 101 frame morph #22
> coordset #22 1,101
> close #21
> morph #18,20
Computed 51 frame morph #21
> coordset #21 1,51
> close #22
> morph #17,20
Computed 51 frame morph #22
> coordset #22 1,51
> hide #!21 models
> hide #!22 models
> show #!17 models
> show #!20 models
> hide #!17 models
> mlp #!20
Map values for surface "230926_MBCD_HC_10.pdb_A SES surface": minimum -28.57,
mean -0.03631, maximum 25.41
Map values for surface "230926_MBCD_HC_10.pdb_B SES surface": minimum -28,
mean -0.02772, maximum 25.92
Map values for surface "230926_MBCD_HC_10.pdb_C SES surface": minimum -28.3,
mean -0.1042, maximum 25.64
Map values for surface "230926_MBCD_HC_10.pdb_D SES surface": minimum -28.28,
mean -0.05149, maximum 25.19
Map values for surface "230926_MBCD_HC_10.pdb_E SES surface": minimum -27.35,
mean -0.03333, maximum 24.83
Map values for surface "230926_MBCD_HC_10.pdb_F SES surface": minimum -27.13,
mean -0.07312, maximum 24.98
To also show corresponding color key, enter the above mlp command and add key
true
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> close #22
> close #21
> hide #!20 models
> morph #18,20
Computed 51 frame morph #21
> coordset #21 1,51
> morph #18,20,17
Computed 101 frame morph #22
> coordset #22 1,101
> close #21
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/230903_All_Align.cxs"
——— End of log from Fri Oct 6 04:37:41 2023 ———
opened ChimeraX session
> close #22
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> open
> C:/Users/OJS/Desktop/Phenix/230320_Cx43_WT_POPE_PIP2/RealSpaceRefine_90/231006_From86_PIO_real_space_refined_090.pdb
Chain information for 231006_From86_PIO_real_space_refined_090.pdb #21
---
Chain | Description
A B C D E F | No description available
> hide #!21 atoms
> show #!21 cartoons
> color #21 #ff557fff
> select ::name="PIO"
282 atoms, 282 bonds, 6 residues, 1 model selected
> show sel atoms
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> select clear
> hide #!2 models
> hide #!1 models
> show #!2 models
> transparency 30
> select add #21
11526 atoms, 11724 bonds, 6 pseudobonds, 1266 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #21,1,0,0,-38.016,0,1,0,-20.413,0,0,1,-99.273
> view matrix models #21,1,0,0,-63.406,0,1,0,-42.853,0,0,1,-124.46
> view matrix models #21,1,0,0,-88.421,0,1,0,-69.632,0,0,1,-109.58
> view matrix models #21,1,0,0,-57.048,0,1,0,-55.647,0,0,1,-83.181
> view matrix models #21,1,0,0,-66.548,0,1,0,-60.717,0,0,1,-79.857
> ui tool show "Fit in Map"
> fitmap #21 inMap #1
Fit molecule 231006_From86_PIO_real_space_refined_090.pdb (#21) to map
WT_PIP2_P68_J150_009_volume_map.mrc (#1) using 11526 atoms
average map value = 0.1004, steps = 132
shifted from previous position = 6.49
rotated from previous position = 12.1 degrees
atoms outside contour = 7089, contour level = 0.097151
Position of 231006_From86_PIO_real_space_refined_090.pdb (#21) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.51764976 0.85559262 -0.00000026 -63.30191413
-0.85559262 0.51764976 -0.00000394 226.91542539
-0.00000324 0.00000227 1.00000001 -5.24153078
Axis 0.00000363 0.00000174 -1.00000000
Axis point 169.60025893 169.60017669 0.00000000
Rotation angle (degrees) 58.82526657
Shift along axis 5.24169647
> view matrix models
> #21,0.97778,-0.20963,1.3479e-05,-22.486,0.20963,0.97778,4.6066e-05,-92.668,-2.2837e-05,-4.2217e-05,1,-69.749
> fitmap #21 inMap #1
Fit molecule 231006_From86_PIO_real_space_refined_090.pdb (#21) to map
WT_PIP2_P68_J150_009_volume_map.mrc (#1) using 11526 atoms
average map value = 0.1776, steps = 68
shifted from previous position = 1.6
rotated from previous position = 1.21 degrees
atoms outside contour = 2082, contour level = 0.097151
Position of 231006_From86_PIO_real_space_refined_090.pdb (#21) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.49950197 0.86631275 -0.00006353 -62.03103824
-0.86631275 0.49950197 0.00004222 231.81045494
0.00006830 0.00003396 1.00000000 -0.01172360
Axis -0.00000477 -0.00007609 -1.00000000
Axis point 169.60500377 169.59003413 0.00000000
Rotation angle (degrees) 60.03294397
Shift along axis -0.00561937
> select clear
> select
73384 atoms, 75154 bonds, 42 pseudobonds, 8310 residues, 42 models selected
> color sel byhetero
> select clear
> clip front 0
> clip front 1
[Repeated 3 time(s)]
> show #!18 models
> hide #!18,21 surfaces
> select ::name="CLR"
504 atoms, 558 bonds, 18 residues, 2 models selected
> show sel atoms
> volume #2 level 0.1459
> hide #!21 models
> hide #!2 models
> show #!1 models
> show #!21 models
> hide #!21 models
> volume #1 level 0.08407
> hide #!18 models
> hide #!1 models
> show #!1 models
> show #!21 models
> hide #!21 models
> show #!18 models
> show #!19 models
> lighting simple
> lighting soft
> hide sel & #!18 surfaces
> select clear
> hide #!19 models
> show #!19 models
> hide #!18-19 surfaces
> ~clip
> hide #!1 models
> select ::name="CLR"
504 atoms, 558 bonds, 18 residues, 2 models selected
> color sel yellow
> color sel byhetero
> select clear
> show #!11 models
> hide #!11 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> rename #11 id #30
> rename #12 id #31
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/N55H_POPE_C2_P58_J151_004_volume_map.mrc"
Opened N55H_POPE_C2_P58_J151_004_volume_map.mrc as #11, grid size 256,256,256,
pixel 1.1, shown at level 0.209, step 1, values float32
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/N55H_POPE_C2_P58_J151_004_volume_map_sharp.mrc"
Opened N55H_POPE_C2_P58_J151_004_volume_map_sharp.mrc as #12, grid size
256,256,256, pixel 1.1, shown at level 0.259, step 1, values float32
> close #9-10
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/N55H_POPE_C6_P58_J139_004_volume_map.mrc"
Opened N55H_POPE_C6_P58_J139_004_volume_map.mrc as #9, grid size 256,256,256,
pixel 1.1, shown at level 0.213, step 1, values float32
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/N55H_POPE_C6_P58_J139_004_volume_map_sharp.mrc"
Opened N55H_POPE_C6_P58_J139_004_volume_map_sharp.mrc as #10, grid size
256,256,256, pixel 1.1, shown at level 0.251, step 1, values float32
> color #9 #ffaaffff models
> color #10 #ffaaffff models
> color #11 #5555ffff models
> color #11 #55aa7fff models
> color #11 #55ff7fff models
> color #12 #55ff00ff models
> color #12 #55ff7fff models
> close #21
> close #17
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Models/231006_PIP2_HC_90.pdb"
Chain information for 231006_PIP2_HC_90.pdb #17
---
Chain | Description
A B C D E F | No description available
> color #17 #ff557fff
> hide #!17-19 atoms
> show #!17-19 cartoons
> color #17 #ff557fff
> ribbon style thickness 0.6
> select clear
> fitmap #17 inMap #1
Fit molecule 231006_PIP2_HC_90.pdb (#17) to map
WT_PIP2_P68_J150_009_volume_map.mrc (#1) using 11526 atoms
average map value = 0.0003365, steps = 464
shifted from previous position = 60.8
rotated from previous position = 24.5 degrees
atoms outside contour = 11526, contour level = 0.084067
Position of 231006_PIP2_HC_90.pdb (#17) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.12268988 0.98521157 -0.11960501 103.51842698
-0.92084376 0.15795414 0.35650704 213.58576967
0.37012696 0.06639772 0.92660530 63.99014458
Axis -0.14583979 -0.24619136 -0.95818608
Axis point 152.16987089 49.52669903 0.00000000
Rotation angle (degrees) 84.05206677
Shift along axis -128.99454312
> ui mousemode right "translate selected models"
> select add #17
11526 atoms, 11724 bonds, 6 pseudobonds, 1266 residues, 2 models selected
> view matrix models
> #17,0.91038,0.17268,-0.37601,-46.057,-0.18495,0.98274,0.0035092,-60.982,0.37013,0.066349,0.92661,-141.03
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.91038,0.17268,-0.37601,-17.729,-0.18495,0.98274,0.0035092,-40.744,0.37013,0.066349,0.92661,-124.51
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.59061,-0.78584,0.1834,102.65,0.78528,0.61203,0.093574,-157.95,-0.18578,0.088755,0.97857,-42.987
> view matrix models
> #17,0.69309,0.31893,-0.64645,40.933,-0.52553,0.83739,-0.15032,68.186,0.49339,0.44392,0.748,-178.67
> view matrix models
> #17,0.25819,0.9349,0.2435,-143.17,-0.95936,0.21841,0.17868,190.03,0.11387,-0.27974,0.9533,-26.955
> view matrix models
> #17,-0.49385,0.68738,-0.53256,160.12,-0.83163,-0.55225,0.058386,319.81,-0.25398,0.47173,0.84437,-73.242
> view matrix models
> #17,-0.88482,0.43784,0.15932,149.5,-0.38946,-0.88272,0.26291,265.61,0.25574,0.17058,0.95158,-127.09
> view matrix models
> #17,-0.95517,0.26487,-0.13229,241.03,-0.26326,-0.96426,-0.029796,308.49,-0.13546,0.0063684,0.99076,-39.65
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.95517,0.26487,-0.13229,255.7,-0.26326,-0.96426,-0.029796,315.7,-0.13546,0.0063684,0.99076,-43.241
> fitmap #17 inMap #1
Fit molecule 231006_PIP2_HC_90.pdb (#17) to map
WT_PIP2_P68_J150_009_volume_map.mrc (#1) using 11526 atoms
average map value = 0.1776, steps = 108
shifted from previous position = 10.7
rotated from previous position = 9 degrees
atoms outside contour = 1312, contour level = 0.084067
Position of 231006_PIP2_HC_90.pdb (#17) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.49939248 -0.86637588 -0.00007891 401.24114656
0.86637588 -0.49939248 -0.00000801 107.35493075
-0.00003246 -0.00007237 1.00000001 0.02478257
Axis -0.00003714 -0.00002680 1.00000000
Axis point 169.60477101 169.59963292 0.00000000
Rotation angle (degrees) 119.95981452
Shift along axis 0.00700158
> view matrix models
> #17,-0.98201,0.18885,-8.3786e-06,248.32,-0.18885,-0.98201,-2.9595e-05,309.49,-1.3816e-05,-2.748e-05,1,-71.796
> view matrix models
> #17,-0.98201,0.18885,-8.3786e-06,246.28,-0.18885,-0.98201,-2.9595e-05,308.4,-1.3816e-05,-2.748e-05,1,-71.813
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.55538,-0.62177,-0.55222,406.59,0.79754,-0.58633,-0.14194,98.465,-0.23553,-0.51925,0.82152,86.954
> view matrix models
> #17,-0.32594,-0.93222,0.15723,298.04,0.91303,-0.26726,0.30815,-52.814,-0.24524,0.244,0.93825,-60.966
> view matrix models
> #17,0.24737,-0.9686,0.025075,229.76,0.9688,0.24686,-0.022042,-92.554,0.01516,0.029745,0.99944,-79.34
> view matrix models
> #17,0.57134,-0.79843,-0.18995,183.01,0.79497,0.59591,-0.11367,-106.48,0.20395,-0.08606,0.97519,-87.538
> view matrix models
> #17,0.73963,-0.65643,0.14848,72.057,0.65382,0.75314,0.072749,-141.34,-0.15958,0.043274,0.98624,-49.721
> view matrix models
> #17,0.91,-0.41459,-0.0024811,28.167,0.41448,0.90987,-0.018234,-111.65,0.0098171,0.015564,0.99983,-76.096
> fitmap #17 inMap #1
Fit molecule 231006_PIP2_HC_90.pdb (#17) to map
WT_PIP2_P68_J150_009_volume_map.mrc (#1) using 11526 atoms
average map value = 0.1776, steps = 108
shifted from previous position = 3.55
rotated from previous position = 13.6 degrees
atoms outside contour = 1311, contour level = 0.084067
Position of 231006_PIP2_HC_90.pdb (#17) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.49939449 0.86637472 -0.00015750 -62.01244167
-0.86637473 0.49939446 -0.00017212 231.86485271
-0.00007047 0.00022241 0.99999999 -0.02032724
Axis 0.00022769 -0.00005023 -0.99999997
Axis point 169.63264160 169.59345189 0.00000000
Rotation angle (degrees) 60.04005412
Shift along axis -0.00543780
> select clear
> hide #!19 models
> hide #!18 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!18 models
> select add #17
11526 atoms, 11724 bonds, 6 pseudobonds, 1266 residues, 2 models selected
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.3
Changed 11724 bond radii
> setattr =sel p display false
Assigning display attribute to 6 items
> select #17:200
48 atoms, 42 bonds, 6 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 0
Assigning ss_type attribute to 6 items
> show #!20 models
> hide sel surfaces
[Repeated 1 time(s)]
> select add #20
11832 atoms, 12108 bonds, 6 pseudobonds, 1242 residues, 3 models selected
> hide sel surfaces
> select subtract #20
48 atoms, 42 bonds, 6 residues, 7 models selected
> show #!19 models
> hide #!20 models
> hide #!19 models
> hide #!18 models
> select #17:45-52
396 atoms, 408 bonds, 48 residues, 1 model selected
> select #17:45-54
498 atoms, 510 bonds, 60 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 0
Assigning ss_type attribute to 60 items
> select clear
> select ::name="PIO"
282 atoms, 282 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel orange
> color sel byhetero
> select clear
> select down
Nothing selected
> select down
Nothing selected
> select ::name="PIO"
282 atoms, 282 bonds, 6 residues, 1 model selected
> color sel green
> color sel cyan
> color sel byhetero
> select clear
> show #!18 models
> select ::name="CLR"
504 atoms, 558 bonds, 18 residues, 2 models selected
> show sel atoms
> hide #!17 models
> mlp sel & #!18
mlp: no amino acids specified
> select add #20
11952 atoms, 12252 bonds, 6 pseudobonds, 1242 residues, 3 models selected
> select subtract #20
168 atoms, 186 bonds, 6 residues, 7 models selected
> select add #18
11400 atoms, 11652 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> select subtract #18
6 models selected
> select add #18
11400 atoms, 11652 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> mlp sel
Map values for surface "230904_Chol_HC_150.pdb_A SES surface": minimum -27.81,
mean 0.2399, maximum 23.77
Map values for surface "230904_Chol_HC_150.pdb_B SES surface": minimum -28.02,
mean 0.1571, maximum 25.31
Map values for surface "230904_Chol_HC_150.pdb_C SES surface": minimum -27.97,
mean 0.1452, maximum 24.75
Map values for surface "230904_Chol_HC_150.pdb_D SES surface": minimum -27.84,
mean 0.223, maximum 24.9
Map values for surface "230904_Chol_HC_150.pdb_E SES surface": minimum -27.89,
mean 0.1406, maximum 24.79
Map values for surface "230904_Chol_HC_150.pdb_F SES surface": minimum -27.69,
mean 0.1485, maximum 25.26
To also show corresponding color key, enter the above mlp command and add key
true
> clip front 0
> ~clip
> hide sel cartoons
> hide sel surfaces
> show sel cartoons
> select clear
> show #!17 models
> morph #17,18
Computed 51 frame morph #21
> coordset #21 1,51
> close #17
> close #21
> undo
[Repeated 1 time(s)]
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Models/231006_PIP2_HC_90.pdb"
Chain information for 231006_PIP2_HC_90.pdb #17
---
Chain | Description
A B C D E F | No description available
> color #17 #ff557fff
> hide #!17 atoms
> show #!17 cartoons
> color #17 #ff557fff
> fitmap #17 inMap #1
Fit molecule 231006_PIP2_HC_90.pdb (#17) to map
WT_PIP2_P68_J150_009_volume_map.mrc (#1) using 11526 atoms
average map value = 0.0003365, steps = 464
shifted from previous position = 60.8
rotated from previous position = 24.5 degrees
atoms outside contour = 11526, contour level = 0.084067
Position of 231006_PIP2_HC_90.pdb (#17) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.12268988 0.98521157 -0.11960501 103.51842698
-0.92084376 0.15795414 0.35650704 213.58576967
0.37012696 0.06639772 0.92660530 63.99014458
Axis -0.14583979 -0.24619136 -0.95818608
Axis point 152.16987089 49.52669903 0.00000000
Rotation angle (degrees) 84.05206677
Shift along axis -128.99454312
> show #!3 models
> hide #!3 models
> show #!18 models
> select subtract #18
6 models selected
> ui mousemode right "translate selected models"
> select add #17
11526 atoms, 11724 bonds, 6 pseudobonds, 1266 residues, 2 models selected
> view matrix models
> #17,0.91038,0.17268,-0.37601,63.716,-0.18495,0.98274,0.0035092,-71.828,0.37013,0.066349,0.92661,-126.45
> view matrix models
> #17,0.91038,0.17268,-0.37601,-13.502,-0.18495,0.98274,0.0035092,-22.938,0.37013,0.066349,0.92661,-115.33
> view matrix models
> #17,0.91038,0.17268,-0.37601,-2.7055,-0.18495,0.98274,0.0035092,-24.895,0.37013,0.066349,0.92661,-133.5
> fitmap #17 inMap #1
Fit molecule 231006_PIP2_HC_90.pdb (#17) to map
WT_PIP2_P68_J150_009_volume_map.mrc (#1) using 11526 atoms
average map value = 0.06834, steps = 72
shifted from previous position = 2.99
rotated from previous position = 5.25 degrees
atoms outside contour = 8196, contour level = 0.084067
Position of 231006_PIP2_HC_90.pdb (#17) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.12947023 0.98727610 -0.09232209 0.97975031
-0.94974864 0.15022797 0.27460717 251.30132577
0.28498245 0.05212933 0.95711418 -47.66813956
Axis -0.11202700 -0.18998880 -0.97537388
Axis point 148.17541530 129.81546918 0.00000000
Rotation angle (degrees) 83.19987218
Shift along axis -1.35993665
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.77406,-0.62014,-0.12751,112.21,0.3209,0.55791,-0.76535,93.893,0.54576,0.5515,0.63086,-191.51
> view matrix models
> #17,0.41356,-0.90536,0.096395,183.12,0.90974,0.40664,-0.083773,-97.818,0.036647,0.12234,0.99181,-94.607
> fitmap #17 inMap #1
Fit molecule 231006_PIP2_HC_90.pdb (#17) to map
WT_PIP2_P68_J150_009_volume_map.mrc (#1) using 11526 atoms
average map value = 0.1779, steps = 144
shifted from previous position = 8.28
rotated from previous position = 9 degrees
atoms outside contour = 1297, contour level = 0.084067
Position of 231006_PIP2_HC_90.pdb (#17) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.99999975 0.00070003 0.00011261 -0.12840814
-0.00070003 0.99999976 0.00001442 0.11692133
-0.00011260 -0.00001449 1.00000000 0.02751741
Axis -0.02038098 0.15877969 -0.98710366
Axis point 168.31477364 183.66649757 0.00000000
Rotation angle (degrees) 0.04063292
Shift along axis -0.00598071
> view matrix models
> #17,0.57709,-0.80933,0.10933,129.09,0.78258,0.5863,0.20932,-159.69,-0.23351,-0.035237,0.97172,-20.706
> view matrix models
> #17,0.84555,-0.52807,-0.078665,68.264,0.49174,0.82766,-0.27049,-68.586,0.20795,0.19003,0.9595,-131.68
> view matrix models
> #17,0.95288,-0.29805,-0.056488,7.226,0.29421,0.95336,-0.067378,-91.418,0.073935,0.047584,0.99613,-91.104
> fitmap #17 inMap #1
Fit molecule 231006_PIP2_HC_90.pdb (#17) to map
WT_PIP2_P68_J150_009_volume_map.mrc (#1) using 11526 atoms
average map value = 0.1776, steps = 100
shifted from previous position = 0.229
rotated from previous position = 8.13 degrees
atoms outside contour = 1305, contour level = 0.084067
Position of 231006_PIP2_HC_90.pdb (#17) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.49936269 0.86639304 0.00002022 -62.03372790
-0.86639303 0.49936268 0.00018202 231.82679916
0.00014760 -0.00010840 0.99999999 0.00003691
Axis -0.00016760 -0.00007352 -0.99999998
Axis point 169.58057604 169.59057282 0.00000000
Rotation angle (degrees) 60.04215595
Shift along axis -0.00668272
> select clear
> select #17:200
48 atoms, 42 bonds, 6 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 0
Assigning ss_type attribute to 6 items
> select #17:46-55
462 atoms, 462 bonds, 60 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 0
Assigning ss_type attribute to 60 items
> select clear
> select add #17
11526 atoms, 11724 bonds, 6 pseudobonds, 1266 residues, 2 models selected
> ui tool show "Selection Inspector"
> setattr =sel p display false
Assigning display attribute to 6 items
> size =sel stickRadius 0.3
Changed 11724 bond radii
> select clear
> ribbon style thickness 0.6
> select clear
> select ::name="PIO"
282 atoms, 282 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel cyan
> color sel byhetero
> select clear
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> select clear
> show #!20 models
> color #20 #aaaaffff
> color #20 magenta
> color #20 #ffaaffff
> color #7 #ffaaffb3 models
> color #8 #ffaaffb3 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/230903_All_Align.cxs"
> color #9 #aa5500ff models
> color #10 #aa5500ff models
> color #11 #00aa00ff models
> color #12 #00aa00ff models
> hide #!20 models
> show #!20 models
> hide #!20 models
> hide #!18 models
> hide #!17 models
> show #!4 models
> hide #!4 models
> show #!3 models
> transparency 0
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!3 models
> show #!3 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.1805
> hide #!7 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!7 models
> show #!20 models
> hide #!7 models
> show #!3 models
> hide #!3 models
> show #!18 models
> morph #18,20,17
Computed 101 frame morph #21
> coordset #21 1,101
> hide #!21 models
> close #21
> show #!5 models
> hide #!5 models
> show #!7 models
> show #!9 models
> volume #9 level 0.6345
> show #!10 models
> hide #!10 models
> fitmap #9 inMap #1
Fit map N55H_POPE_C6_P58_J139_004_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 29710 points
correlation = 0.7241, correlation about mean = 0.1056, overlap = 1838
steps = 260, shift = 32.7, angle = 16.5 degrees
Position of N55H_POPE_C6_P58_J139_004_volume_map.mrc (#9) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.33525711 0.89895582 -0.28192393 63.01461047
-0.93379245 0.35677972 0.02720110 239.33114414
0.12503732 0.25413908 0.95905110 -4.81702597
Axis 0.12000610 -0.21520342 -0.96916770
Axis point 198.19355642 71.21595615 0.00000000
Rotation angle (degrees) 71.00146607
Shift along axis -39.27423735
> ui mousemode right "rotate selected models"
> select add #9
2 models selected
> view matrix models
> #9,0.97202,0.2346,0.011801,-46.176,-0.23019,0.96135,-0.15105,50.824,-0.046781,0.1441,0.98846,-40.308
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.97202,0.2346,0.011801,-65.054,-0.23019,0.96135,-0.15105,29.672,-0.046781,0.1441,0.98846,-49.027
> view matrix models
> #9,0.97202,0.2346,0.011801,-69.753,-0.23019,0.96135,-0.15105,21.828,-0.046781,0.1441,0.98846,-49.368
> view matrix models
> #9,0.97202,0.2346,0.011801,-66.31,-0.23019,0.96135,-0.15105,31.882,-0.046781,0.1441,0.98846,-56.283
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.99375,0.10519,-0.037404,-44.443,-0.10609,0.9941,-0.022722,-7.6899,0.034793,0.026548,0.99904,-52.66
> view matrix models
> #9,0.99775,-0.065319,-0.015173,-24.028,0.061278,0.98,-0.18932,-6.567,0.027236,0.18797,0.9818,-71.974
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.99775,-0.065319,-0.015173,-21.575,0.061278,0.98,-0.18932,-14.341,0.027236,0.18797,0.9818,-74.116
> fitmap #9 inMap #1
Fit map N55H_POPE_C6_P58_J139_004_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 29710 points
correlation = 0.9011, correlation about mean = 0.3642, overlap = 4905
steps = 100, shift = 5.56, angle = 11 degrees
Position of N55H_POPE_C6_P58_J139_004_volume_map.mrc (#9) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40874414 0.91264902 -0.00000336 -16.45053949
-0.91264902 0.40874414 -0.00002185 240.54929908
-0.00001857 0.00001201 1.00000001 30.15206210
Axis 0.00001855 0.00000833 -1.00000000
Axis point 177.42840075 132.97068170 0.00000000
Rotation angle (degrees) 65.87403199
Shift along axis -30.15036328
> fitmap #9 inMap #1
Fit map N55H_POPE_C6_P58_J139_004_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 29710 points
correlation = 0.9012, correlation about mean = 0.3644, overlap = 4905
steps = 48, shift = 0.0038, angle = 0.0154 degrees
Position of N55H_POPE_C6_P58_J139_004_volume_map.mrc (#9) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40898936 0.91253915 0.00000223 -16.46790190
-0.91253915 0.40898936 -0.00003981 240.49880525
-0.00003724 0.00001425 1.00000001 30.15418165
Axis 0.00002962 0.00002163 -1.00000000
Axis point 177.43588722 132.96252036 0.00000000
Rotation angle (degrees) 65.85863600
Shift along axis -30.14946832
> fitmap #9 inMap #1
Fit map N55H_POPE_C6_P58_J139_004_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 29710 points
correlation = 0.9012, correlation about mean = 0.3643, overlap = 4905
steps = 28, shift = 0.017, angle = 0.014 degrees
Position of N55H_POPE_C6_P58_J139_004_volume_map.mrc (#9) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40877490 0.91263525 -0.00000446 -16.45953480
-0.91263525 0.40877490 0.00002735 240.54773100
0.00002678 -0.00000711 1.00000001 30.14676293
Axis -0.00001888 -0.00001711 -1.00000000
Axis point 177.42839260 132.97779659 0.00000000
Rotation angle (degrees) 65.87210099
Shift along axis -30.15056838
> view matrix models
> #9,0.99611,-0.088091,-1.7463e-05,-19.746,0.088091,0.99611,5.2324e-05,-45.183,1.2786e-05,-5.3659e-05,1,-42.381
> fitmap #9 inMap #1
Fit map N55H_POPE_C6_P58_J139_004_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 29710 points
correlation = 0.9012, correlation about mean = 0.3643, overlap = 4905
steps = 56, shift = 1.79, angle = 0.00141 degrees
Position of N55H_POPE_C6_P58_J139_004_volume_map.mrc (#9) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40877252 0.91263631 -0.00000384 -16.45891324
-0.91263631 0.40877252 0.00000287 240.54535440
0.00000418 0.00000234 1.00000001 30.14932904
Axis -0.00000029 -0.00000440 -1.00000000
Axis point 177.42691471 132.97585146 0.00000000
Rotation angle (degrees) 65.87225037
Shift along axis -30.15038159
> fitmap #9 inMap #1
Fit map N55H_POPE_C6_P58_J139_004_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 29710 points
correlation = 0.9012, correlation about mean = 0.3644, overlap = 4905
steps = 44, shift = 0.0159, angle = 0.0132 degrees
Position of N55H_POPE_C6_P58_J139_004_volume_map.mrc (#9) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40897100 0.91254738 0.00005459 -16.46693254
-0.91254738 0.40897100 -0.00004666 240.50711129
-0.00006490 -0.00003072 1.00000000 30.16495060
Axis 0.00000873 0.00006547 -1.00000000
Axis point 177.43939564 132.96679241 0.00000000
Rotation angle (degrees) 65.85978897
Shift along axis -30.14934828
> fitmap #9 inMap #1
Fit map N55H_POPE_C6_P58_J139_004_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 29710 points
correlation = 0.9012, correlation about mean = 0.3644, overlap = 4905
steps = 40, shift = 0.0179, angle = 0.0082 degrees
Position of N55H_POPE_C6_P58_J139_004_volume_map.mrc (#9) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40895999 0.91255232 -0.00006546 -16.46769070
-0.91255232 0.40895999 0.00003038 240.50164754
0.00005449 0.00004732 1.00000000 30.13646863
Axis 0.00000928 -0.00006572 -1.00000000
Axis point 177.42929860 132.96248706 0.00000000
Rotation angle (degrees) 65.86048018
Shift along axis -30.15242789
> fitmap #9 inMap #1
Fit map N55H_POPE_C6_P58_J139_004_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 29710 points
correlation = 0.9012, correlation about mean = 0.3642, overlap = 4905
steps = 40, shift = 0.00294, angle = 0.0137 degrees
Position of N55H_POPE_C6_P58_J139_004_volume_map.mrc (#9) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40875338 0.91264487 -0.00014222 -16.44358710
-0.91264488 0.40875340 0.00003684 240.54107813
0.00009176 0.00011475 1.00000000 30.12118952
Axis 0.00004268 -0.00012819 -0.99999999
Axis point 177.42478055 132.95872863 0.00000000
Rotation angle (degrees) 65.87345156
Shift along axis -30.15272579
> fitmap #9 inMap #1
Fit map N55H_POPE_C6_P58_J139_004_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 29710 points
correlation = 0.9012, correlation about mean = 0.3643, overlap = 4905
steps = 40, shift = 0.0151, angle = 0.013 degrees
Position of N55H_POPE_C6_P58_J139_004_volume_map.mrc (#9) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40879877 0.91262455 0.00007654 -16.46213826
-0.91262455 0.40879877 0.00000936 240.54024547
-0.00002275 -0.00007367 1.00000000 30.16398353
Axis -0.00004549 0.00005440 -1.00000000
Axis point 177.42789760 132.97812510 0.00000000
Rotation angle (degrees) 65.87060228
Shift along axis -30.15014956
> fitmap #9 inMap #1
Fit map N55H_POPE_C6_P58_J139_004_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 29710 points
correlation = 0.9012, correlation about mean = 0.3644, overlap = 4905
steps = 40, shift = 0.0056, angle = 0.0101 degrees
Position of N55H_POPE_C6_P58_J139_004_volume_map.mrc (#9) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40895855 0.91255296 0.00008860 -16.47310036
-0.91255296 0.40895855 0.00002954 240.50960092
-0.00000928 -0.00009293 1.00000000 30.16546844
Axis -0.00006710 0.00005363 -1.00000000
Axis point 177.43403883 132.97419523 0.00000000
Rotation angle (degrees) 65.86057067
Shift along axis -30.15146436
> show #!10 models
> hide #!9 models
> view matrix models
> #9,0.99609,-0.088291,1.0874e-05,-25.247,0.088291,0.99609,0.00014099,-56.878,-2.328e-05,-0.00013948,1,-61.109
> select subtract #9
Nothing selected
> show #!9 models
> fitmap #9 inMap #1
Fit map N55H_POPE_C6_P58_J139_004_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 29710 points
correlation = 0.9012, correlation about mean = 0.3643, overlap = 4905
steps = 196, shift = 24.5, angle = 0.0121 degrees
Position of N55H_POPE_C6_P58_J139_004_volume_map.mrc (#9) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40878315 0.91263155 0.00000213 -16.45417490
-0.91263155 0.40878315 0.00000930 240.53510094
0.00000762 -0.00000574 1.00000001 30.14999359
Axis -0.00000824 -0.00000301 -1.00000000
Axis point 177.42365263 132.96743568 0.00000000
Rotation angle (degrees) 65.87158281
Shift along axis -30.15058144
> select add #10
2 models selected
> view matrix models #10,1,0,0,-13.919,0,1,0,-37.915,0,0,1,-41.314
> view matrix models #10,1,0,0,-24.288,0,1,0,-36.559,0,0,1,-48.086
> view matrix models #10,1,0,0,-26.82,0,1,0,-34.667,0,0,1,-47.904
> view matrix models #10,1,0,0,-26.329,0,1,0,-34.246,0,0,1,-46.821
> volume #10 level 0.8465
> fitmap #9 inMap #1
Fit map N55H_POPE_C6_P58_J139_004_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 29710 points
correlation = 0.9012, correlation about mean = 0.3643, overlap = 4905
steps = 40, shift = 0.0161, angle = 0.0103 degrees
Position of N55H_POPE_C6_P58_J139_004_volume_map.mrc (#9) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40877232 0.91263640 0.00001451 -16.46019496
-0.91263639 0.40877231 0.00018814 240.52859413
0.00016577 -0.00009014 0.99999999 30.13976421
Axis -0.00015246 -0.00008287 -0.99999998
Axis point 177.40917383 132.97081684 0.00000000
Rotation angle (degrees) 65.87226369
Shift along axis -30.15718633
> fitmap #10 inMap #1
Fit map N55H_POPE_C6_P58_J139_004_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 36934 points
correlation = 0.8863, correlation about mean = 0.4119, overlap = 9897
steps = 92, shift = 8.59, angle = 4.99 degrees
Position of N55H_POPE_C6_P58_J139_004_volume_map_sharp.mrc (#10) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40781172 0.91306605 -0.00003523 -16.37612283
-0.91306604 0.40781172 -0.00011985 240.74713954
-0.00009507 0.00008105 1.00000000 30.25073311
Axis 0.00011002 0.00003277 -0.99999999
Axis point 177.41246647 132.99627023 0.00000000
Rotation angle (degrees) 65.93255577
Shift along axis -30.24464639
> select clear
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!11 models
> volume #11 level 0.3969
> volume #12 level 0.5738
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!7 models
> show #!1 models
> select add #11
2 models selected
> volume #1 level 0.1232
> view matrix models #11,1,0,0,-1.812,0,1,0,-2.1757,0,0,1,-99.584
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.83034,0.55005,-0.089292,191.72,0.48927,0.79632,0.35564,-95.245,0.26673,0.25162,-0.93035,114.33
> view matrix models
> #11,-0.82989,0.55031,0.091836,164.7,0.55297,0.78941,0.26658,-90.002,0.074204,0.27201,-0.95943,142.89
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.90721,0.38715,0.1646,187.75,0.41221,0.8962,0.16406,-69.983,-0.084002,0.21668,-0.97262,174.92
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.90721,0.38715,0.1646,159.25,0.41221,0.8962,0.16406,-93.449,-0.084002,0.21668,-0.97262,220.86
> view matrix models
> #11,-0.90721,0.38715,0.1646,157.82,0.41221,0.8962,0.16406,-97.959,-0.084002,0.21668,-0.97262,221.04
> fitmap #11 inMap #1
Fit map N55H_POPE_C2_P58_J151_004_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 62015 points
correlation = 0.7958, correlation about mean = 0.3491, overlap = 5144
steps = 228, shift = 2.1, angle = 26.9 degrees
Position of N55H_POPE_C2_P58_J151_004_volume_map.mrc (#11) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.47291422 0.88110847 -0.00009613 -21.03134436
0.88110846 -0.47291422 -0.00007861 112.13161583
-0.00011472 -0.00004753 -0.99999999 314.73122979
Axis 0.85826414 0.51320821 -0.00008484
Axis point 0.00000000 62.35210624 157.36506009
Rotation angle (degrees) 179.99896243
Shift along axis 39.46971640
> fitmap #11 inMap #1
Fit map N55H_POPE_C2_P58_J151_004_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 62015 points
correlation = 0.7958, correlation about mean = 0.3491, overlap = 5144
steps = 24, shift = 0.0032, angle = 0.0236 degrees
Position of N55H_POPE_C2_P58_J151_004_volume_map.mrc (#11) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.47296324 0.88108216 0.00005720 -21.05803408
0.88108211 -0.47296323 0.00029930 112.08402861
0.00029077 -0.00009116 -0.99999996 314.68247501
Axis -0.85817764 -0.51335283 -0.00010323
Axis point 0.00000000 62.36121640 157.33641962
Rotation angle (degrees) 179.98696528
Shift along axis -39.49960319
> fitmap #11 inMap #1
Fit map N55H_POPE_C2_P58_J151_004_volume_map.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 62015 points
correlation = 0.7958, correlation about mean = 0.3491, overlap = 5144
steps = 24, shift = 0.00353, angle = 0.0161 degrees
Position of N55H_POPE_C2_P58_J151_004_volume_map.mrc (#11) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.47287464 0.88112971 0.00008749 -21.05659220
0.88112955 -0.47287461 0.00056058 112.02267496
0.00053532 -0.00018799 -0.99999984 314.66106472
Axis -0.85815538 -0.51339002 -0.00018241
Axis point 0.00000000 62.34985300 157.32111320
Rotation angle (degrees) 179.97501047
Shift along axis -39.49889255
> select add #12
4 models selected
> select subtract #11
2 models selected
> view matrix models #12,1,0,0,-42.098,0,1,0,51.193,0,0,1,-54.94
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.93262,-0.015062,0.36056,178.32,-0.23686,0.77934,-0.58011,202.19,-0.27226,-0.62642,-0.73039,329.84
> view matrix models
> #12,-0.88284,-0.45953,0.097047,273.22,-0.46951,0.86881,-0.15724,159.24,-0.012057,-0.18439,-0.98278,268.64
> view matrix models
> #12,-0.88152,-0.46593,-0.076302,299.81,-0.46169,0.8845,-0.06718,142.49,0.09879,-0.023993,-0.99482,232.24
> view matrix models
> #12,-0.68232,-0.37191,-0.62938,341.07,-0.39981,0.9106,-0.10465,135.69,0.61204,0.18023,-0.77002,97.675
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.68232,-0.37191,-0.62938,356.61,-0.39981,0.9106,-0.10465,52.559,0.61204,0.18023,-0.77002,108.01
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.79949,-0.59033,-0.11102,326.5,-0.59843,0.79876,0.062196,71.372,0.05196,0.11616,-0.99187,229
> fitmap #12 inMap #1
Fit map N55H_POPE_C2_P58_J151_004_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 60925 points
correlation = 0.6371, correlation about mean = 0.08177, overlap = 5462
steps = 84, shift = 5.08, angle = 7.31 degrees
Position of N55H_POPE_C2_P58_J151_004_volume_map_sharp.mrc (#12) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.81866939 0.57340622 0.03139652 201.57314020
0.56201085 0.78876723 0.24897806 -62.89701946
0.11800102 0.22147591 -0.96800010 267.41680881
Axis -0.30031340 -0.94568928 -0.12443327
Axis point 107.58640960 0.00000000 140.16278109
Rotation angle (degrees) 177.37556104
Shift along axis -34.32962586
> view matrix models
> #12,-0.95982,-0.22242,-0.17108,306.1,-0.23089,0.97248,0.031101,-0.18635,0.15946,0.069354,-0.98477,214.33
> fitmap #12 inMap #1
Fit map N55H_POPE_C2_P58_J151_004_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 60925 points
correlation = 0.7905, correlation about mean = 0.3902, overlap = 8881
steps = 120, shift = 7.97, angle = 9.99 degrees
Position of N55H_POPE_C2_P58_J151_004_volume_map_sharp.mrc (#12) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.52571249 0.85066225 0.00035241 123.78995881
0.85066221 0.52571217 0.00071906 -24.30442978
0.00042641 0.00067780 -0.99999968 314.23055756
Axis -0.48692116 -0.87344583 -0.00039378
Axis point 68.66568299 0.00000000 157.12202710
Rotation angle (degrees) 179.99757277
Shift along axis -39.17108455
> hide #!1 models
> volume #12 level 1.031
> hide #!12 models
> show #!12 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> view matrix models
> #12,-0.98416,-0.1763,0.018707,269.16,-0.17625,0.98434,0.0043907,-5.892,-0.019188,0.0010241,-0.99982,245.75
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.98416,-0.1763,0.018707,268.16,-0.17625,0.98434,0.0043907,-5.1865,-0.019188,0.0010241,-0.99982,240.89
> fitmap #12 inMap #1
Fit map N55H_POPE_C2_P58_J151_004_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 28800 points
correlation = 0.8142, correlation about mean = 0.3067, overlap = 6964
steps = 88, shift = 4.93, angle = 2.72 degrees
Position of N55H_POPE_C2_P58_J151_004_volume_map_sharp.mrc (#12) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.52560458 0.85072899 -0.00013292 123.84850017
0.85072899 0.52560459 0.00006149 -24.20616178
0.00012218 -0.00008075 -0.99999999 314.30337194
Axis -0.48701413 -0.87339409 0.00000720
Axis point 68.65992225 0.00000000 157.15596584
Rotation angle (degrees) 179.99163258
Shift along axis -39.17218753
> fitmap #12 inMap #1
Fit map N55H_POPE_C2_P58_J151_004_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 28800 points
correlation = 0.8141, correlation about mean = 0.3066, overlap = 6964
steps = 48, shift = 0.0198, angle = 0.0108 degrees
Position of N55H_POPE_C2_P58_J151_004_volume_map_sharp.mrc (#12) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.52569534 0.85067291 0.00000428 123.83458467
0.85067291 0.52569535 -0.00001073 -24.18586712
-0.00001138 -0.00000200 -1.00000000 314.31107552
Axis 0.48723283 0.87327210 0.00002378
Axis point 68.66522185 0.00000000 157.15559831
Rotation angle (degrees) 179.99948646
Shift along axis 39.22290623
> fitmap #12 inMap #1
Fit map N55H_POPE_C2_P58_J151_004_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map.mrc using 28800 points
correlation = 0.8142, correlation about mean = 0.3068, overlap = 6964
steps = 44, shift = 0.00322, angle = 0.026 degrees
Position of N55H_POPE_C2_P58_J151_004_volume_map_sharp.mrc (#12) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.52554464 0.85076599 0.00025590 123.76050051
0.85076592 0.52554470 -0.00034324 -24.12464091
-0.00042650 0.00003733 -0.99999991 314.36398442
Axis 0.48706595 0.87336519 -0.00008694
Axis point 68.64242627 0.00000000 157.16908566
Rotation angle (degrees) 179.97761619
Shift along axis 39.18257426
> hide #!12 models
> show #!12 models
> hide #!11 models
> volume #12 level 0.558
> show #!11 models
> hide #!12 models
> show #!12 models
> hide #!11 models
> volume #12 level 0.8101
> show #!11 models
> hide #!12 models
> show #!13 models
> show #!14 models
> hide #!14 models
> show #!12 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> show #!12 models
> show #!11 models
> hide #!12 models
> show #!15 models
> hide #!11 models
> volume #16 level 0.3389
> show #!12 models
> hide #!12 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/230903_All_Align.cxs"
> hide #!15 models
> hide #!16 models
> show #!9 models
> volume #9 level 0.3437
> volume #9 level 0.2579
> volume #9 level 0.3294
> show #!10 models
> hide #!9 models
> volume #10 level 0.5672
> open
> C:/Users/OJS/Desktop/Phenix/230725_Cx43_N55H_POPE/RealSpaceRefine_27/231009_From25_real_space_refined_027.pdb
Chain information for 231009_From25_real_space_refined_027.pdb #21
---
Chain | Description
A B C D E F | No description available
> select add #21
8706 atoms, 8964 bonds, 6 pseudobonds, 1062 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> color #21 #55ffffff
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.9758,-0.21867,0.00039818,227.55,-0.21867,0.9758,8.2084e-05,-17.604,-0.00040649,-6.9711e-06,-1,202.86,#21,1,0,0,-49.101,0,1,0,-19.525,0,0,1,-40.338
> view matrix models
> #12,-0.9758,-0.21867,0.00039818,244.35,-0.21867,0.9758,8.2084e-05,-29.018,-0.00040649,-6.9711e-06,-1,195.32,#21,1,0,0,-32.3,0,1,0,-30.939,0,0,1,-47.882
> hide #!10 models
> show #!20 models
> view matrix models
> #12,-0.9758,-0.21867,0.00039818,244.97,-0.21867,0.9758,8.2084e-05,-30.095,-0.00040649,-6.9711e-06,-1,202.27,#21,1,0,0,-31.683,0,1,0,-32.016,0,0,1,-40.932
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.73851,-0.64935,0.18152,273.56,-0.61865,0.75965,0.20051,26.235,-0.26809,0.03578,-0.96273,219.95,#21,0.8627,-0.47213,-0.18121,79.871,0.43765,0.87656,-0.20026,-47.823,0.25339,0.093457,0.96284,-84.498
> view matrix models
> #12,-0.44589,-0.85395,-0.26823,322.93,-0.82583,0.50806,-0.2447,133.98,0.34524,0.1124,-0.93176,141.47,#21,0.62172,-0.73581,0.26842,87.058,0.69465,0.67633,0.24503,-119.09,-0.36184,0.034112,0.93162,14.94
> view matrix models
> #12,-0.042345,-0.99023,-0.13287,290.51,-0.99829,0.036571,0.0456,200.16,-0.040295,0.13457,-0.99008,183.11,#21,0.2578,-0.95702,0.13289,188.71,0.96615,0.25398,-0.045194,-56.628,0.0094996,0.14004,0.9901,-60.581
> view matrix models
> #12,0.64273,-0.6971,0.31772,126.51,-0.7608,-0.62948,0.15792,274.57,0.089913,-0.34322,-0.93494,243.16,#21,-0.47461,-0.82075,-0.31798,336.73,0.8801,-0.44787,-0.1576,70.279,-0.013058,-0.35465,0.93491,20.088
> view matrix models
> #12,0.72192,-0.66497,0.19144,125.88,-0.6862,-0.72364,0.074057,290.98,0.089286,-0.18483,-0.97871,221.48,#21,-0.55896,-0.80672,-0.19173,328.7,0.82785,-0.55607,-0.073773,80.961,-0.047099,-0.19996,0.97867,-3.1151
> view matrix models
> #12,0.65181,-0.7487,0.12079,154.02,-0.75799,-0.64825,0.072226,286.05,0.024226,-0.13863,-0.99005,221.65,#21,-0.47228,-0.8731,-0.12105,315.79,0.88143,-0.46681,-0.071914,60.585,0.0062815,-0.14066,0.99004,-20.597
> fitmap #21 inMap #10
Fit molecule 231009_From25_real_space_refined_027.pdb (#21) to map
N55H_POPE_C6_P58_J139_004_volume_map_sharp.mrc (#10) using 8706 atoms
average map value = 1.103, steps = 84
shifted from previous position = 1.33
rotated from previous position = 10.6 degrees
atoms outside contour = 2389, contour level = 0.56725
Position of 231009_From25_real_space_refined_027.pdb (#21) relative to
N55H_POPE_C6_P58_J139_004_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.50003754 -0.86600346 0.00068022 333.04652030
0.86600361 -0.50003772 -0.00010983 89.29271650
0.00043525 0.00053415 0.99999976 -0.18267864
Axis 0.00037181 0.00014144 0.99999992
Axis point 140.74800078 140.78379317 0.00000000
Rotation angle (degrees) 120.00249780
Shift along axis -0.04621835
> select clear
> show #!18 models
> hide #!20 models
> morph #18,21
Computed 51 frame morph #22
> coordset #22 1,51
> morph #21,19
Computed 51 frame morph #23
> coordset #23 1,51
> close #23
> close #22
> morph #21,18
Computed 51 frame morph #22
> coordset #22 1,51
> morph #21,18,20,17
Computed 151 frame morph #23
> coordset #23 1,151
> close #22
> morph #21,17
Computed 51 frame morph #22
> coordset #22 1,51
> hide #!22 models
> show #!22 models
> hide #!23 models
> hide #!22 models
> close #22
> close #23
> show #!21 models
> select #21:200
48 atoms, 42 bonds, 6 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 0
Assigning ss_type attribute to 6 items
> ui tool show "Selection Inspector"
> select #21:196-200
240 atoms, 240 bonds, 30 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 0
Assigning ss_type attribute to 30 items
> setattr sel r ss_type 2
Assigning ss_type attribute to 30 items
> setattr sel r ss_type 0
Assigning ss_type attribute to 30 items
> select down
240 atoms, 240 bonds, 30 residues, 1 model selected
> select #21:196-199
192 atoms, 192 bonds, 24 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 2
Assigning ss_type attribute to 24 items
> select clear
> select #21:196-200
240 atoms, 240 bonds, 30 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 2
Assigning ss_type attribute to 30 items
> select clear
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/230903_All_Align.cxs"
> select :196-200
1680 atoms, 1680 bonds, 210 residues, 7 models selected
> ui tool show "Selection Inspector"
> setattr sel r ss_id 1
Assigning ss_id attribute to 210 items
> setattr sel r ss_type 2
Assigning ss_type attribute to 210 items
> hide #!21 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #!19 models
> show #!18 models
> show #!17 models
> show #!21 models
> select :52-55
1548 atoms, 1566 bonds, 168 residues, 7 models selected
> select :52-54
1176 atoms, 1176 bonds, 126 residues, 7 models selected
> select :52-53
924 atoms, 924 bonds, 84 residues, 7 models selected
> hide #!18 models
> hide #!19 models
> hide #!20 models
> hide #!21 models
> show #!21 models
> select :52-54
1176 atoms, 1176 bonds, 126 residues, 7 models selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 2
Assigning ss_type attribute to 126 items
> setattr sel r ss_id 1
Assigning ss_id attribute to 126 items
> hide #!21 models
> show #!18 models
> show #!19 models
> hide #!18 models
> hide #!17 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #!21 models
> select clear
> show #!18 models
> show #!17 models
> hide #!21 models
> hide #!20 models
> hide #!17 models
> hide #!19 models
> show #!19 models
> show #!21 models
> hide #!21 models
> hide #!19 models
> select add #18
11400 atoms, 11652 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> mlp sel
Map values for surface "230904_Chol_HC_150.pdb_A SES surface": minimum -27.81,
mean 0.2399, maximum 23.77
Map values for surface "230904_Chol_HC_150.pdb_B SES surface": minimum -28.02,
mean 0.1571, maximum 25.31
Map values for surface "230904_Chol_HC_150.pdb_C SES surface": minimum -27.97,
mean 0.1452, maximum 24.75
Map values for surface "230904_Chol_HC_150.pdb_D SES surface": minimum -27.84,
mean 0.223, maximum 24.9
Map values for surface "230904_Chol_HC_150.pdb_E SES surface": minimum -27.89,
mean 0.1406, maximum 24.79
Map values for surface "230904_Chol_HC_150.pdb_F SES surface": minimum -27.69,
mean 0.1485, maximum 25.26
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> hide #!18 models
> show #!17 models
> mlp #!17
Map values for surface "231006_PIP2_HC_90.pdb_A SES surface": minimum -27.87,
mean 0.03369, maximum 24.9
Map values for surface "231006_PIP2_HC_90.pdb_B SES surface": minimum -27.78,
mean 0.02849, maximum 26.04
Map values for surface "231006_PIP2_HC_90.pdb_C SES surface": minimum -28.51,
mean -0.003208, maximum 23.51
Map values for surface "231006_PIP2_HC_90.pdb_D SES surface": minimum -27.99,
mean 0.03851, maximum 26.17
Map values for surface "231006_PIP2_HC_90.pdb_E SES surface": minimum -27.97,
mean 0.03483, maximum 25.07
Map values for surface "231006_PIP2_HC_90.pdb_F SES surface": minimum -27.97,
mean -0.01962, maximum 23.57
To also show corresponding color key, enter the above mlp command and add key
true
> show #!18 models
> hide #!17 models
> show #!19 models
> hide #!18 models
> color bfactor #!19
8634 atoms, 1020 residues, 6 surfaces, atom bfactor range 96.3 to 171
> mlp #!19
Map values for surface "230926_CBX_HC_181.pdb_A SES surface": minimum -27.57,
mean 0.8045, maximum 24.47
Map values for surface "230926_CBX_HC_181.pdb_B SES surface": minimum -26.7,
mean 0.8385, maximum 24.42
Map values for surface "230926_CBX_HC_181.pdb_C SES surface": minimum -28.15,
mean 0.8719, maximum 24.27
Map values for surface "230926_CBX_HC_181.pdb_D SES surface": minimum -27.92,
mean 0.8499, maximum 24.31
Map values for surface "230926_CBX_HC_181.pdb_E SES surface": minimum -27.7,
mean 0.8051, maximum 24.33
Map values for surface "230926_CBX_HC_181.pdb_F SES surface": minimum -28.95,
mean 0.8538, maximum 24.25
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!19 models
> show #!18 models
> hide #!18 models
> show #!18 models
> show #!17 models
> hide #!18 models
> show #!18 models
> hide #!17 models
> show #!19 models
> hide #!18 models
> hide #!19 models
> show #!19 models
> hide #!19 surfaces
> select #19
8634 atoms, 8916 bonds, 6 pseudobonds, 1020 residues, 2 models selected
> color #19 #aa55ffff
> select clear
> select ::name="CBO"
246 atoms, 270 bonds, 6 residues, 1 model selected
> color sel dark green
> color sel byhetero
> select clear
> show #!18 models
> hide #!18-19 surfaces
> select #19:203:235
42 atoms, 42 bonds, 6 residues, 1 model selected
> select #19:203-235
1536 atoms, 1572 bonds, 186 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 1
Assigning ss_type attribute to 186 items
> select clear
> hide #!18 models
> show #!18 models
> select #19:74-110
1686 atoms, 1740 bonds, 192 residues, 1 model selected
> select #19:74-103
1578 atoms, 1632 bonds, 180 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 1
Assigning ss_type attribute to 180 items
> select clear
> select add #18
11400 atoms, 11652 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> select subtract #18
6 models selected
> hide #!19 models
> select add #18
11400 atoms, 11652 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> mlp sel
Map values for surface "230904_Chol_HC_150.pdb_A SES surface": minimum -27.81,
mean 0.2399, maximum 23.77
Map values for surface "230904_Chol_HC_150.pdb_B SES surface": minimum -28.02,
mean 0.1571, maximum 25.31
Map values for surface "230904_Chol_HC_150.pdb_C SES surface": minimum -27.97,
mean 0.1452, maximum 24.75
Map values for surface "230904_Chol_HC_150.pdb_D SES surface": minimum -27.84,
mean 0.223, maximum 24.9
Map values for surface "230904_Chol_HC_150.pdb_E SES surface": minimum -27.89,
mean 0.1406, maximum 24.79
Map values for surface "230904_Chol_HC_150.pdb_F SES surface": minimum -27.69,
mean 0.1485, maximum 25.26
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> show #!19 models
> hide #!18 models
> select add #19
20034 atoms, 20568 bonds, 12 pseudobonds, 2256 residues, 10 models selected
> hide sel & #!19 surfaces
> show sel & #!19 surfaces
> mlp sel & #!19
Map values for surface "230926_CBX_HC_181.pdb_A SES surface": minimum -27.57,
mean 0.8045, maximum 24.47
Map values for surface "230926_CBX_HC_181.pdb_B SES surface": minimum -26.7,
mean 0.8385, maximum 24.42
Map values for surface "230926_CBX_HC_181.pdb_C SES surface": minimum -28.15,
mean 0.8719, maximum 24.27
Map values for surface "230926_CBX_HC_181.pdb_D SES surface": minimum -27.92,
mean 0.8499, maximum 24.31
Map values for surface "230926_CBX_HC_181.pdb_E SES surface": minimum -27.7,
mean 0.8051, maximum 24.33
Map values for surface "230926_CBX_HC_181.pdb_F SES surface": minimum -28.95,
mean 0.8538, maximum 24.25
To also show corresponding color key, enter the above mlp command and add key
true
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #!19 models
> show #!18 models
> select #18:1-21
876 atoms, 888 bonds, 120 residues, 1 model selected
> hide sel surfaces
> hide sel ribbons
> show #!19 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #!19 surfaces
> show #!18 models
> hide sel surfaces
> select add #18
11400 atoms, 11652 bonds, 6 pseudobonds, 1236 residues, 8 models selected
> select subtract #18
6 models selected
> hide #!18-19 surfaces
> hide #!19 models
> select add #18
11400 atoms, 11652 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> hide sel surfaces
> show sel surfaces
> hide #!18 models
> show #!19 models
> select subtract #18
6 models selected
> select add #19
8634 atoms, 8916 bonds, 6 pseudobonds, 1020 residues, 2 models selected
> show sel surfaces
> show #!18 models
> hide #!18 models
> show #!18 models
> select #18:1-20
852 atoms, 864 bonds, 114 residues, 1 model selected
> hide sel ribbons
> hide sel surfaces
> hide #!19 models
> show #!19 models
> hide #!19 models
> hide sel surfaces
[Repeated 1 time(s)]
> select add #18
11400 atoms, 11652 bonds, 6 pseudobonds, 1236 residues, 8 models selected
> select subtract #18
6 models selected
> hide #!18 surfaces
> select #17
11526 atoms, 11724 bonds, 6 pseudobonds, 1266 residues, 2 models selected
> select #18
11400 atoms, 11652 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> show sel atoms
> undo
> show sel ribbons
> select clear
> show #!19 models
> hide #!19 models
> mlp #!18
Map values for surface "230904_Chol_HC_150.pdb_A SES surface": minimum -27.81,
mean 0.2399, maximum 23.77
Map values for surface "230904_Chol_HC_150.pdb_B SES surface": minimum -28.02,
mean 0.1571, maximum 25.31
Map values for surface "230904_Chol_HC_150.pdb_C SES surface": minimum -27.97,
mean 0.1452, maximum 24.75
Map values for surface "230904_Chol_HC_150.pdb_D SES surface": minimum -27.84,
mean 0.223, maximum 24.9
Map values for surface "230904_Chol_HC_150.pdb_E SES surface": minimum -27.89,
mean 0.1406, maximum 24.79
Map values for surface "230904_Chol_HC_150.pdb_F SES surface": minimum -27.69,
mean 0.1485, maximum 25.26
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!18 models
> show #!19 models
> mlp #!19
Map values for surface "230926_CBX_HC_181.pdb_A SES surface": minimum -27.57,
mean 0.8045, maximum 24.47
Map values for surface "230926_CBX_HC_181.pdb_B SES surface": minimum -26.7,
mean 0.8385, maximum 24.42
Map values for surface "230926_CBX_HC_181.pdb_C SES surface": minimum -28.15,
mean 0.8719, maximum 24.27
Map values for surface "230926_CBX_HC_181.pdb_D SES surface": minimum -27.92,
mean 0.8499, maximum 24.31
Map values for surface "230926_CBX_HC_181.pdb_E SES surface": minimum -27.7,
mean 0.8051, maximum 24.33
Map values for surface "230926_CBX_HC_181.pdb_F SES surface": minimum -28.95,
mean 0.8538, maximum 24.25
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!19 models
> show #!18 models
> hide #!18 models
> show #!19 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> show #!18 models
> hide #!19 models
> hide #!18 models
> show #!18 models
> hide #!18 surfaces
> mlp #!18
Map values for surface "230904_Chol_HC_150.pdb_A SES surface": minimum -27.81,
mean 0.2399, maximum 23.77
Map values for surface "230904_Chol_HC_150.pdb_B SES surface": minimum -28.02,
mean 0.1571, maximum 25.31
Map values for surface "230904_Chol_HC_150.pdb_C SES surface": minimum -27.97,
mean 0.1452, maximum 24.75
Map values for surface "230904_Chol_HC_150.pdb_D SES surface": minimum -27.84,
mean 0.223, maximum 24.9
Map values for surface "230904_Chol_HC_150.pdb_E SES surface": minimum -27.89,
mean 0.1406, maximum 24.79
Map values for surface "230904_Chol_HC_150.pdb_F SES surface": minimum -27.69,
mean 0.1485, maximum 25.26
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!18 models
> show #!19 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> hide #!18 models
> show #!18 models
> show #!19 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> hide #!18 surfaces
> show #!19 models
> hide #!18-19 surfaces
> morph #18,19
Computed 51 frame morph #22
> coordset #22 1,51
> hide #!22 models
> show #!19 models
> show #!18 models
> show #!22 models
> hide #!19 models
> hide #!18 models
> hide #!22 models
> show #!18 models
> color bfactor #!18
11400 atoms, 1236 residues, 6 surfaces, atom bfactor range 0 to 142
> mlp #!18
Map values for surface "230904_Chol_HC_150.pdb_A SES surface": minimum -27.81,
mean 0.2399, maximum 23.77
Map values for surface "230904_Chol_HC_150.pdb_B SES surface": minimum -28.02,
mean 0.1571, maximum 25.31
Map values for surface "230904_Chol_HC_150.pdb_C SES surface": minimum -27.97,
mean 0.1452, maximum 24.75
Map values for surface "230904_Chol_HC_150.pdb_D SES surface": minimum -27.84,
mean 0.223, maximum 24.9
Map values for surface "230904_Chol_HC_150.pdb_E SES surface": minimum -27.89,
mean 0.1406, maximum 24.79
Map values for surface "230904_Chol_HC_150.pdb_F SES surface": minimum -27.69,
mean 0.1485, maximum 25.26
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!18 models
> show #!18 models
> hide #!18 surfaces
> select #18
11400 atoms, 11652 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> color #18 #00aaffff
> select ::name="CLR"
504 atoms, 558 bonds, 18 residues, 2 models selected
> color sel yellow
> select #18
11400 atoms, 11652 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> color sel byhetero
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/230903_All_Align.cxs"
> hide #!18 models
> show #!22 models
> show #!18 models
> hide #!22 models
> show #!19 models
> select clear
> hide #!19 models
> hide #!18 models
> show #!20 models
> select ::name="6OU"
3528 atoms, 3456 bonds, 72 residues, 3 models selected
> show sel atoms
> color sel byhetero
> select clear
> select ::name="6OU"
3528 atoms, 3456 bonds, 72 residues, 3 models selected
> color sel gray
> color sel byhetero
> select clear
> show #!22 models
> hide #!22 models
> select clear
> show #!19 models
> hide #!20 models
> select ::name="CBO"
246 atoms, 270 bonds, 6 residues, 1 model selected
> show sel atoms
> select clear
> show #!18 models
> show #!22 models
> hide #!19 models
> hide #!18 models
> hide #!22 models
> morph #17,20
Computed 51 frame morph #23
> coordset #23 1,51
> select #23
9606 atoms, 9882 bonds, 6 pseudobonds, 1182 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 9606 atom styles
> color sel byhetero
> select clear
> select #23/b,c,e,f
6404 atoms, 6588 bonds, 4 pseudobonds, 788 residues, 2 models selected
> hide sel ribbons
> hide sel atoms
> select up
9606 atoms, 9882 bonds, 6 pseudobonds, 1182 residues, 2 models selected
> select down
6404 atoms, 6588 bonds, 4 pseudobonds, 788 residues, 2 models selected
> select up
9606 atoms, 9882 bonds, 6 pseudobonds, 1182 residues, 2 models selected
> select up
88570 atoms, 90922 bonds, 6 pseudobonds, 10296 residues, 42 models selected
> select clear
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!20 models
> hide #!23 models
> show #!18 models
> nirog #18,20
Unknown command: nirog #18,20
> morph #18,20
Computed 51 frame morph #24
> coordset #24 1,51
> close #23
> close #22
> hide #!24 models
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Models/231009_CBX_HC_185.pdb"
Chain information for 231009_CBX_HC_185.pdb #22
---
Chain | Description
A B C D E F | No description available
> color #22 #aa55ffff
> select add #22
8550 atoms, 8838 bonds, 6 pseudobonds, 1014 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> show #!19 models
> ribbon style thickness 0.6
> ui tool show "Selection Inspector"
> setattr =sel p display false
Assigning display attribute to 6 items
> size =sel stickRadius 0.3
Changed 8838 bond radii
> ui mousemode right "translate selected models"
> view matrix models #22,1,0,0,-61.977,0,1,0,-58.498,0,0,1,-12.461
> view matrix models #22,1,0,0,-39.409,0,1,0,-50.734,0,0,1,-44.154
> view matrix models #22,1,0,0,-54.676,0,1,0,-57.409,0,0,1,-63.388
> fitmap #22 inMap #4
Fit molecule 231009_CBX_HC_185.pdb (#22) to map
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) using 8550 atoms
average map value = 0.07426, steps = 60
shifted from previous position = 0.805
rotated from previous position = 2.27 degrees
atoms outside contour = 7588, contour level = 0.28686
Position of 231009_CBX_HC_185.pdb (#22) relative to
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99143154 -0.13062735 -0.00002495 25.76792514
0.13061225 0.99131981 -0.01501571 -16.68051252
0.00198619 0.01488379 0.99988726 -1.81490954
Axis 0.11370673 -0.00764831 0.99348492
Axis point 140.06320313 186.98348468 0.00000000
Rotation angle (degrees) 7.55491475
Shift along axis 1.25447903
> view matrix models
> #22,0.99932,0.036698,-0.0025584,-60.11,-0.036731,0.99922,-0.014759,-50.082,0.0020148,0.014843,0.99989,-69.396
> view matrix models
> #22,0.99932,0.036698,-0.0025584,-64.711,-0.036731,0.99922,-0.014759,-51.573,0.0020148,0.014843,0.99989,-69.749
> ui mousemode right "rotate selected models"
> view matrix models
> #22,-0.66458,-0.73684,0.12412,319.43,0.68264,-0.53117,0.50185,-0.40154,-0.30386,0.41825,0.856,-62.696
> view matrix models
> #22,-0.68358,-0.72103,0.11329,321.71,0.72987,-0.67604,0.10127,80.504,0.0035655,0.15191,0.98839,-90.901
> view matrix models
> #22,-0.091595,-0.99507,-0.037941,293.35,0.99499,-0.092987,0.036715,-49.858,-0.040062,-0.034388,0.99861,-54.385
> view matrix models
> #22,-0.12199,-0.98526,-0.11995,310.01,0.99248,-0.11985,-0.024859,-35.037,0.010116,-0.12208,0.99247,-47.168
> view matrix models
> #22,-0.12106,-0.98901,-0.084909,304.82,0.97743,-0.10384,-0.184,-9.4926,0.17316,-0.10527,0.97925,-74.889
> view matrix models
> #22,-0.63138,0.70869,0.31483,43.177,-0.51434,-0.68654,0.51393,222.13,0.58036,0.16255,0.79797,-157.66
> view matrix models
> #22,-0.61598,0.73656,0.27937,41.724,-0.73832,-0.66346,0.12129,318.9,0.27469,-0.13155,0.95249,-83.057
> view matrix models
> #22,-0.23087,0.92155,0.31215,-58.206,-0.90911,-0.31864,0.26832,266.27,0.34674,-0.22183,0.91135,-73.387
> view matrix models
> #22,-0.1927,0.98125,-0.0050125,-23.225,-0.97988,-0.19215,0.053985,291.64,0.052009,0.015314,0.99853,-77.907
> fitmap #22 inMap #4
Fit molecule 231009_CBX_HC_185.pdb (#22) to map
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) using 8550 atoms
average map value = 0.3149, steps = 92
shifted from previous position = 5.53
rotated from previous position = 8.26 degrees
atoms outside contour = 5217, contour level = 0.28686
Position of 231009_CBX_HC_185.pdb (#22) relative to
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.10742601 0.99421305 0.00021706 -16.90770752
-0.99421307 0.10742599 0.00011727 313.16910087
0.00009328 -0.00022840 0.99999996 1.38485607
Axis -0.00017384 0.00006225 -0.99999998
Axis point 165.96120129 166.00123546 0.00000000
Rotation angle (degrees) 83.83304408
Shift along axis -1.36242139
> select clear
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> fitmap #22 inMap #4
Fit molecule 231009_CBX_HC_185.pdb (#22) to map
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) using 8550 atoms
average map value = 0.315, steps = 28
shifted from previous position = 0.0228
rotated from previous position = 0.0138 degrees
atoms outside contour = 5212, contour level = 0.28686
Position of 231009_CBX_HC_185.pdb (#22) relative to
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.10758166 0.99419624 0.00011349 -16.92937765
-0.99419621 0.10758163 0.00026806 313.13387605
0.00025429 -0.00014167 0.99999995 1.34446101
Axis -0.00020606 -0.00007081 -0.99999998
Axis point 165.95809172 165.99711052 0.00000000
Rotation angle (degrees) 83.82407491
Shift along axis -1.36314582
> fitmap #22 inMap #4
Fit molecule 231009_CBX_HC_185.pdb (#22) to map
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) using 8550 atoms
average map value = 0.315, steps = 36
shifted from previous position = 0.00466
rotated from previous position = 0.00577 degrees
atoms outside contour = 5211, contour level = 0.28686
Position of 231009_CBX_HC_185.pdb (#22) relative to
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.10763247 0.99419075 0.00005485 -16.92478353
-0.99419070 0.10763244 0.00033211 313.11074633
0.00032427 -0.00009028 0.99999993 1.32426515
Axis -0.00021243 -0.00013550 -0.99999997
Axis point 165.95642037 165.98343403 0.00000000
Rotation angle (degrees) 83.82114690
Shift along axis -1.36309530
> fitmap #22 inMap #4
Fit molecule 231009_CBX_HC_185.pdb (#22) to map
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) using 8550 atoms
average map value = 0.315, steps = 28
shifted from previous position = 0.0137
rotated from previous position = 0.0105 degrees
atoms outside contour = 5220, contour level = 0.28686
Position of 231009_CBX_HC_185.pdb (#22) relative to
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.10767053 0.99418661 0.00017475 -16.93930578
-0.99418661 0.10767049 0.00019963 313.11528995
0.00017966 -0.00019523 0.99999996 1.36568073
Axis -0.00019858 -0.00000247 -0.99999998
Axis point 165.95851113 165.99423628 0.00000000
Rotation angle (degrees) 83.81895333
Shift along axis -1.36308978
> fitmap #22 inMap #4
Fit molecule 231009_CBX_HC_185.pdb (#22) to map
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) using 8550 atoms
average map value = 0.315, steps = 28
shifted from previous position = 0.0193
rotated from previous position = 0.0119 degrees
atoms outside contour = 5208, contour level = 0.28686
Position of 231009_CBX_HC_185.pdb (#22) relative to
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.10765536 0.99418827 0.00002763 -16.92860828
-0.99418821 0.10765535 0.00034662 313.10736323
0.00034163 -0.00006478 0.99999993 1.31758225
Axis -0.00020691 -0.00015792 -0.99999997
Axis point 165.95665162 165.98407308 0.00000000
Rotation angle (degrees) 83.81982732
Shift along axis -1.36352567
> fitmap #22 inMap #4
Fit molecule 231009_CBX_HC_185.pdb (#22) to map
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) using 8550 atoms
average map value = 0.315, steps = 40
shifted from previous position = 0.0178
rotated from previous position = 0.0106 degrees
atoms outside contour = 5219, contour level = 0.28686
Position of 231009_CBX_HC_185.pdb (#22) relative to
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.10761681 0.99419243 0.00015601 -16.92946496
-0.99419242 0.10761677 0.00022040 313.12299434
0.00020233 -0.00017883 0.99999995 1.35915099
Axis -0.00020078 -0.00002329 -0.99999998
Axis point 165.95822724 165.99208140 0.00000000
Rotation angle (degrees) 83.82204911
Shift along axis -1.36304552
> fitmap #22 inMap #4
Fit molecule 231009_CBX_HC_185.pdb (#22) to map
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) using 8550 atoms
average map value = 0.315, steps = 28
shifted from previous position = 0.0151
rotated from previous position = 0.0112 degrees
atoms outside contour = 5208, contour level = 0.28686
Position of 231009_CBX_HC_185.pdb (#22) relative to
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.10767950 0.99418566 0.00001893 -16.92906219
-0.99418560 0.10767949 0.00034485 313.10108602
0.00034080 -0.00005596 0.99999993 1.31590365
Axis -0.00020157 -0.00016187 -0.99999997
Axis point 165.95718860 165.98141112 0.00000000
Rotation angle (degrees) 83.81843603
Shift along axis -1.36317433
> select clear
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!22 models
> show #!22 models
> hide #!19 models
> select #22:74-103
1578 atoms, 1632 bonds, 180 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 1
Assigning ss_type attribute to 180 items
> select clear
> select #22:203-235
1536 atoms, 1572 bonds, 186 residues, 1 model selected
> select #22:203-230
1362 atoms, 1386 bonds, 168 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 1
Assigning ss_type attribute to 168 items
> select clear
> color #19 #ffff7fff
> show #!19 models
> hide #!19 models
> morph #18,22
Computed 51 frame morph #23
> coordset #23 1,51
> close #19
> rename #22 id #19
> select clear
> close #24
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/230903_All_Align.cxs"
> hide #!23 models
> show #!19 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> hide #!19 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!19 models
> mlp #!19
Map values for surface "231009_CBX_HC_185.pdb_A SES surface": minimum -27.25,
mean 0.8939, maximum 24.32
Map values for surface "231009_CBX_HC_185.pdb_B SES surface": minimum -27.68,
mean 0.9203, maximum 24.56
Map values for surface "231009_CBX_HC_185.pdb_C SES surface": minimum -27.75,
mean 0.9056, maximum 24.54
Map values for surface "231009_CBX_HC_185.pdb_D SES surface": minimum -27.64,
mean 0.9218, maximum 24.13
Map values for surface "231009_CBX_HC_185.pdb_E SES surface": minimum -27.6,
mean 0.8945, maximum 23.94
Map values for surface "231009_CBX_HC_185.pdb_F SES surface": minimum -26.79,
mean 0.9031, maximum 24.3
To also show corresponding color key, enter the above mlp command and add key
true
> select #19/b,c,e,f
5700 atoms, 5892 bonds, 4 pseudobonds, 676 residues, 2 models selected
> hide sel surfaces
> select clear
> select #19/b,c,e,f
5700 atoms, 5892 bonds, 4 pseudobonds, 676 residues, 2 models selected
> show sel surfaces
> select #19/b,c,d,e,
Expected an objects specifier or a keyword
> select #19/b,c,d,e
5700 atoms, 5892 bonds, 4 pseudobonds, 676 residues, 2 models selected
> hide sel surfaces
> select clear
> show #!5 models
> hide #!5 models
> show #!6 models
> show #!5 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!19 surfaces
> hide #!19 models
> show #!19 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!18 models
> hide #!18 models
> show #!18 models
> select ::name="CBO"
246 atoms, 270 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel dark green
> color sel byhetero
> select clear
> show #!5 models
> hide #!5 models
> show #!6 models
> volume #6 level 0.1169
> show #!5 models
> hide #!6 models
> volume #5 level 0.07217
> volume #5 level 0.06717
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/C1/cryosparc_P52_J654_003_volume_map.mrc"
Opened cryosparc_P52_J654_003_volume_map.mrc as #22, grid size 400,400,400,
pixel 0.83, shown at level 0.0434, step 2, values float32
> volume #22 step 1
> volume #22 level 0.08678
> volume #22 level 0.07438
> fitmap #22 inMap #4
Fit map cryosparc_P52_J654_003_volume_map.mrc in map
N55H_CBX_P52_J575_011_volume_map_sharp.mrc using 165931 points
correlation = 0.3467, correlation about mean = 0.06451, overlap = 1020
steps = 572, shift = 66.6, angle = 13.5 degrees
Position of cryosparc_P52_J654_003_volume_map.mrc (#22) relative to
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.96842316 -0.20253930 -0.14537678 79.98562775
0.17515572 0.96768712 -0.18138941 36.16399589
0.17741772 0.15019813 0.97260654 -34.22847996
Axis 0.55511851 -0.54039787 0.63230814
Axis point -141.10209622 408.09928033 0.00000000
Rotation angle (degrees) 17.37736162
Shift along axis 3.21560923
> select add #22
2 models selected
> view matrix models
> #22,0.98592,0.0050434,-0.16715,-6.5265,-0.042711,0.97399,-0.22255,17.631,0.16167,0.22655,0.96049,-106.2
> ui mousemode right "translate selected models"
> view matrix models
> #22,0.98592,0.0050434,-0.16715,-31.173,-0.042711,0.97399,-0.22255,-17.116,0.16167,0.22655,0.96049,-111.92
> fitmap #22 inMap #4
Fit map cryosparc_P52_J654_003_volume_map.mrc in map
N55H_CBX_P52_J575_011_volume_map_sharp.mrc using 165931 points
correlation = 0.3213, correlation about mean = 0.05285, overlap = 1453
steps = 128, shift = 9.51, angle = 9.02 degrees
Position of cryosparc_P52_J654_003_volume_map.mrc (#22) relative to
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.97945409 -0.20054069 0.02128659 32.70629724
0.20011701 0.95343264 -0.22565323 3.84721168
0.02495733 0.22527679 0.97397510 -36.84600292
Axis 0.74753457 -0.00608522 0.66419503
Axis point 0.00000000 161.53781159 -16.28811236
Rotation angle (degrees) 17.55441842
Shift along axis -0.04725542
> fitmap #22 inMap #4
Fit map cryosparc_P52_J654_003_volume_map.mrc in map
N55H_CBX_P52_J575_011_volume_map_sharp.mrc using 165931 points
correlation = 0.3214, correlation about mean = 0.05297, overlap = 1453
steps = 28, shift = 0.00919, angle = 0.00766 degrees
Position of cryosparc_P52_J654_003_volume_map.mrc (#22) relative to
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.97945312 -0.20053508 0.02138361 32.68653409
0.20013112 0.95340858 -0.22574237 3.85542181
0.02488195 0.22538359 0.97395232 -36.85123096
Axis 0.74767209 -0.00579796 0.66404279
Axis point 0.00000000 161.46661792 -16.24795805
Rotation angle (degrees) 17.55895877
Shift along axis -0.05433839
> view matrix models
> #22,0.99912,-0.038564,-0.016629,-48.006,0.033812,0.97352,-0.2261,-18.585,0.024908,0.22534,0.97396,-95.994
> fitmap #22 inMap #4
Fit map cryosparc_P52_J654_003_volume_map.mrc in map
N55H_CBX_P52_J575_011_volume_map_sharp.mrc using 165931 points
correlation = 0.3069, correlation about mean = 0.02999, overlap = 1323
steps = 68, shift = 2.74, angle = 4.15 degrees
Position of cryosparc_P52_J654_003_volume_map.mrc (#22) relative to
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.96580729 -0.25894060 0.01288570 48.17115881
0.25310559 0.93094561 -0.26320682 15.23376552
0.05615905 0.25746851 0.96465337 -42.89725488
Axis 0.71174179 -0.05915289 0.69994611
Axis point 0.00000000 177.40180007 12.08958003
Rotation angle (degrees) 21.45531225
Shift along axis 3.35853846
> view matrix models
> #22,0.99451,-0.099901,-0.031261,-32.996,0.088323,0.96112,-0.26162,-23.268,0.056182,0.25743,0.96466,-106.78
> ui mousemode right "rotate selected models"
> view matrix models
> #22,0.94056,-0.33741,0.038869,3.6007,0.33686,0.9121,-0.23366,-61.125,0.043385,0.23286,0.97154,-101.73
> fitmap #22 inMap #4
Fit map cryosparc_P52_J654_003_volume_map.mrc in map
N55H_CBX_P52_J575_011_volume_map_sharp.mrc using 165931 points
correlation = 0.6097, correlation about mean = 0.3097, overlap = 3564
steps = 144, shift = 2.74, angle = 15.3 degrees
Position of cryosparc_P52_J654_003_volume_map.mrc (#22) relative to
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.80390349 -0.59475705 0.00179629 130.97442642
0.59475832 0.80390453 -0.00022466 -66.15064711
-0.00131042 0.00124897 0.99999836 1.08546927
Axis 0.00123884 0.00261174 0.99999582
Axis point 165.80842923 165.54430252 0.00000000
Rotation angle (degrees) 36.49553695
Shift along axis 1.07495343
> select clear
> hide #!19 models
> hide #!5 models
> volume #22 level 0.08213
> close #23
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/C1/cryosparc_P52_J576_005_volume_map_sharp.mrc"
Opened cryosparc_P52_J576_005_volume_map_sharp.mrc as #23, grid size
400,400,400, pixel 0.83, shown at level 0.0627, step 2, values float32
> volume #23 step 1
> volume #23 level 0.1292
> ui mousemode right "translate selected models"
> select add #23
2 models selected
> view matrix models #23,1,0,0,-118.06,0,1,0,10.474,0,0,1,-51.83
> ui mousemode right "rotate selected models"
> view matrix models
> #23,0.15214,-0.9763,0.15391,158.38,-0.97312,-0.17521,-0.14945,390.98,0.17287,-0.12704,-0.97672,269.02
> view matrix models
> #23,0.15108,-0.97253,0.1771,154.08,-0.9771,-0.17408,-0.12239,386.96,0.14986,-0.15455,-0.97655,277.36
> ui mousemode right "translate selected models"
> view matrix models
> #23,0.15108,-0.97253,0.1771,213.39,-0.9771,-0.17408,-0.12239,314.96,0.14986,-0.15455,-0.97655,273.58
> fitmap #23 inMap #4
Fit map cryosparc_P52_J576_005_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map_sharp.mrc using 135057 points
correlation = 0.305, correlation about mean = 0.04649, overlap = 2002
steps = 108, shift = 3.09, angle = 6.14 degrees
Position of cryosparc_P52_J576_005_volume_map_sharp.mrc (#23) relative to
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.40209643 -0.88761580 0.22462557 209.98474510
-0.90584892 -0.42136236 -0.04349136 385.87731932
0.13325238 -0.18598911 -0.97347412 345.78265697
Axis -0.83696156 0.53668108 -0.10709234
Axis point 0.00000000 269.05537442 149.54960651
Rotation angle (degrees) 175.11661382
Shift along axis -5.68677532
> view matrix models
> #23,0.24523,-0.9455,0.21424,187.97,-0.96026,-0.26728,-0.080421,327.55,0.1333,-0.186,-0.97346,280.59
> fitmap #23 inMap #4
Fit map cryosparc_P52_J576_005_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map_sharp.mrc using 135057 points
correlation = 0.8603, correlation about mean = 0.647, overlap = 9416
steps = 160, shift = 8.45, angle = 14.6 degrees
Position of cryosparc_P52_J576_005_volume_map_sharp.mrc (#23) relative to
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.31563628 -0.94888011 0.00052745 271.02238398
-0.94887884 -0.31563672 -0.00154948 376.18647696
0.00163676 -0.00001141 -0.99999866 331.69993023
Axis 0.81105923 -0.58496366 0.00066653
Axis point 0.00000000 285.73160074 165.84854606
Rotation angle (degrees) 179.94567290
Shift along axis -0.01912620
> fitmap #23 inMap #4
Fit map cryosparc_P52_J576_005_volume_map_sharp.mrc in map
N55H_CBX_P52_J575_011_volume_map_sharp.mrc using 135057 points
correlation = 0.8602, correlation about mean = 0.6468, overlap = 9418
steps = 28, shift = 0.0154, angle = 0.0139 degrees
Position of cryosparc_P52_J576_005_volume_map_sharp.mrc (#23) relative to
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.31567177 -0.94886832 0.00049440 271.02375417
-0.94886741 -0.31567215 -0.00131212 376.13442832
0.00140110 -0.00005492 -0.99999902 331.74657898
Axis 0.81107004 -0.58494875 0.00058357
Axis point 0.00000000 285.71997067 165.86564190
Rotation angle (degrees) 179.95559425
Shift along axis -0.00651986
> fitmap #22 inMap #5
Fit map cryosparc_P52_J654_003_volume_map.mrc in map
N55H_CBX_P52_J650_003_volume_map.mrc using 130729 points
correlation = 0.9632, correlation about mean = 0.7971, overlap = 2392
steps = 44, shift = 0.254, angle = 0.091 degrees
Position of cryosparc_P52_J654_003_volume_map.mrc (#22) relative to
N55H_CBX_P52_J650_003_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
0.99999955 0.00001703 0.00094844 -0.16665372
-0.00001626 0.99999966 -0.00081873 0.12291641
-0.00094845 0.00081871 0.99999922 0.02575101
Axis 0.65338259 0.75691131 -0.01328377
Axis point 26.78752666 0.00000000 164.57025866
Rotation angle (degrees) 0.07179440
Shift along axis -0.01619388
> fitmap #22 inMap #5
Fit map cryosparc_P52_J654_003_volume_map.mrc in map
N55H_CBX_P52_J650_003_volume_map.mrc using 130729 points
correlation = 0.9633, correlation about mean = 0.7973, overlap = 2392
steps = 44, shift = 0.0151, angle = 0.00594 degrees
Position of cryosparc_P52_J654_003_volume_map.mrc (#22) relative to
N55H_CBX_P52_J650_003_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
0.99999949 -0.00003922 0.00100982 -0.16368183
0.00004011 0.99999961 -0.00088034 0.13810945
-0.00100979 0.00088038 0.99999910 0.02611190
Axis 0.65685378 0.75343694 0.02959526
Axis point 25.79503361 0.00000000 160.35609606
Rotation angle (degrees) 0.07679147
Shift along axis -0.00268547
> fitmap #22 inMap #5
Fit map cryosparc_P52_J654_003_volume_map.mrc in map
N55H_CBX_P52_J650_003_volume_map.mrc using 130729 points
correlation = 0.9633, correlation about mean = 0.7973, overlap = 2392
steps = 44, shift = 0.00341, angle = 0.0132 degrees
Position of cryosparc_P52_J654_003_volume_map.mrc (#22) relative to
N55H_CBX_P52_J650_003_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
0.99999950 0.00018527 0.00097840 -0.19810161
-0.00018445 0.99999963 -0.00083669 0.16586021
-0.00097855 0.00083651 0.99999917 0.02726457
Axis 0.64325441 0.75234295 -0.14214026
Axis point 26.74699936 0.00000000 198.20125343
Rotation angle (degrees) 0.07451734
Shift along axis -0.00652137
> fitmap #22 inMap #5
Fit map cryosparc_P52_J654_003_volume_map.mrc in map
N55H_CBX_P52_J650_003_volume_map.mrc using 130729 points
correlation = 0.9633, correlation about mean = 0.7971, overlap = 2392
steps = 40, shift = 0.0132, angle = 0.00959 degrees
Position of cryosparc_P52_J654_003_volume_map.mrc (#22) relative to
N55H_CBX_P52_J650_003_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
0.99999956 0.00002401 0.00094127 -0.16855976
-0.00002324 0.99999967 -0.00081166 0.12248084
-0.00094129 0.00081163 0.99999923 0.02597335
Axis 0.65291425 0.75719336 -0.01900510
Axis point 27.09713293 0.00000000 166.73849084
Rotation angle (degrees) 0.07122507
Shift along axis -0.01780702
> fitmap #22 inMap #5
Fit map cryosparc_P52_J654_003_volume_map.mrc in map
N55H_CBX_P52_J650_003_volume_map.mrc using 130729 points
correlation = 0.9633, correlation about mean = 0.7972, overlap = 2392
steps = 40, shift = 0.0103, angle = 0.00611 degrees
Position of cryosparc_P52_J654_003_volume_map.mrc (#22) relative to
N55H_CBX_P52_J650_003_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
0.99999954 0.00013015 0.00094930 -0.18396882
-0.00012938 0.99999966 -0.00081834 0.15073787
-0.00094941 0.00081822 0.99999921 0.02542331
Axis 0.64940673 0.75343561 -0.10298388
Axis point 25.69858790 0.00000000 187.97907948
Rotation angle (degrees) 0.07219485
Shift along axis -0.00851751
> select clear
> hide #!22 models
> volume #23 level 0.1577
> hide #!23 models
> show #!22 models
> hide #!22 models
> show #!23 models
> volume #23 level 0.1406
> hide #!23 models
> show #!22 models
> hide #!18 models
> volume #22 level 0.07671
> show #!18 models
> volume #22 level 0.07129
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!18 models
> hide #!22 models
> hide #!18 models
> show #!18 models
> show #!22 models
> hide #!22 models
> open
> C:/Users/OJS/Desktop/Phenix/220302_Cx43_N55H_CBX/RealSpaceRefine_186/231006_From150_real_space_refined_186.pdb
Chain information for 231006_From150_real_space_refined_186.pdb #24
---
Chain | Description
A B C D E F | No description available
> select add #24
11400 atoms, 11652 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> hide sel atoms
> show sel cartoons
[Repeated 1 time(s)]
> color #24 cyan
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #24,1,0,0,17.94,0,1,0,-55.06,0,0,1,-46.911
> view matrix models #24,1,0,0,-29.604,0,1,0,-53.506,0,0,1,-14.078
> view matrix models #24,1,0,0,-51.608,0,1,0,-56.51,0,0,1,-69.13
> view matrix models #24,1,0,0,-55.583,0,1,0,-56.931,0,0,1,-65.026
> view matrix models #24,1,0,0,-57.655,0,1,0,-56.087,0,0,1,-63.3
> ui mousemode right "rotate selected models"
> view matrix models
> #24,0.99475,0.097018,-0.032611,-67.517,-0.093494,0.99096,0.096206,-54.914,0.04165,-0.092651,0.99483,-53.981
> view matrix models
> #24,0.98922,0.14641,-0.003361,-79.616,-0.14642,0.98922,-0.0028217,-29.532,0.0029117,0.0032834,0.99999,-64.327
> fitmap #24 inMap #4
Fit molecule 231006_From150_real_space_refined_186.pdb (#24) to map
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) using 11400 atoms
average map value = 0.3613, steps = 68
shifted from previous position = 1.53
rotated from previous position = 1.22 degrees
atoms outside contour = 6635, contour level = 0.28686
Position of 231006_From150_real_space_refined_186.pdb (#24) relative to
N55H_CBX_P52_J575_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99999999 -0.00000349 0.00012771 -0.01838810
0.00000351 0.99999999 -0.00012401 0.01842138
-0.00012771 0.00012401 0.99999998 -0.01640801
Axis 0.69651395 0.71727430 0.01964457
Axis point -128.51406025 0.00000000 144.43406313
Rotation angle (degrees) 0.01020110
Shift along axis 0.00008328
> select clear
> morph #18,24
Computed 51 frame morph #25
> coordset #25 1,51
> hide #!25 models
> show #!25 models
> close #25
> morph #24,19
Computed 51 frame morph #25
> coordset #25 1,51
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!25 models
> show #!18 models
> morph #18,19
Computed 51 frame morph #26
> coordset #26 1,51
> hide #!24 models
> select #25,26
16608 atoms, 17136 bonds, 12 pseudobonds, 2016 residues, 4 models selected
> show sel atoms
> style sel stick
Changed 16608 atom styles
> select clear
> select #25,26/b,c,e,f
11072 atoms, 11424 bonds, 8 pseudobonds, 1344 residues, 4 models selected
> hide sel ribbons
> hide sel atoms
> select #26/A:86
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #26/A:89@CA
1 atom, 1 residue, 1 model selected
> select #26/A:84
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #26/A:87
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #26/A:37
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #26/A:83
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #26/A:86
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #26/A:82@CA
1 atom, 1 residue, 1 model selected
> select #26/A:86
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #26/A:82@CA
1 atom, 1 residue, 1 model selected
> select #26:82-85
204 atoms, 204 bonds, 24 residues, 1 model selected
> color sel black
> color sel byhetero
> color sel gray
> color sel magenta
> select #26/A:86
6 atoms, 5 bonds, 1 residue, 1 model selected
> undo
[Repeated 5 time(s)]
> select clear
> hide #!26 models
> show #!25 models
> select #25
8304 atoms, 8568 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> color sel byhetero
> select clear
> show #!26 models
> hide #!25 models
> hide #!26 models
> show #!24 models
> show #!21 models
> hide #!21 models
> show #!18 models
> hide #!18 models
> select #24/b,c,e,f
7600 atoms, 7768 bonds, 4 pseudobonds, 824 residues, 2 models selected
> hide sel ribbons
> show #!18 models
> select #18/b,c,e,f
7600 atoms, 7768 bonds, 4 pseudobonds, 824 residues, 2 models selected
> hide sel ribbons
> select clear
> hide #!24 models
> hide #!18 models
> show #!24 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #!24 models
> show #!18 models
> hide #!18 models
> show #!24 models
> show #!18 models
> hide #!24 models
> hide #!18 models
> show #!24 models
> ribbon style thickness 0.6
> show #!18 models
> hide #!24 models
> show #!24 models
> hide #!18 models
> hide #!24 models
> show #!18 models
> show #!19 models
> hide #!19 models
> hide #!18 models
> show #!26 models
> hide #!26 models
> show #!25 models
> select
98584 atoms, 101182 bonds, 60 pseudobonds, 11352 residues, 56 models selected
> select #25
8304 atoms, 8568 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> ribbon style thickness 0.6
> select
98584 atoms, 101182 bonds, 60 pseudobonds, 11352 residues, 56 models selected
> select #25,26
16608 atoms, 17136 bonds, 12 pseudobonds, 2016 residues, 4 models selected
> hide sel atoms
> select clear
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> hide #!26 models
> show #!25 models
> hide #!25 models
> show #!26 models
> hide #!26 models
> show #!25 models
> hide #!25 models
> show #!19 models
> close #26
> close #25
> show #!18 models
> hide #!19 models
> show #!24 models
> show #!19 models
> hide #!18 models
> hide #!24 models
> select add #19
8550 atoms, 8838 bonds, 6 pseudobonds, 1014 residues, 2 models selected
> mlp sel
Map values for surface "231009_CBX_HC_185.pdb_A SES surface": minimum -27.25,
mean 0.8939, maximum 24.32
Map values for surface "231009_CBX_HC_185.pdb_B SES surface": minimum -27.68,
mean 0.9203, maximum 24.56
Map values for surface "231009_CBX_HC_185.pdb_C SES surface": minimum -27.75,
mean 0.9056, maximum 24.54
Map values for surface "231009_CBX_HC_185.pdb_D SES surface": minimum -27.64,
mean 0.9218, maximum 24.13
Map values for surface "231009_CBX_HC_185.pdb_E SES surface": minimum -27.6,
mean 0.8945, maximum 23.94
Map values for surface "231009_CBX_HC_185.pdb_F SES surface": minimum -26.79,
mean 0.9031, maximum 24.3
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> show #!20 models
> hide #!19 models
> mlp #!20
Map values for surface "230926_MBCD_HC_10.pdb_A SES surface": minimum -28.57,
mean -0.03631, maximum 25.41
Map values for surface "230926_MBCD_HC_10.pdb_B SES surface": minimum -28,
mean -0.02772, maximum 25.92
Map values for surface "230926_MBCD_HC_10.pdb_C SES surface": minimum -28.3,
mean -0.1041, maximum 25.64
Map values for surface "230926_MBCD_HC_10.pdb_D SES surface": minimum -28.28,
mean -0.05149, maximum 25.19
Map values for surface "230926_MBCD_HC_10.pdb_E SES surface": minimum -27.35,
mean -0.03333, maximum 24.83
Map values for surface "230926_MBCD_HC_10.pdb_F SES surface": minimum -27.13,
mean -0.07316, maximum 24.98
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!20 models
> show #!19 models
> hide #!19 models
> show #!18 models
> mlp #!18
Map values for surface "230904_Chol_HC_150.pdb_A SES surface": minimum -27.81,
mean 0.2399, maximum 23.77
Map values for surface "230904_Chol_HC_150.pdb_B SES surface": minimum -28.02,
mean 0.1571, maximum 25.31
Map values for surface "230904_Chol_HC_150.pdb_C SES surface": minimum -27.97,
mean 0.1452, maximum 24.75
Map values for surface "230904_Chol_HC_150.pdb_D SES surface": minimum -27.84,
mean 0.223, maximum 24.9
Map values for surface "230904_Chol_HC_150.pdb_E SES surface": minimum -27.89,
mean 0.1406, maximum 24.79
Map values for surface "230904_Chol_HC_150.pdb_F SES surface": minimum -27.69,
mean 0.1485, maximum 25.26
To also show corresponding color key, enter the above mlp command and add key
true
> undo
[Repeated 1 time(s)]
> show #!18 models
> hide #!18 models
> show #!18 models
> select #18
11400 atoms, 11652 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> hide sel surfaces
> select #18/a,d
3800 atoms, 3884 bonds, 2 pseudobonds, 412 residues, 2 models selected
> show sel surfaces
> mlp sel
Map values for surface "230904_Chol_HC_150.pdb_A SES surface": minimum -27.81,
mean 0.2399, maximum 23.77
Map values for surface "230904_Chol_HC_150.pdb_D SES surface": minimum -27.84,
mean 0.223, maximum 24.9
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> show #!17 models
> hide #!18 models
> select #17
11526 atoms, 11724 bonds, 6 pseudobonds, 1266 residues, 2 models selected
> hide sel surfaces
> select #17/b,c,e,f
7684 atoms, 7816 bonds, 4 pseudobonds, 844 residues, 2 models selected
> hide sel ribbons
> select #17/a,d
3842 atoms, 3908 bonds, 2 pseudobonds, 422 residues, 2 models selected
> show sel surfaces
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 231006_PIP2_HC_90.pdb_A SES surface #17.2: minimum,
-10.90, mean 0.18, maximum 12.83
Coulombic values for 231006_PIP2_HC_90.pdb_D SES surface #17.5: minimum,
-10.87, mean 0.17, maximum 12.73
To also show corresponding color key, enter the above coulombic command and
add key true
> select #17
11526 atoms, 11724 bonds, 6 pseudobonds, 1266 residues, 2 models selected
> hide sel surfaces
> show sel atoms
> style sel stick
Changed 11526 atom styles
> color sel byhetero
> select #17/b,c,e,f
7684 atoms, 7816 bonds, 4 pseudobonds, 844 residues, 2 models selected
> hide sel atoms
> view matrix models
> #17,0.89118,-0.15271,0.42717,-89.601,0.13778,0.98827,0.065846,-93.665,-0.43222,0.00017537,0.90177,18.875
> select #17/a,d
3842 atoms, 3908 bonds, 2 pseudobonds, 422 residues, 2 models selected
> show sel surfaces
> coulombic sel
Coulombic values for 231006_PIP2_HC_90.pdb_A SES surface #17.2: minimum,
-10.90, mean 0.18, maximum 12.83
Coulombic values for 231006_PIP2_HC_90.pdb_D SES surface #17.5: minimum,
-10.87, mean 0.17, maximum 12.73
To also show corresponding color key, enter the above coulombic command and
add key true
> select #17/a,d:1-24
332 atoms, 336 bonds, 46 residues, 1 model selected
> hide sel surfaces
> select #17/a,d:1-24
332 atoms, 336 bonds, 46 residues, 1 model selected
> show sel surfaces
> select #17/a,d:1-10
132 atoms, 134 bonds, 18 residues, 1 model selected
> hide sel surfaces
> show sel surfaces
> select clear
> select add #17
11526 atoms, 11724 bonds, 6 pseudobonds, 1266 residues, 2 models selected
> hide sel surfaces
> select clear
> select add #17
11526 atoms, 11724 bonds, 6 pseudobonds, 1266 residues, 2 models selected
> hide sel atoms
> undo
> hide sel atoms
> select ::name="PIO"
282 atoms, 282 bonds, 6 residues, 1 model selected
> show sel atoms
> select clear
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/230903_All_Align.cxs"
> select #17/b,c,e,f
7684 atoms, 7816 bonds, 4 pseudobonds, 844 residues, 2 models selected
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> show #!21 models
> hide #!21 models
> show #!21 models
> show #!20 models
> hide #!20 models
> ui tool show "Fit in Map"
> fitmap #21 inMap #9
Fit molecule 231009_From25_real_space_refined_027.pdb (#21) to map
N55H_POPE_C6_P58_J139_004_volume_map.mrc (#9) using 8706 atoms
average map value = 0.5856, steps = 48
shifted from previous position = 0.132
rotated from previous position = 0.0452 degrees
atoms outside contour = 2555, contour level = 0.32943
Position of 231009_From25_real_space_refined_027.pdb (#21) relative to
N55H_POPE_C6_P58_J139_004_volume_map.mrc (#9) coordinates:
Matrix rotation and translation
-0.49881499 -0.86670840 0.00040190 333.00119717
0.86670849 -0.49881496 0.00016782 88.99067360
0.00005503 0.00043205 0.99999990 -0.14454104
Axis 0.00015243 0.00020011 0.99999997
Axis point 140.77062126 140.77640419 0.00000000
Rotation angle (degrees) 119.92163353
Shift along axis -0.07597335
> select add #21
8706 atoms, 8964 bonds, 6 pseudobonds, 1062 residues, 2 models selected
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide sel surfaces
> select add #19
17256 atoms, 17802 bonds, 12 pseudobonds, 2076 residues, 4 models selected
> hide sel surfaces
> fitmap #21 inMap #9
Fit molecule 231009_From25_real_space_refined_027.pdb (#21) to map
N55H_POPE_C6_P58_J139_004_volume_map.mrc (#9) using 8706 atoms
average map value = 0.5856, steps = 40
shifted from previous position = 0.018
rotated from previous position = 0.0171 degrees
atoms outside contour = 2552, contour level = 0.32943
Position of 231009_From25_real_space_refined_027.pdb (#21) relative to
N55H_POPE_C6_P58_J139_004_volume_map.mrc (#9) coordinates:
Matrix rotation and translation
-0.49894784 -0.86663183 0.00056367 333.00382739
0.86663196 -0.49894793 -0.00002960 89.04113276
0.00030690 0.00047372 0.99999984 -0.18533346
Axis 0.00029039 0.00014814 0.99999995
Axis point 140.76191983 140.78535862 0.00000000
Rotation angle (degrees) 119.93042251
Shift along axis -0.07544115
> fitmap #21 inMap #9
Fit molecule 231009_From25_real_space_refined_027.pdb (#21) to map
N55H_POPE_C6_P58_J139_004_volume_map.mrc (#9) using 8706 atoms
average map value = 0.5856, steps = 44
shifted from previous position = 0.0183
rotated from previous position = 0.0121 degrees
atoms outside contour = 2550, contour level = 0.32943
Position of 231009_From25_real_space_refined_027.pdb (#21) relative to
N55H_POPE_C6_P58_J139_004_volume_map.mrc (#9) coordinates:
Matrix rotation and translation
-0.49911103 -0.86653791 0.00046898 333.01099065
0.86653800 -0.49911110 -0.00004957 89.07043372
0.00027702 0.00038165 0.99999988 -0.16715924
Axis 0.00024881 0.00011076 0.99999996
Axis point 140.76261974 140.78116041 0.00000000
Rotation angle (degrees) 119.94120973
Shift along axis -0.07443617
> fitmap #21 inMap #9
Fit molecule 231009_From25_real_space_refined_027.pdb (#21) to map
N55H_POPE_C6_P58_J139_004_volume_map.mrc (#9) using 8706 atoms
average map value = 0.5856, steps = 40
shifted from previous position = 0.0184
rotated from previous position = 0.00607 degrees
atoms outside contour = 2552, contour level = 0.32943
Position of 231009_From25_real_space_refined_027.pdb (#21) relative to
N55H_POPE_C6_P58_J139_004_volume_map.mrc (#9) coordinates:
Matrix rotation and translation
-0.49906117 -0.86656658 0.00055023 333.01394615
0.86656671 -0.49906125 -0.00001310 89.06128702
0.00028595 0.00047028 0.99999984 -0.18133126
Axis 0.00027890 0.00015249 0.99999995
Axis point 140.76503600 140.78383528 0.00000000
Rotation angle (degrees) 119.93791479
Shift along axis -0.07487231
> show #!18 models
> select add #18
28656 atoms, 29454 bonds, 18 pseudobonds, 3312 residues, 12 models selected
> hide sel surfaces
> select #17,18,19,20,21
51966 atoms, 53244 bonds, 30 pseudobonds, 5814 residues, 10 models selected
> show sel ribbons
> select clear
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/230903_All_Align.cxs"
> hide #!18 models
> show #!18 models
> hide #!21 models
> show #!7 models
> hide #!7 models
> show #!9 models
> hide #!9 models
> color #21 #aa5500ff
> show #!21 models
> hide #!19 models
> hide #!18 models
> show #!9 models
> show #!10 models
> hide #!10 models
> volume #9 level 0.274
> hide #!9 models
> show #!11 models
> hide #!11 models
> show #!1 models
> hide #!1 models
> hide #!21 models
> show #!18 models
> show #!19 models
> hide #!19 models
> hide #!18 models
> show #!23 models
> hide #!23 models
> show #!20 models
> hide #!20 models
> show #!20 models
> select add #20
11784 atoms, 12066 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> select subtract #20
6 models selected
> hide #!20 surfaces
> select #20/b,c,e,f
7856 atoms, 8044 bonds, 4 pseudobonds, 824 residues, 2 models selected
> hide sel ribbons
> hide sel atoms
> show #!18 models
> select #18/b,c,e,f
7600 atoms, 7768 bonds, 4 pseudobonds, 824 residues, 2 models selected
> hide sel ribbons
> hide sel atoms
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!20 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> volume #4 level 0.1208
> volume #4 level 0.19
> hide #!4 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!20 models
> select #20,18
23184 atoms, 23718 bonds, 12 pseudobonds, 2472 residues, 4 models selected
> select #20,18:30
132 atoms, 132 bonds, 12 residues, 2 models selected
> select #20,18/a,d
7728 atoms, 7906 bonds, 4 pseudobonds, 824 residues, 4 models selected
> select #20,18:30
132 atoms, 132 bonds, 12 residues, 2 models selected
> show sel atoms
> select #18/A:7
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #18/A:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!20 models
> select #18/A:27
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #18/a
1900 atoms, 1942 bonds, 1 pseudobond, 206 residues, 2 models selected
> show sel atoms
> select clear
> show #!20 models
> select ::name="6OU"
4704 atoms, 4608 bonds, 96 residues, 4 models selected
> help help:user
> hide sel atoms
> select clear
> hide #!20 models
> show #!20 models
> select #20/a
1964 atoms, 2011 bonds, 1 pseudobond, 206 residues, 2 models selected
> show sel atoms
> select clear
> select #20
11784 atoms, 12066 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> color sel byhetero
> select ::name="6OU"
4704 atoms, 4608 bonds, 96 residues, 4 models selected
> hide sel atoms
> select clear
> select ::name="6OU"
4704 atoms, 4608 bonds, 96 residues, 4 models selected
> show sel atoms
> select #20/b,c,e,f
7856 atoms, 8044 bonds, 4 pseudobonds, 824 residues, 2 models selected
> hide sel atoms
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!18 models
> select #20/b
1964 atoms, 2011 bonds, 1 pseudobond, 206 residues, 2 models selected
> show sel ribbons
> show sel atoms
> show #!18 models
> show #!17 models
> select add #17
13490 atoms, 13735 bonds, 7 pseudobonds, 1472 residues, 5 models selected
> fitmap #17 inMap #1
Fit molecule 231006_PIP2_HC_90.pdb (#17) to map
WT_PIP2_P68_J150_009_volume_map.mrc (#1) using 11526 atoms
average map value = 0.07176, steps = 100
shifted from previous position = 0.97
rotated from previous position = 4.14 degrees
atoms outside contour = 9330, contour level = 0.12324
Position of 231006_PIP2_HC_90.pdb (#17) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.43716680 0.87933724 0.18881531 -85.41819673
-0.76178368 0.47363148 -0.44199418 293.02168898
-0.47809082 0.04938877 0.87692071 93.64250597
Axis 0.26729691 0.36277601 -0.89271828
Axis point 220.22249076 238.05740158 0.00000000
Rotation angle (degrees) 66.80513742
Shift along axis -0.12715882
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.87426,0.40254,-0.27135,-2.5398,-0.37324,0.91478,0.15452,34.893,0.31042,-0.033811,0.95,-25.534,#17,0.95013,0.24343,0.1949,-125.69,-0.24579,0.96924,-0.012398,-11.758,-0.19192,-0.036123,0.98075,-29.453
> select add #20
23310 atoms, 23790 bonds, 12 pseudobonds, 2502 residues, 11 models selected
> select subtract #20
11526 atoms, 11724 bonds, 6 pseudobonds, 1266 residues, 14 models selected
> select clear
> undo
[Repeated 1 time(s)]
> select clear
> select add #20
11784 atoms, 12066 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> hide #!18 models
> hide #!17 models
> show #!7 models
> hide #!7 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!18 models
> view matrix models
> #20,0.98567,0.12363,0.11473,-22.214,-0.10818,0.98528,-0.13234,27.816,-0.1294,0.11803,0.98454,1.1307
> fitmap #20 inMap #7
Fit molecule 230926_MBCD_HC_10.pdb (#20) to map
MBCD_P41_J50_013_volume_map.mrc (#7) using 11784 atoms
average map value = 0.1298, steps = 112
shifted from previous position = 2.33
rotated from previous position = 12.1 degrees
atoms outside contour = 5794, contour level = 0.11674
Position of 230926_MBCD_HC_10.pdb (#20) relative to
MBCD_P41_J50_013_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.99999995 0.00032196 0.00004132 -0.03936431
-0.00032196 0.99999995 -0.00005833 0.04120307
-0.00004134 0.00005832 1.00000000 -0.01066129
Axis 0.17684872 0.12530643 -0.97622888
Axis point 124.60457629 127.01376510 0.00000000
Rotation angle (degrees) 0.01889610
Shift along axis 0.00860934
> select clear
> hide #!20 models
> show #!20 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> select #18
11400 atoms, 11652 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> select ::name="6OU"
4704 atoms, 4608 bonds, 96 residues, 4 models selected
> show sel atoms
> select clear
> hide #!20 models
> select #18/b,c,e
5700 atoms, 5826 bonds, 3 pseudobonds, 618 residues, 2 models selected
> hide sel atoms
> select ::name="PTY"
594 atoms, 576 bonds, 18 residues, 3 models selected
> select clear
> show #!20 models
> open
> C:/Users/OJS/Desktop/Phenix/230901_MBCD_Chol_N55H/2301009_From10_POPEHEAD.pdb
Summary of feedback from opening
C:/Users/OJS/Desktop/Phenix/230901_MBCD_Chol_N55H/2301009_From10_POPEHEAD.pdb
---
warnings | Duplicate atom serial number found: 5893
Duplicate atom serial number found: 5894
Duplicate atom serial number found: 5895
Duplicate atom serial number found: 5896
Duplicate atom serial number found: 5897
9815 messages similar to the above omitted
Chain information for 2301009_From10_POPEHEAD.pdb #25
---
Chain | Description
A B C D E F | No description available
> hide #!20 models
> hide #!18 models
> color #25 lime
> select add #25
11784 atoms, 12054 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> show #!7 models
> select
> ::name="6OU"::name="CBO"::name="CLR"::name="MC3"::name="PIO"::name="PTY"
9942 atoms, 9816 bonds, 294 residues, 6 models selected
> show sel atoms
> color sel byhetero
> select clear
> hide #!7 models
> show #!18 models
> show #!20 models
> hide #!20 models
> hide #!18 models
> show #!17 models
> hide #!25 models
> select
> ::name="6OU"::name="CBO"::name="CLR"::name="MC3"::name="PIO"::name="PTY"
9942 atoms, 9816 bonds, 294 residues, 6 models selected
> show sel atoms
> select clear
> show #!18 models
> select add #17
11526 atoms, 11724 bonds, 6 pseudobonds, 1266 residues, 2 models selected
> fitmap #17 inMap #1
Fit molecule 231006_PIP2_HC_90.pdb (#17) to map
WT_PIP2_P68_J150_009_volume_map.mrc (#1) using 11526 atoms
average map value = 0.07335, steps = 112
shifted from previous position = 2.45
rotated from previous position = 5.97 degrees
atoms outside contour = 9303, contour level = 0.12324
Position of 231006_PIP2_HC_90.pdb (#17) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.07402966 0.99644500 0.04021172 -18.54660546
-0.99327025 0.07727530 -0.08627143 336.88328831
-0.08907211 -0.03355446 0.99545983 23.15033210
Axis 0.02642974 0.06481667 -0.99754713
Axis point 172.83135861 179.17407947 0.00000000
Rotation angle (degrees) 85.79171561
Shift along axis -1.74807722
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.97936,-0.14347,-0.14238,-5.7938,0.089552,0.93948,-0.3307,-9.6199,0.18121,0.31113,0.93293,-141.54
> view matrix models
> #17,0.95021,-0.3093,0.037966,-3.809,0.30924,0.92087,-0.23742,-59.803,0.038472,0.23733,0.97067,-111.32
> view matrix models
> #17,0.89573,-0.44248,0.043242,27.107,0.44446,0.89359,-0.062881,-108.19,-0.010817,0.075544,0.99708,-80.072
> fitmap #17 inMap #1
Fit molecule 231006_PIP2_HC_90.pdb (#17) to map
WT_PIP2_P68_J150_009_volume_map.mrc (#1) using 11526 atoms
average map value = 0.07812, steps = 92
shifted from previous position = 3.72
rotated from previous position = 5.23 degrees
atoms outside contour = 9110, contour level = 0.12324
Position of 231006_PIP2_HC_90.pdb (#17) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.66957884 0.74242814 0.02155522 -71.86318179
-0.74109869 0.66974576 -0.04704617 183.65657547
-0.04936492 0.01552659 0.99866012 6.22775039
Axis 0.04209293 0.04770824 -0.99797400
Axis point 170.84211235 172.80177961 0.00000000
Rotation angle (degrees) 48.01065757
Shift along axis -0.47813322
> view matrix models
> #17,0.84862,-0.36767,-0.38034,98.914,0.43958,0.89011,0.12032,-138.09,0.29431,-0.2693,0.91699,-60.844
> view matrix models
> #17,0.94575,0.16677,-0.27881,-25.702,-0.066436,0.93933,0.33651,-97.878,0.31802,-0.29973,0.89946,-56.682
> view matrix models
> #17,0.92214,0.21324,-0.32279,-21.998,-0.2274,0.97378,-0.0063197,-17.33,0.31298,0.079228,0.94645,-128.2
> view matrix models
> #17,0.83467,0.19445,-0.51528,29.201,-0.3504,0.90931,-0.22444,52.061,0.42491,0.36789,0.82711,-175.57
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.83467,0.19445,-0.51528,22.682,-0.3504,0.90931,-0.22444,48.046,0.42491,0.36789,0.82711,-175
> fitmap #17 inMap #1
Fit molecule 231006_PIP2_HC_90.pdb (#17) to map
WT_PIP2_P68_J150_009_volume_map.mrc (#1) using 11526 atoms
average map value = 0.06975, steps = 96
shifted from previous position = 3.12
rotated from previous position = 3.42 degrees
atoms outside contour = 9462, contour level = 0.12324
Position of 231006_PIP2_HC_90.pdb (#17) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.05668158 0.94151932 -0.33215744 72.14363881
-0.91442852 0.08458668 0.39581003 243.59131623
0.40075888 0.32616938 0.85615762 -96.38639745
Axis -0.03487898 -0.36707543 -0.92953703
Axis point 161.08524950 104.25035395 0.00000000
Rotation angle (degrees) 93.32322155
Shift along axis -2.33795941
> hide #!18 models
> show #!1 models
> view matrix models
> #17,0.8457,0.22774,-0.48262,5.0618,-0.35238,0.91748,-0.18453,39.918,0.40077,0.32612,0.85617,-164.88
> view matrix models
> #17,0.8457,0.22774,-0.48262,-5.6919,-0.35238,0.91748,-0.18453,42.428,0.40077,0.32612,0.85617,-168.9
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.89294,0.15756,-0.42171,-12.299,-0.26426,0.94183,-0.20767,27.344,0.36445,0.29688,0.88263,-162.34
> view matrix models
> #17,0.87103,0.21801,-0.44021,-15.646,-0.17947,0.97541,0.12795,-50.582,0.45728,-0.032444,0.88873,-123.28
> view matrix models
> #17,0.90901,0.11131,-0.40163,-10.643,-0.074858,0.99161,0.1054,-67.185,0.40999,-0.065749,0.90972,-113.23
> view matrix models
> #17,0.91035,0.02355,-0.41317,6.006,-0.12841,0.96518,-0.22791,3.8323,0.39342,0.26054,0.88167,-160.92
> view matrix models
> #17,0.94848,-0.11094,-0.29679,2.2879,0.034409,0.96723,-0.25157,-20.052,0.31497,0.2284,0.92121,-148.98
> view matrix models
> #17,0.88801,-0.18295,-0.42186,46.315,0.11788,0.97736,-0.17571,-49.003,0.44446,0.10631,0.88947,-144.77
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.88801,-0.18295,-0.42186,53.262,0.11788,0.97736,-0.17571,-48.255,0.44446,0.10631,0.88947,-143.56
> fitmap #17 inMap #1
Fit molecule 231006_PIP2_HC_90.pdb (#17) to map
WT_PIP2_P68_J150_009_volume_map.mrc (#1) using 11526 atoms
average map value = 0.1776, steps = 204
shifted from previous position = 7.77
rotated from previous position = 27.2 degrees
atoms outside contour = 3807, contour level = 0.12324
Position of 231006_PIP2_HC_90.pdb (#17) relative to
WT_PIP2_P68_J150_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.49939923 0.86637198 -0.00004010 -62.03278309
-0.86637198 0.49939924 0.00002960 231.82502572
0.00004567 0.00001997 1.00000000 -0.00561421
Axis -0.00000556 -0.00004950 -1.00000000
Axis point 169.58928151 169.59148137 0.00000000
Rotation angle (degrees) 60.03973817
Shift along axis -0.00551651
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!18 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> select clear
> hide #!18 models
> select #17/b,c,e,f
7684 atoms, 7816 bonds, 4 pseudobonds, 844 residues, 2 models selected
> hide sel ribbons
> hide sel atoms
> select #17/a:95-110
145 atoms, 147 bonds, 16 residues, 1 model selected
> show sel atoms
> select clear
> select #17/b
1921 atoms, 1954 bonds, 1 pseudobond, 211 residues, 2 models selected
> show sel ribbons
> select clear
> morph #18,20,17
Computed 101 frame morph #26
> coordset #26 1,101
> select #26
9582 atoms, 9858 bonds, 6 pseudobonds, 1182 residues, 2 models selected
> hide sel atoms
> select clear
> morph #18,20
Computed 51 frame morph #27
> coordset #27 1,51
> hide #!26 models
> close #26
> close #27
> morph #18,20
Computed 51 frame morph #26
> coordset #26 1,51
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/Models/Previous_Models/Nanodisc/WT-pope-chs-
> ph8/Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb"
Summary of feedback from opening C:/Users/OJS/OneDrive -
korea.ac.kr/MCSB/논문/Models/Previous_Models/Nanodisc/WT-pope-chs-ph8/Cx43-nano-
pope-chs-pH8-rs37-final-for-revision.pdb
---
warnings | Ignored bad PDB record found on line 193
Ignored bad PDB record found on line 194
Ignored bad PDB record found on line 195
ALLOWED : 4.25 %
Ignored bad PDB record found on line 196
CIS-PROLINE : 16.6666666667
Ignored bad PDB record found on line 197
CIS-GENERAL : 0.0
18 messages similar to the above omitted
Chain information for Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb #27
---
Chain | Description
A B C D E F G H I J K L | No description available
> color #27 #aaaaffff
> hide #!26-27 atoms
> show #!26-27 cartoons
> select add #27
48276 atoms, 48744 bonds, 12 pseudobonds, 2568 residues, 2 models selected
> view matrix models #27,1,0,0,-38.184,0,1,0,-15.794,0,0,1,-84.832
> view matrix models #27,1,0,0,-30.731,0,1,0,-34.825,0,0,1,-87.356
> select #27/g-n
24138 atoms, 24372 bonds, 6 pseudobonds, 1284 residues, 2 models selected
> delete sel
> select add #27
24138 atoms, 24372 bonds, 6 pseudobonds, 1284 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #27,0.29316,0.94254,-0.16026,-48.228,0.94996,-0.30607,-0.06234,21.823,-0.10781,-0.13397,-0.9851,143.88
> ui mousemode right "translate selected models"
> view matrix models
> #27,0.29316,0.94254,-0.16026,-55.707,0.94996,-0.30607,-0.06234,31.65,-0.10781,-0.13397,-0.9851,229.94
> view matrix models
> #27,0.29316,0.94254,-0.16026,-45.989,0.94996,-0.30607,-0.06234,25.77,-0.10781,-0.13397,-0.9851,226.77
> view matrix models
> #27,0.29316,0.94254,-0.16026,-51.794,0.94996,-0.30607,-0.06234,25.724,-0.10781,-0.13397,-0.9851,236.57
> ui mousemode right "rotate selected models"
> view matrix models
> #27,0.40113,0.91577,-0.021501,-77.074,0.91052,-0.40118,-0.10002,48.536,-0.10022,0.020543,-0.99475,214.55
> view matrix models
> #27,0.55984,0.76443,-0.31972,-48.531,0.76805,-0.62354,-0.14595,104.81,-0.31092,-0.16385,-0.9362,264.75
> view matrix models
> #27,0.87698,0.47984,0.025595,-87.413,0.47923,-0.86947,-0.11981,178.02,-0.035237,0.11734,-0.99247,191.39
> view matrix models
> #27,0.82866,0.54418,0.13114,-100.15,0.55599,-0.82731,-0.080246,157.23,0.064824,0.13941,-0.98811,173.65
> view matrix models
> #27,0.82734,0.54116,0.15052,-101.46,0.5597,-0.81685,-0.13962,161.12,0.047391,0.19976,-0.9787,166.63
> ui mousemode right "translate selected models"
> view matrix models
> #27,0.82734,0.54116,0.15052,-98.873,0.5597,-0.81685,-0.13962,159.42,0.047391,0.19976,-0.9787,163.86
> ui mousemode right "rotate selected models"
> view matrix models
> #27,0.70793,0.68188,0.18403,-105.22,0.70438,-0.70075,-0.11314,119.82,0.051814,0.20972,-0.97639,161.59
> ui mousemode right "translate selected models"
> view matrix models
> #27,0.70793,0.68188,0.18403,-102.67,0.70438,-0.70075,-0.11314,117.25,0.051814,0.20972,-0.97639,161.53
> fitmap #27 inMap #3
Fit molecule Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 24138 atoms
average map value = 0.1152, steps = 108
shifted from previous position = 4.75
rotated from previous position = 12.9 degrees
atoms outside contour = 18957, contour level = 0.18046
Position of Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) relative
to N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.53799775 0.84294625 0.00024963 -29.76097737
0.84294627 -0.53799776 -0.00001904 122.75614070
0.00011825 0.00022067 -0.99999997 265.31002431
Axis 0.87692439 0.48062834 0.00009903
Axis point 0.00000000 69.52349257 132.66085903
Rotation angle (degrees) 179.99216915
Shift along axis 32.92822703
> select clear
> show #!20 models
> select
127504 atoms, 130360 bonds, 66 pseudobonds, 13038 residues, 58 models selected
> hide sel atoms
> select clear
> select #20,18,27
47322 atoms, 48090 bonds, 18 pseudobonds, 3756 residues, 6 models selected
> select #20,18,27/b,c,e,f
31548 atoms, 32060 bonds, 12 pseudobonds, 2504 residues, 6 models selected
> hide sel ribbons
> select add #20
35476 atoms, 36082 bonds, 14 pseudobonds, 2916 residues, 14 models selected
> select subtract #20
23692 atoms, 24016 bonds, 8 pseudobonds, 1680 residues, 14 models selected
> select add #20
35476 atoms, 36082 bonds, 14 pseudobonds, 2916 residues, 10 models selected
> ui mousemode right "rotate selected models"
> select add #18
39276 atoms, 39966 bonds, 16 pseudobonds, 3328 residues, 16 models selected
> select subtract #18
27876 atoms, 28314 bonds, 10 pseudobonds, 2092 residues, 16 models selected
> select add #18
39276 atoms, 39966 bonds, 16 pseudobonds, 3328 residues, 12 models selected
> select subtract #18
27876 atoms, 28314 bonds, 10 pseudobonds, 2092 residues, 16 models selected
> select subtract #20
16092 atoms, 16248 bonds, 4 pseudobonds, 856 residues, 8 models selected
> select add #20
27876 atoms, 28314 bonds, 10 pseudobonds, 2092 residues, 4 models selected
> select subtract #20
16092 atoms, 16248 bonds, 4 pseudobonds, 856 residues, 8 models selected
> select #20,18,27/b,c,e,f
31548 atoms, 32060 bonds, 12 pseudobonds, 2504 residues, 6 models selected
> hide #!26 models
> select add #27
39594 atoms, 40184 bonds, 14 pseudobonds, 2932 residues, 14 models selected
> select subtract #27
15456 atoms, 15812 bonds, 8 pseudobonds, 1648 residues, 12 models selected
> select add #27
39594 atoms, 40184 bonds, 14 pseudobonds, 2932 residues, 14 models selected
> view matrix models
> #18,0.98017,0.14589,0.13408,-100.71,-0.14135,0.98903,-0.042817,-25.064,-0.13885,0.023016,0.99005,-43.062,#20,0.99075,-0.01978,0.13425,-10.62,0.025726,0.99876,-0.042703,1.7119,-0.13324,0.045762,0.99003,10.465,#27,0.64943,0.74854,-0.13391,-76.374,0.75842,-0.65037,0.042665,88.972,-0.055155,-0.12927,-0.99007,226.57
> ui mousemode right "rotate selected models"
> select add #20
43522 atoms, 44206 bonds, 16 pseudobonds, 3344 residues, 14 models selected
> select subtract #20
31738 atoms, 32140 bonds, 10 pseudobonds, 2108 residues, 14 models selected
> select subtract #27
7600 atoms, 7768 bonds, 4 pseudobonds, 824 residues, 6 models selected
> select add #27
31738 atoms, 32140 bonds, 10 pseudobonds, 2108 residues, 8 models selected
> view matrix models
> #18,0.55806,0.74737,0.36056,-168.15,-0.82938,0.48854,0.27102,120.1,0.026406,-0.45029,0.89249,24.305,#27,0.93015,0.069493,-0.36055,2.527,-0.033273,-0.96194,-0.27124,276.51,-0.36567,0.26429,-0.89243,205.15
> view matrix models
> #18,0.39533,0.90526,0.15562,-133.31,-0.91574,0.40165,-0.010091,195.56,-0.071641,-0.13852,0.98776,-27.017,#27,0.97595,-0.15261,-0.15566,7.1698,-0.15295,-0.98818,0.0098661,269.3,-0.15533,0.014179,-0.98776,220.22
> fitmap #27 inMap #3
Fit molecule Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 24138 atoms
average map value = 0.1152, steps = 104
shifted from previous position = 0.256
rotated from previous position = 9.56 degrees
atoms outside contour = 18945, contour level = 0.18046
Position of Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) relative
to N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99900649 -0.04456506 0.00008172 30.69516423
-0.04456504 -0.99900646 -0.00024822 313.93619642
0.00009270 0.00024433 -0.99999997 265.30492652
Axis 0.99975163 -0.02228646 0.00004452
Axis point 0.00000000 157.29388403 132.67115042
Rotation angle (degrees) 179.98588611
Shift along axis 23.70282638
> view matrix models
> #18,0.42934,0.88656,0.17226,-138.61,-0.89874,0.43821,-0.015303,187.53,-0.089051,-0.14824,0.98493,-22.041,#27,0.98495,-0.17206,-0.016494,-5.0575,-0.17189,-0.98505,0.011214,271.4,-0.018177,-0.0082097,-0.9998,205.15
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.42934,0.88656,0.17226,-138.34,-0.89874,0.43821,-0.015303,188.01,-0.089051,-0.14824,0.98493,-18.388,#27,0.98495,-0.17206,-0.016494,-4.7865,-0.17189,-0.98505,0.011214,271.88,-0.018177,-0.0082097,-0.9998,208.81
> fitmap #27 inMap #3
Fit molecule Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 24138 atoms
average map value = 0.1152, steps = 64
shifted from previous position = 3.69
rotated from previous position = 2.5 degrees
atoms outside contour = 18948, contour level = 0.18046
Position of Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) relative
to N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99901091 -0.04446596 -0.00001510 30.70041734
-0.04446596 -0.99901087 -0.00025656 313.92295641
-0.00000368 0.00025698 -0.99999997 265.31893759
Axis 0.99975273 -0.02223694 -0.00000383
Axis point 0.00000000 157.28586431 132.67972293
Rotation angle (degrees) 179.98528450
Shift along axis 23.71112558
> view matrix models
> #18,0.42934,0.88656,0.17226,-143.22,-0.89874,0.43821,-0.015303,186.99,-0.089051,-0.14824,0.98493,-20.607,#27,0.97768,-0.2101,-1.7211e-05,-5.1351,-0.2101,-0.97768,-0.00021188,275.89,2.769e-05,0.00021077,-1,199.18
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.43545,0.86682,0.24291,-152.44,-0.89455,0.44689,0.0088969,180.91,-0.10084,-0.22117,0.97001,-4.0935,#27,0.97823,-0.19463,-0.071987,-0.26359,-0.19667,-0.98021,-0.022387,276.55,-0.066206,0.036057,-0.99715,203.21
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.43545,0.86682,0.24291,-146.78,-0.89455,0.44689,0.0088969,182.07,-0.10084,-0.22117,0.97001,-1.3774,#27,0.97823,-0.19463,-0.071987,5.3896,-0.19667,-0.98021,-0.022387,277.7,-0.066206,0.036057,-0.99715,205.93
> fitmap #27 inMap #3
Fit molecule Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 24138 atoms
average map value = 0.1152, steps = 64
shifted from previous position = 0.877
rotated from previous position = 4.4 degrees
atoms outside contour = 18961, contour level = 0.18046
Position of Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) relative
to N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99901339 -0.04441019 0.00004124 30.67584011
-0.04441018 -0.99901335 -0.00026996 313.91851147
0.00005318 0.00026787 -0.99999997 265.32198490
Axis 0.99975335 -0.02220910 0.00002444
Axis point 0.00000000 157.28213507 132.68176775
Rotation angle (degrees) 179.98458849
Shift along axis 23.70291089
> select add #18
35538 atoms, 36024 bonds, 12 pseudobonds, 2520 residues, 8 models selected
> show #!18 models
> hide #!18 models
> select subtract #18
24138 atoms, 24372 bonds, 6 pseudobonds, 1284 residues, 8 models selected
> show #!18 models
> select #18-30
106330 atoms, 108712 bonds, 54 pseudobonds, 10584 residues, 22 models selected
> show sel ribbons
> select clear
> show #!3 models
> hide #!27 models
> hide #!20 models
> hide #!18 models
> show #!18 models
> select add #18
11400 atoms, 11652 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> view matrix models
> #18,0.43545,0.86682,0.24291,-144.01,-0.89455,0.44689,0.0088969,179.42,-0.10084,-0.22117,0.97001,-4.1112
> fitmap #18 inMap #3
Fit molecule 230904_Chol_HC_150.pdb (#18) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11400 atoms
average map value = 0.166, steps = 116
shifted from previous position = 4.03
rotated from previous position = 15.4 degrees
atoms outside contour = 7012, contour level = 0.18046
Position of 230904_Chol_HC_150.pdb (#18) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.49900007 0.86660194 -0.00004538 -60.68494796
-0.86660194 0.49900007 -0.00008250 227.04136658
-0.00004885 0.00008049 1.00000000 -0.01100686
Axis 0.00009404 0.00000200 -1.00000000
Axis point 166.01932001 166.00541576 0.00000000
Rotation angle (degrees) 60.06613282
Shift along axis 0.00575510
> select clear
> hide #!18 models
> show #!18 models
> hide #!3 models
> show #!20 models
> show #!7 models
> fitmap #20 inMap #7
Fit molecule 230926_MBCD_HC_10.pdb (#20) to map
MBCD_P41_J50_013_volume_map.mrc (#7) using 11784 atoms
average map value = 0.1298, steps = 84
shifted from previous position = 0.231
rotated from previous position = 8.21 degrees
atoms outside contour = 5793, contour level = 0.11674
Position of 230926_MBCD_HC_10.pdb (#20) relative to
MBCD_P41_J50_013_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.99999997 0.00021565 -0.00007063 -0.01562552
-0.00021566 0.99999996 -0.00019277 0.04475525
0.00007058 0.00019279 0.99999998 -0.03065823
Axis 0.64744849 -0.23712894 -0.72427917
Axis point 209.13353167 76.91398535 0.00000000
Rotation angle (degrees) 0.01705982
Shift along axis 0.00147563
> hide #!7 models
> hide #!20 models
> hide #!18 models
> show #!20 models
> show #!27 models
> select clear
> show #!18 models
> select #18,20,27
47322 atoms, 48090 bonds, 18 pseudobonds, 3756 residues, 6 models selected
> select #18,20,27/b
7887 atoms, 8015 bonds, 3 pseudobonds, 626 residues, 6 models selected
> select #18,20,27/a
7887 atoms, 8015 bonds, 3 pseudobonds, 626 residues, 6 models selected
> select #18,20,27/b-f
39435 atoms, 40075 bonds, 15 pseudobonds, 3130 residues, 6 models selected
> hide sel ribbons
> select add #20
41399 atoms, 42086 bonds, 16 pseudobonds, 3336 residues, 16 models selected
> select subtract #20
29615 atoms, 30020 bonds, 10 pseudobonds, 2100 residues, 15 models selected
> select add #18
31515 atoms, 31962 bonds, 11 pseudobonds, 2306 residues, 9 models selected
> select subtract #18
20115 atoms, 20310 bonds, 5 pseudobonds, 1070 residues, 8 models selected
> select add #18
31515 atoms, 31962 bonds, 11 pseudobonds, 2306 residues, 4 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.3232,0.94598,0.025928,-106.87,-0.94591,0.32375,-0.021132,215.14,-0.028385,-0.017696,0.99944,-56.712,#27,0.97157,-0.23533,-0.026,6.3311,-0.23483,-0.97181,0.020787,277.31,-0.030159,-0.01409,-0.99945,207.14
> fitmap #27 inMap #7
Fit molecule Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) to map
MBCD_P41_J50_013_volume_map.mrc (#7) using 24138 atoms
average map value = 0.09324, steps = 72
shifted from previous position = 0.769
rotated from previous position = 2.36 degrees
atoms outside contour = 16407, contour level = 0.11674
Position of Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) relative
to MBCD_P41_J50_013_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.97738895 -0.21144938 0.00007412 -0.04081000
-0.21144935 -0.97738891 -0.00033092 277.08117276
0.00014242 0.00030776 -0.99999995 201.47105643
Axis 0.99433106 -0.10632850 0.00005322
Axis point 0.00000000 138.52213579 100.75764995
Rotation angle (degrees) 179.98159875
Shift along axis -29.49148207
> fitmap #27 inMap #7
Fit molecule Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) to map
MBCD_P41_J50_013_volume_map.mrc (#7) using 24138 atoms
average map value = 0.09324, steps = 40
shifted from previous position = 0.00292
rotated from previous position = 0.0199 degrees
atoms outside contour = 16401, contour level = 0.11674
Position of Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) relative
to MBCD_P41_J50_013_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.97746003 -0.21112057 -0.00000429 -0.09081784
-0.21112055 -0.97745997 -0.00037320 277.05106037
0.00007460 0.00036570 -0.99999993 201.47399420
Axis 0.99434894 -0.10616111 0.00001662
Axis point 0.00000000 138.50186135 100.76258610
Rotation angle (degrees) 179.97871180
Shift along axis -29.49900450
> fitmap #27 inMap #7
Fit molecule Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) to map
MBCD_P41_J50_013_volume_map.mrc (#7) using 24138 atoms
average map value = 0.09324, steps = 28
shifted from previous position = 0.00625
rotated from previous position = 0.00545 degrees
atoms outside contour = 16401, contour level = 0.11674
Position of Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) relative
to MBCD_P41_J50_013_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.97745198 -0.21115783 0.00006353 -0.09183431
-0.21115780 -0.97745194 -0.00031840 277.04913807
0.00012933 0.00029780 -0.99999995 201.46967316
Axis 0.99434690 -0.10618024 0.00004722
Axis point 0.00000000 138.50397053 100.75617783
Rotation angle (degrees) 179.98224678
Shift along axis -29.49894571
> fitmap #27 inMap #7
Fit molecule Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) to map
MBCD_P41_J50_013_volume_map.mrc (#7) using 24138 atoms
average map value = 0.09324, steps = 28
shifted from previous position = 0.0224
rotated from previous position = 0.000781 degrees
atoms outside contour = 16415, contour level = 0.11674
Position of Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) relative
to MBCD_P41_J50_013_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.97745096 -0.21116256 0.00006167 -0.08869672
-0.21116253 -0.97745091 -0.00033100 277.05256975
0.00013017 0.00031051 -0.99999995 201.49000011
Axis 0.99434665 -0.10618260 0.00004701
Axis point 0.00000000 138.50520754 100.76721790
Rotation angle (degrees) 179.98151767
Shift along axis -29.49688549
> fitmap #18 inMap #3
Fit molecule 230904_Chol_HC_150.pdb (#18) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11400 atoms
average map value = 0.166, steps = 60
shifted from previous position = 0.741
rotated from previous position = 2.41 degrees
atoms outside contour = 7015, contour level = 0.18046
Position of 230904_Chol_HC_150.pdb (#18) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.49898756 0.86660915 0.00010479 -60.69842360
-0.86660912 0.49898757 -0.00020368 227.04693194
-0.00022880 0.00001082 0.99999998 0.02958979
Axis 0.00012376 0.00019247 -0.99999997
Axis point 166.01412712 166.01898214 0.00000000
Rotation angle (degrees) 60.06696066
Shift along axis 0.00659721
> select add #27
35538 atoms, 36024 bonds, 12 pseudobonds, 2520 residues, 10 models selected
> select subtract #27
11400 atoms, 11652 bonds, 6 pseudobonds, 1236 residues, 8 models selected
> view matrix models
> #18,0.46068,0.88268,0.093064,-128.01,-0.88754,0.45897,0.040206,175.24,-0.0072253,-0.10112,0.99485,-46.293
> view matrix models
> #18,0.92146,0.29989,0.24693,-129.57,-0.25001,0.94432,-0.2139,49.125,-0.29733,0.13537,0.94513,-32.792
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.92146,0.29989,0.24693,-124.16,-0.25001,0.94432,-0.2139,38.972,-0.29733,0.13537,0.94513,-38.297
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.92146,0.29989,0.24693,-120.71,-0.25001,0.94432,-0.2139,35.72,-0.29733,0.13537,0.94513,-37.004
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.98081,0.17494,0.086011,-83.362,-0.17665,0.98419,0.012558,-18.454,-0.082454,-0.027511,0.99622,-51.264
> fitmap #18 inMap #3
Fit molecule 230904_Chol_HC_150.pdb (#18) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11400 atoms
average map value = 0.06518, steps = 116
shifted from previous position = 7.86
rotated from previous position = 3.23 degrees
atoms outside contour = 10302, contour level = 0.18046
Position of 230904_Chol_HC_150.pdb (#18) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99027672 0.01461111 0.13834211 -15.61961396
-0.01889220 0.99938081 0.02968319 6.55327789
-0.13782275 -0.03200816 0.98993958 29.21169812
Axis -0.21650044 0.96917657 -0.11757696
Axis point 208.73133255 0.00000000 117.71961422
Rotation angle (degrees) 8.19102944
Shift along axis 6.29831400
> fitmap #18 inMap #3
Fit molecule 230904_Chol_HC_150.pdb (#18) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11400 atoms
average map value = 0.06518, steps = 44
shifted from previous position = 0.00738
rotated from previous position = 0.00541 degrees
atoms outside contour = 10301, contour level = 0.18046
Position of 230904_Chol_HC_150.pdb (#18) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99027435 0.01464938 0.13835497 -15.62603126
-0.01894225 0.99937751 0.02976232 6.54991886
-0.13783285 -0.03209362 0.98993540 29.22107744
Axis -0.21702600 0.96902479 -0.11785865
Axis point 208.78814122 0.00000000 117.74493355
Rotation angle (degrees) 8.19300689
Shift along axis 6.29433210
> view matrix models
> #18,0.87475,0.4503,0.17902,-130.92,-0.47248,0.87462,0.10867,23.459,-0.10764,-0.17964,0.97783,-14.13
> view matrix models
> #18,0.98354,0.0067218,0.18056,-77.959,-0.071079,0.93313,0.35245,-84.066,-0.16611,-0.35948,0.91825,32.15
> view matrix models
> #18,0.37408,-0.87094,0.31863,124.24,0.49079,0.47744,0.72882,-156.74,-0.78688,-0.11626,0.60605,135.85
> view matrix models
> #18,0.77562,-0.24762,0.58061,-74.165,0.23646,0.96684,0.096453,-91.738,-0.58524,0.062481,0.80845,45.421
> view matrix models
> #18,0.39114,-0.91167,0.12599,159.85,0.67272,0.18979,-0.71514,99.609,0.62805,0.36448,0.68753,-157.67
> view matrix models
> #18,0.93213,-0.28393,0.22477,-32.574,0.17004,-0.20485,-0.96391,274.94,0.31973,0.93671,-0.14267,-65.11
> view matrix models
> #18,0.45081,0.83032,0.32763,-153.02,-0.89147,0.43743,0.11806,150.71,-0.04529,-0.34529,0.9374,9.2544
> view matrix models
> #18,0.067468,0.9917,-0.10948,-50.455,-0.98658,0.049956,-0.15547,269.87,-0.14871,0.1185,0.98176,-55.198
> view matrix models
> #18,0.1434,0.9854,-0.091772,-63.413,-0.98409,0.13215,-0.11879,250.68,-0.10493,0.10735,0.98867,-60.955
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.1434,0.9854,-0.091772,-71.947,-0.98409,0.13215,-0.11879,249.67,-0.10493,0.10735,0.98867,-64.273
> fitmap #18 inMap #3
Fit molecule 230904_Chol_HC_150.pdb (#18) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11400 atoms
average map value = 0.06183, steps = 128
shifted from previous position = 7.57
rotated from previous position = 6.33 degrees
atoms outside contour = 10468, contour level = 0.18046
Position of 230904_Chol_HC_150.pdb (#18) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.23669356 0.95891439 -0.15639475 -12.91849740
-0.96869598 0.22050971 -0.11403305 295.38063165
-0.07486137 0.17848986 0.98108976 -14.37878155
Axis 0.14990536 -0.04178234 -0.98781710
Axis point 179.26573138 156.15783373 0.00000000
Rotation angle (degrees) 77.34109132
Shift along axis -0.07463916
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.17963,0.92096,-0.34579,-23.963,-0.98303,0.15477,-0.098462,251.12,-0.037163,0.35761,0.93313,-103.73
> view matrix models
> #18,0.052928,0.85988,-0.50775,30.617,-0.91757,-0.15875,-0.3645,334.24,-0.39403,0.48519,0.7806,-46.65
> view matrix models
> #18,0.31441,0.73382,-0.60221,27.856,-0.92387,0.38234,-0.016453,193.62,0.21818,0.56154,0.79817,-150.25
> view matrix models
> #18,0.6711,0.6985,-0.24844,-76.714,-0.59217,0.70667,0.38723,28.502,0.44605,-0.11275,0.88788,-93.211
> view matrix models
> #18,0.76794,0.64052,0.0032238,-123.23,-0.57343,0.68525,0.44901,18.933,0.28539,-0.34666,0.89352,-34.444
> view matrix models
> #18,0.99827,-0.034034,0.047927,-59.083,0.042263,0.98224,-0.18279,-12.466,-0.040855,0.1845,0.98198,-84.313
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.99827,-0.034034,0.047927,-67.51,0.042263,0.98224,-0.18279,-17.224,-0.040855,0.1845,0.98198,-83.208
> view matrix models
> #18,0.99827,-0.034034,0.047927,-65.117,0.042263,0.98224,-0.18279,-24.891,-0.040855,0.1845,0.98198,-86.953
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.97308,-0.17178,-0.15363,-6.8126,0.18318,0.98104,0.063301,-85.712,0.13984,-0.089739,0.9861,-71.19
> fitmap #18 inMap #3
Fit molecule 230904_Chol_HC_150.pdb (#18) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11400 atoms
average map value = 0.06771, steps = 100
shifted from previous position = 5.3
rotated from previous position = 9.22 degrees
atoms outside contour = 10137, contour level = 0.18046
Position of 230904_Chol_HC_150.pdb (#18) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.96280912 -0.26344655 -0.05995400 56.00286217
0.26057269 0.96406949 -0.05169006 -22.19165970
0.07141739 0.03414529 0.99686189 -18.61055148
Axis 0.15691671 -0.24016172 0.95796633
Axis point 115.94540238 198.41996026 0.00000000
Rotation angle (degrees) 15.87300668
Shift along axis -3.71090990
> fitmap #18 inMap #3
Fit molecule 230904_Chol_HC_150.pdb (#18) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11400 atoms
average map value = 0.06771, steps = 60
shifted from previous position = 0.00507
rotated from previous position = 0.00694 degrees
atoms outside contour = 10135, contour level = 0.18046
Position of 230904_Chol_HC_150.pdb (#18) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.96282043 -0.26338544 -0.06004089 56.00239638
0.26051287 0.96408891 -0.05162936 -22.19053373
0.07148318 0.03406838 0.99685980 -18.60769559
Axis 0.15669400 -0.24048514 0.95792165
Axis point 115.96556600 198.46445446 0.00000000
Rotation angle (degrees) 15.87000672
Shift along axis -3.71298169
> fitmap #18 inMap #3
Fit molecule 230904_Chol_HC_150.pdb (#18) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11400 atoms
average map value = 0.06771, steps = 76
shifted from previous position = 0.0103
rotated from previous position = 0.0116 degrees
atoms outside contour = 10135, contour level = 0.18046
Position of 230904_Chol_HC_150.pdb (#18) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.96281647 -0.26343186 -0.05990055 55.99354026
0.26055410 0.96407023 -0.05176980 -22.17993574
0.07138615 0.03423749 0.99686096 -18.62102041
Axis 0.15723828 -0.24001796 0.95794963
Axis point 115.90376552 198.40878973 0.00000000
Rotation angle (degrees) 15.87225605
Shift along axis -3.71008851
> show #!3 models
> view matrix models
> #18,0.96675,-0.23848,0.092346,-32.207,0.24055,0.97056,-0.011828,-80.689,-0.086807,0.033649,0.99566,-59.297
> fitmap #18 inMap #3
Fit molecule 230904_Chol_HC_150.pdb (#18) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11400 atoms
average map value = 0.166, steps = 180
shifted from previous position = 12
rotated from previous position = 24.1 degrees
atoms outside contour = 7011, contour level = 0.18046
Position of 230904_Chol_HC_150.pdb (#18) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999931 0.00116491 -0.00001064 -0.18360613
-0.00116491 0.99999930 -0.00008849 0.20975451
0.00001053 0.00008850 0.99999998 -0.02241553
Axis 0.07574667 -0.00905799 -0.99708595
Axis point 180.01837363 158.14393864 0.00000000
Rotation angle (degrees) 0.06693969
Shift along axis 0.00654270
> fitmap #18 inMap #3
Fit molecule 230904_Chol_HC_150.pdb (#18) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11400 atoms
average map value = 0.166, steps = 24
shifted from previous position = 0.00496
rotated from previous position = 0.00177 degrees
atoms outside contour = 7006, contour level = 0.18046
Position of 230904_Chol_HC_150.pdb (#18) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999930 0.00116960 -0.00002147 -0.18213232
-0.00116960 0.99999930 -0.00005994 0.20987990
0.00002140 0.00005996 0.99999998 -0.02238291
Axis 0.05118001 -0.01829945 -0.99852178
Axis point 179.49830139 156.22934560 0.00000000
Rotation angle (degrees) 0.06711223
Shift along axis 0.00918760
> fitmap #18 inMap #3
Fit molecule 230904_Chol_HC_150.pdb (#18) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11400 atoms
average map value = 0.166, steps = 28
shifted from previous position = 0.0202
rotated from previous position = 0.00202 degrees
atoms outside contour = 7011, contour level = 0.18046
Position of 230904_Chol_HC_150.pdb (#18) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999931 0.00116654 0.00000171 -0.19898984
-0.00116654 0.99999930 -0.00008634 0.19873886
-0.00000181 0.00008634 0.99999998 -0.02264338
Axis 0.07381505 0.00150394 -0.99727081
Axis point 170.25522301 171.19898456 0.00000000
Rotation angle (degrees) 0.06702071
Shift along axis 0.00819203
> fitmap #18 inMap #3
Fit molecule 230904_Chol_HC_150.pdb (#18) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11400 atoms
average map value = 0.166, steps = 28
shifted from previous position = 0.0182
rotated from previous position = 0.000706 degrees
atoms outside contour = 7004, contour level = 0.18046
Position of 230904_Chol_HC_150.pdb (#18) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999931 0.00116709 0.00000492 -0.18663747
-0.00116709 0.99999930 -0.00009823 0.21314736
-0.00000504 0.00009823 0.99999998 -0.02740001
Axis 0.08387007 0.00425057 -0.99646763
Axis point 182.49170589 160.92614808 0.00000000
Rotation angle (degrees) 0.06710621
Shift along axis 0.01255592
> fitmap #18 inMap #3
Fit molecule 230904_Chol_HC_150.pdb (#18) to map
N55H_CBX_P52_J575_011_volume_map.mrc (#3) using 11400 atoms
average map value = 0.166, steps = 28
shifted from previous position = 0.00515
rotated from previous position = 0.00329 degrees
atoms outside contour = 7006, contour level = 0.18046
Position of 230904_Chol_HC_150.pdb (#18) relative to
N55H_CBX_P52_J575_011_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999930 0.00117384 0.00005665 -0.19556550
-0.00117383 0.99999929 -0.00007429 0.20783145
-0.00005674 0.00007423 0.99999998 -0.01926749
Axis 0.06306348 0.04814536 -0.99684754
Axis point 176.26253215 167.61410103 0.00000000
Rotation angle (degrees) 0.06746852
Shift along axis 0.01687983
> hide #!3 models
> show #!3 models
> hide #!3 models
> select clear
> select #18,20,27/b,e
15774 atoms, 16030 bonds, 6 pseudobonds, 1252 residues, 6 models selected
> select #18,20,27/a-f
47322 atoms, 48090 bonds, 18 pseudobonds, 3756 residues, 6 models selected
> show sel ribbons
> select #18,20,27/b,c,e
23661 atoms, 24045 bonds, 9 pseudobonds, 1878 residues, 6 models selected
> select #18,20,27/b,c,e,f
31548 atoms, 32060 bonds, 12 pseudobonds, 2504 residues, 6 models selected
> hide sel ribbons
> select clear
> show #!17 models
> select #17/b/
Expected an objects specifier or a keyword
> select #17/b
1921 atoms, 1954 bonds, 1 pseudobond, 211 residues, 2 models selected
> hide sel ribbons
> select clear
> morph #18,20,17
Computed 101 frame morph #28
> coordset #28 1,101
> hide #!27 models
> close #26
> select #17,20
23310 atoms, 23790 bonds, 12 pseudobonds, 2502 residues, 4 models selected
> show sel atoms
> undo
> select #17,20/a,d
7770 atoms, 7930 bonds, 4 pseudobonds, 834 residues, 4 models selected
> show sel atoms
> hide #!28 models
> show #!17 models
> show #!20 models
> select add #20
15626 atoms, 15974 bonds, 8 pseudobonds, 1658 residues, 8 models selected
> select add #17
23310 atoms, 23790 bonds, 12 pseudobonds, 2502 residues, 12 models selected
> select subtract #20
11526 atoms, 11724 bonds, 6 pseudobonds, 1266 residues, 14 models selected
> select subtract #17
6 models selected
> select clear
> select
> ::name="6OU"::name="CBO"::name="CLR"::name="MC3"::name="PIO"::name="PTY"::name="Y01"
14490 atoms, 14322 bonds, 384 residues, 7 models selected
> hide sel atoms
> select clear
> hide #!20 models
> show #!28 models
> hide #!17 models
> show #!19 models
> hide #!19 models
> show #!4 models
> hide #!4 models
> show #!3 models
> volume #3 level 0.1695
> hide #!3 models
> hide #!28 models
> show #!3 models
> show #!5 models
> hide #!5 models
> hide #!3 models
> show #!18 models
> show #!20 models
> show #!17 models
> select #17,18,20
34710 atoms, 35442 bonds, 18 pseudobonds, 3738 residues, 6 models selected
> hide sel atoms
> select #17,18,20:189
198 atoms, 180 bonds, 18 residues, 3 models selected
> show sel atoms
> undo
> select #17,18,20/a,d:189
66 atoms, 60 bonds, 6 residues, 3 models selected
> show sel atoms
> select clear
> show #!7 models
> hide #!7 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!19 models
> hide #!20 models
> hide #!18 models
> hide #!17 models
> show #!6 models
> clip front 0
> transparency 50
> select add #19
8550 atoms, 8838 bonds, 6 pseudobonds, 1014 residues, 2 models selected
> toolshed show
> ui tool show "Map Coordinates"
> mlp sel
Map values for surface "231009_CBX_HC_185.pdb_A SES surface": minimum -27.25,
mean 0.8939, maximum 24.32
Map values for surface "231009_CBX_HC_185.pdb_B SES surface": minimum -27.68,
mean 0.9203, maximum 24.56
Map values for surface "231009_CBX_HC_185.pdb_C SES surface": minimum -27.75,
mean 0.9056, maximum 24.54
Map values for surface "231009_CBX_HC_185.pdb_D SES surface": minimum -27.64,
mean 0.9218, maximum 24.13
Map values for surface "231009_CBX_HC_185.pdb_E SES surface": minimum -27.6,
mean 0.8945, maximum 23.94
Map values for surface "231009_CBX_HC_185.pdb_F SES surface": minimum -26.79,
mean 0.9031, maximum 24.3
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> ~clip
> hide #!6 models
> select clear
> show #!18 models
> select #19/b,c,e,f
5700 atoms, 5892 bonds, 4 pseudobonds, 676 residues, 2 models selected
> hide sel ribbons
> select clear
> select #19/A:189
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select clear
> show #!17 models
> select #18,19
19950 atoms, 20490 bonds, 12 pseudobonds, 2250 residues, 4 models selected
> show sel ribbons
> select clear
> select add #17
11526 atoms, 11724 bonds, 6 pseudobonds, 1266 residues, 2 models selected
> select add #18
22926 atoms, 23376 bonds, 12 pseudobonds, 2502 residues, 10 models selected
> select add #19
31476 atoms, 32214 bonds, 18 pseudobonds, 3516 residues, 18 models selected
> mlp sel
Map values for surface "230904_Chol_HC_150.pdb_A SES surface": minimum -27.81,
mean 0.2398, maximum 23.77
Map values for surface "230904_Chol_HC_150.pdb_B SES surface": minimum -28.02,
mean 0.1575, maximum 25.32
Map values for surface "230904_Chol_HC_150.pdb_C SES surface": minimum -27.98,
mean 0.1448, maximum 24.75
Map values for surface "230904_Chol_HC_150.pdb_D SES surface": minimum -27.85,
mean 0.2229, maximum 24.89
Map values for surface "230904_Chol_HC_150.pdb_E SES surface": minimum -27.89,
mean 0.1407, maximum 24.78
Map values for surface "230904_Chol_HC_150.pdb_F SES surface": minimum -27.69,
mean 0.1488, maximum 25.26
Map values for surface "231006_PIP2_HC_90.pdb_A SES surface": minimum -27.87,
mean 0.03368, maximum 24.91
Map values for surface "231006_PIP2_HC_90.pdb_B SES surface": minimum -27.78,
mean 0.02854, maximum 26.05
Map values for surface "231006_PIP2_HC_90.pdb_C SES surface": minimum -28.52,
mean -0.002751, maximum 23.5
Map values for surface "231006_PIP2_HC_90.pdb_D SES surface": minimum -27.98,
mean 0.0383, maximum 26.17
Map values for surface "231006_PIP2_HC_90.pdb_E SES surface": minimum -27.97,
mean 0.03508, maximum 25.06
Map values for surface "231006_PIP2_HC_90.pdb_F SES surface": minimum -27.96,
mean -0.0197, maximum 23.57
Map values for surface "231009_CBX_HC_185.pdb_A SES surface": minimum -27.25,
mean 0.8939, maximum 24.32
Map values for surface "231009_CBX_HC_185.pdb_B SES surface": minimum -27.68,
mean 0.9203, maximum 24.56
Map values for surface "231009_CBX_HC_185.pdb_C SES surface": minimum -27.75,
mean 0.9056, maximum 24.54
Map values for surface "231009_CBX_HC_185.pdb_D SES surface": minimum -27.64,
mean 0.9218, maximum 24.13
Map values for surface "231009_CBX_HC_185.pdb_E SES surface": minimum -27.6,
mean 0.8945, maximum 23.94
Map values for surface "231009_CBX_HC_185.pdb_F SES surface": minimum -26.79,
mean 0.9031, maximum 24.3
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!19 models
> hide #!18 models
> select subtract #19
22926 atoms, 23376 bonds, 12 pseudobonds, 2502 residues, 22 models selected
> select subtract #18
11526 atoms, 11724 bonds, 6 pseudobonds, 1266 residues, 14 models selected
> select subtract #17
6 models selected
> select clear
> show #!18 models
> hide #!17 models
> show #!19 models
> hide #!18 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> select ::name="CBO"
246 atoms, 270 bonds, 6 residues, 1 model selected
> show sel atoms
> select clear
> show #!18 models
> hide #!18 models
> show #!5 models
> hide #!5 models
> show #!6 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/230903_All_Align.cxs"
——— End of log from Mon Oct 9 18:51:11 2023 ———
opened ChimeraX session
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231011_All_Align_wo_POPE.cxs"
> close #9-12
> close #13-16
> show #!17 models
> hide #!17 models
> hide #!6 models
> hide #!19 models
> show #!27 models
> close #28
> close #30-31
> show #!23 models
> close #21
> hide #!23 models
> hide #!27 models
> show #!1 models
> hide #!1 models
> show #!17 models
> hide #!17 atoms
> show #!17 cartoons
> hide #!17 surfaces
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231011_All_Align_wo_POPE.cxs"
——— End of log from Wed Oct 11 22:08:58 2023 ———
opened ChimeraX session
> close #1
> close #5-6
> close #24-25
> close #23
> close #22
> rename #2 id #1
> select clear
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/N55H_Chol_P52_J694_007_volume_map_sharp.mrc"
Opened N55H_Chol_P52_J694_007_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.83, shown at level 0.0479, step 2, values float32
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/N55H_MBCD_P74_J90_011_volume_map_sharp.mrc"
Opened N55H_MBCD_P74_J90_011_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.848, shown at level 0.0961, step 2, values float32
> close #17
> hide #!3 models
> show #!3 models
> hide #!3 models
> color #2 #00aaffff models
> color #3 #aaff7fff models
> volume #3 step 1
> volume #2 step 1
> volume #2 level 0.1116
> volume #3 level 0.2065
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!1 models
> transparency 0
> select clear
> volume #1 level 0.1806
> select add #1
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.79312,0.52083,-0.31575,208.34,0.41275,0.84084,0.35017,-163.53,0.44788,0.1474,-0.88186,147.46
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.79312,0.52083,-0.31575,244.16,0.41275,0.84084,0.35017,-141.54,0.44788,0.1474,-0.88186,187.53
> view matrix models
> #1,-0.79312,0.52083,-0.31575,226.98,0.41275,0.84084,0.35017,-127.74,0.44788,0.1474,-0.88186,196.76
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.92951,0.14352,-0.33972,318.17,0.028796,0.9466,0.32112,-75.624,0.36767,0.2887,-0.88401,186.76
> view matrix models
> #1,-0.98197,0.12694,-0.14005,295.97,0.089563,0.96495,0.24666,-76.397,0.16646,0.22967,-0.95893,243.62
> toolshed show
> ui tool show "Fit in Map"
> fitmap #1 inMap #3
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 103096 points
correlation = 0.248, correlation about mean = 0.03376, overlap = 2667
steps = 76, shift = 2.69, angle = 4.35 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.96800472 0.13024566 -0.21448297 305.25999499
0.07646141 0.96719665 0.24224841 -72.08097845
0.23899901 0.21809793 -0.94620969 233.17143977
Axis -0.05281119 -0.99165425 -0.11761300
Axis point 140.73621938 0.00000000 138.77882372
Rotation angle (degrees) 166.78244019
Shift along axis 27.93427222
> view matrix models
> #1,-0.69836,0.63297,-0.33412,194.58,0.58026,0.77399,0.25345,-126.66,0.41903,-0.016874,-0.90782,235.97
> view matrix models
> #1,-0.72837,0.67163,-0.13563,159.41,0.68297,0.72755,-0.06494,-82.133,0.05506,-0.13993,-0.98863,332.29
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.72837,0.67163,-0.13563,165.63,0.68297,0.72755,-0.06494,-91.481,0.05506,-0.13993,-0.98863,325.42
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.70787,0.70342,0.064143,122.83,0.69248,0.70902,-0.13328,-78.344,-0.13923,-0.04993,-0.989,343.17
> view matrix models
> #1,-0.80406,0.59026,0.071239,157.13,0.58326,0.80635,-0.098009,-82.318,-0.11529,-0.037254,-0.99263,337.58
> view matrix models
> #1,-0.80153,0.59795,-0.00097825,167.66,0.59723,0.80048,-0.050363,-91.785,-0.029332,-0.040952,-0.99873,324.66
> view matrix models
> #1,-0.99762,0.056818,-0.03917,299.18,0.055237,0.99766,0.040323,-48.704,0.041369,0.038063,-0.99842,299.22
> fitmap #1 inMap #3
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 103096 points
correlation = 0.8993, correlation about mean = 0.7271, overlap = 1.914e+04
steps = 68, shift = 3.26, angle = 4.36 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.99998879 0.00473509 0.00001750 304.47209732
0.00473509 0.99998879 -0.00001293 -34.72064256
-0.00001756 -0.00001284 -1.00000000 314.58735126
Axis 0.00237420 0.99999718 -0.00000513
Axis point 152.27864430 0.00000000 157.29225175
Rotation angle (degrees) 179.99899558
Shift along axis -33.99928351
> fitmap #1 inMap #3
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 103096 points
correlation = 0.8992, correlation about mean = 0.727, overlap = 1.915e+04
steps = 28, shift = 0.00965, angle = 0.014 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.99998926 0.00463256 0.00016946 304.47199012
0.00463253 0.99998926 -0.00017326 -34.68167225
-0.00017026 -0.00017248 -0.99999997 314.63977891
Axis 0.00231696 0.99999731 -0.00008630
Axis point 152.28953408 0.00000000 157.30546041
Rotation angle (degrees) 179.99026794
Shift along axis -34.00328200
> fitmap #1 inMap #3
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 103096 points
correlation = 0.8992, correlation about mean = 0.727, overlap = 1.915e+04
steps = 28, shift = 0.00937, angle = 0.0112 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.99998933 0.00461524 0.00021359 304.47096569
0.00461524 0.99998935 0.00001560 -34.70185674
-0.00021351 0.00001659 -0.99999998 314.61478599
Axis 0.00230817 0.99999734 0.00000815
Axis point 152.29232858 0.00000000 157.29127515
Rotation angle (degrees) 179.98776438
Shift along axis -33.99642777
> select clear
> rename #3 id #4
> select clear
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/N55H_CBX_P52_J660_003_volume_map_sharp.mrc"
Opened N55H_CBX_P52_J660_003_volume_map_sharp.mrc as #3, grid size
400,400,400, pixel 0.83, shown at level 0.0426, step 2, values float32
> color #3 #aa55ffff models
> volume #3 step 1
> volume #3 level 0.07019
> ui mousemode right "rotate selected models"
> select add #3
2 models selected
> view matrix models
> #3,-0.45256,-0.89173,-0.0031919,389.67,-0.88947,0.45167,-0.069603,249.9,0.063508,-0.028661,-0.99757,316.42
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.45256,-0.89173,-0.0031919,383.69,-0.88947,0.45167,-0.069603,217.56,0.063508,-0.028661,-0.99757,325.58
> view matrix models
> #3,-0.45256,-0.89173,-0.0031919,365.91,-0.88947,0.45167,-0.069603,227.14,0.063508,-0.028661,-0.99757,306.19
> view matrix models
> #3,-0.45256,-0.89173,-0.0031919,358.12,-0.88947,0.45167,-0.069603,223.17,0.063508,-0.028661,-0.99757,306.19
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.67587,-0.73692,0.011781,367.08,-0.7363,0.67443,-0.05472,158.37,0.032379,-0.045659,-0.99843,314.32
> view matrix models
> #3,-0.67692,-0.73329,-0.063747,378.83,-0.73518,0.6778,0.0099676,147.19,0.035899,0.053613,-0.99792,297.17
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.67692,-0.73329,-0.063747,378.4,-0.73518,0.6778,0.0099676,142.95,0.035899,0.053613,-0.99792,297.64
> ui tool show "Fit in Map"
> fitmap #1 inMap #4
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 103096 points
correlation = 0.8993, correlation about mean = 0.7271, overlap = 1.913e+04
steps = 40, shift = 0.0183, angle = 0.0205 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.99998848 0.00480089 -0.00008628 304.47230288
0.00480090 0.99998848 -0.00004151 -34.72885365
0.00008608 -0.00004193 -1.00000000 314.57499947
Axis -0.00239910 -0.99999712 0.00002113
Axis point 152.27103308 0.00000000 157.29369455
Rotation angle (degrees) 179.99506223
Shift along axis 34.00493870
> fitmap #1 inMap #4
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 103096 points
correlation = 0.8993, correlation about mean = 0.7271, overlap = 1.913e+04
steps = 40, shift = 0.0122, angle = 0.0122 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.99998873 0.00474826 0.00009038 304.46153879
0.00474827 0.99998873 0.00006400 -34.73078697
-0.00009007 0.00006443 -1.00000000 314.58645395
Axis 0.00237543 0.99999718 0.00003236
Axis point 152.27911560 0.00000000 157.28691968
Rotation angle (degrees) 179.99483056
Shift along axis -33.99728205
> fitmap #3 inMap #4
Fit map N55H_CBX_P52_J660_003_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 148192 points
correlation = 0.3593, correlation about mean = 0.113, overlap = 2580
steps = 80, shift = 6.8, angle = 5.24 degrees
Position of N55H_CBX_P52_J660_003_volume_map_sharp.mrc (#3) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.72412235 -0.68967154 0.00003392 370.35945177
-0.68967154 0.72412235 0.00000524 129.96262540
-0.00002818 -0.00001960 -1.00000000 306.21828459
Axis -0.37140363 0.92847151 -0.00000463
Axis point 211.17606000 0.00000000 153.10618832
Rotation angle (degrees) 179.99808406
Shift along axis -16.88766962
> fitmap #3 inMap #4
Fit map N55H_CBX_P52_J660_003_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 148192 points
correlation = 0.3593, correlation about mean = 0.113, overlap = 2580
steps = 48, shift = 0.00534, angle = 0.00559 degrees
Position of N55H_CBX_P52_J660_003_volume_map_sharp.mrc (#3) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.72415435 -0.68963794 -0.00005170 370.36932586
-0.68963794 0.72415435 0.00001126 129.95481598
0.00002967 0.00004381 -1.00000000 306.19705658
Axis 0.37137775 -0.92848186 -0.00001542
Axis point 211.17096401 0.00000000 153.10174492
Rotation angle (degrees) 179.99748956
Shift along axis 16.88151512
> select clear
[Repeated 1 time(s)]
> close #18-20
> hide #!3 models
> hide #!4 models
> hide #!1 models
> show #!4 models
> open
> C:/Users/OJS/Desktop/Phenix/230901_MBCD_Chol_N55H/RealSpaceRefine_37/231026_From37_real_space_refined_037.pdb
Chain information for 231026_From37_real_space_refined_037.pdb #5
---
Chain | Description
A B C D E F | No description available
> hide #!5 atoms
> show #!5 cartoons
> color #4 #aaff7fff models
> color #5 #aaff7fff
> transparency 10
> transparency 50
> transparency 80
> select clear
> transparency 50
> transparency 10
> lighting simple
> transparency 30
> transparency 50
> select clear
> volume #4 level 0.2772
> close #5
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/231026_N55H_MBCD_37_wo_water.pdb"
Chain information for 231026_N55H_MBCD_37_wo_water.pdb #5
---
Chain | Description
A B C D E F | No description available
> volume #4 level 0.2065
> volume #4 level 0.1411
> hide #!5 models
> open
> C:/Users/OJS/Desktop/Phenix/230901_MBCD_Chol_N55H/RealSpaceRefine_39/231030_From37_real_space_refined_037-coot-0_real_space_refined_039.pdb
Chain information for
231030_From37_real_space_refined_037-coot-0_real_space_refined_039.pdb #6
---
Chain | Description
A B C D E F | No description available
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!6 atoms
> show #!6 cartoons
> close #6
> rename #5 id #8
> select clear
> show #!8 models
> hide #!8 atoms
> show #!8 cartoons
> color #8 #aaff7fff
> select clear
> show #!3 models
> hide #!3 models
> show #!2 models
> combine #4
No structures specified
> combine #8
> select add #5
11646 atoms, 11886 bonds, 6 pseudobonds, 1230 residues, 2 models selected
> ui mousemode right "rotate selected models"
> hide #!5 models
> show #!5 models
> hide #!8 models
> hide #!4 models
> view matrix models
> #5,0.99888,-0.042557,-0.020451,8.8276,0.038163,0.98274,-0.18101,22.85,0.027802,0.18003,0.98327,-25.824
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.99888,-0.042557,-0.020451,46.966,0.038163,0.98274,-0.18101,45.263,0.027802,0.18003,0.98327,-16.32
> view matrix models
> #5,0.99888,-0.042557,-0.020451,46.151,0.038163,0.98274,-0.18101,48.522,0.027802,0.18003,0.98327,0.076006
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.97918,0.15163,0.13495,0.42631,-0.1337,0.98202,-0.1333,65.168,-0.15273,0.11248,0.98185,33.937
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.97918,0.15163,0.13495,-4.5765,-0.1337,0.98202,-0.1333,67.53,-0.15273,0.11248,0.98185,29.115
> view matrix models
> #5,0.97918,0.15163,0.13495,-3.136,-0.1337,0.98202,-0.1333,66.674,-0.15273,0.11248,0.98185,29.005
> view matrix models
> #5,0.97918,0.15163,0.13495,-5.0975,-0.1337,0.98202,-0.1333,66.444,-0.15273,0.11248,0.98185,33.531
> fitmap #3 inMap #4
Fit map N55H_CBX_P52_J660_003_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 148192 points
correlation = 0.3593, correlation about mean = 0.113, overlap = 2580
steps = 44, shift = 0.00592, angle = 0.00353 degrees
Position of N55H_CBX_P52_J660_003_volume_map_sharp.mrc (#3) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.72414853 -0.68964405 0.00000850 370.36472276
-0.68964405 0.72414853 0.00000079 129.95511441
-0.00000670 -0.00000529 -1.00000000 306.21206689
Axis -0.37139361 0.92847552 -0.00000437
Axis point 211.17429793 0.00000000 153.10553603
Rotation angle (degrees) 179.99953072
Shift along axis -16.89228728
> fitmap #5 inMap #2
Fit molecule copy of 231026_N55H_MBCD_37_wo_water.pdb (#5) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 11646 atoms
average map value = 0.1957, steps = 112
shifted from previous position = 3.98
rotated from previous position = 10.9 degrees
atoms outside contour = 5015, contour level = 0.11163
Position of copy of 231026_N55H_MBCD_37_wo_water.pdb (#5) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.98819065 0.15322939 0.00004404 11.12409425
-0.15322938 0.98819064 -0.00012641 52.73700166
-0.00006289 0.00011817 0.99999999 24.64088949
Axis 0.00079811 0.00034889 -0.99999962
Axis point 347.76565965 -45.92363449 0.00000000
Rotation angle (degrees) 8.81412433
Shift along axis -24.61360236
> select clear
> save
> C:/Users/OJS/Desktop/Phenix/220302_Cx43_N55H_CBX/MBCD_37_N55H_Chol_P52_J694_Fit.pdb
> models #5
> hide #!5 models
> close #5
> show #!8 models
> show #!4 models
> hide #!2 models
> volume #4 level 0.2579
> combine #8
> hide #!4 models
> hide #!8 models
> show #!2 models
> hide #!2 models
> show #!3 models
> volume #3 level 0.05963
> close #5
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!4 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> volume #2 level 0.1711
> volume #3 level 0.07263
> ui mousemode right "translate selected models"
> select add #2
2 models selected
> view matrix models #2,1,0,0,-38.708,0,1,0,-17.382,0,0,1,-23.787
> view matrix models #2,1,0,0,-28.694,0,1,0,-27.85,0,0,1,-19.125
> fitmap #2 inMap #4
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 59871 points
correlation = 0.4013, correlation about mean = 0.1603, overlap = 3522
steps = 72, shift = 2.96, angle = 6.4 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99375857 -0.11155222 -0.00000012 -10.76624969
0.11155222 0.99375857 -0.00000003 -47.80157480
0.00000012 0.00000002 1.00000000 -19.30991453
Axis 0.00000023 -0.00000109 1.00000000
Axis point 421.79280241 -120.11266469 0.00000000
Rotation angle (degrees) 6.40480171
Shift along axis -19.30986500
> fitmap #2 inMap #4
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 59871 points
correlation = 0.4013, correlation about mean = 0.1603, overlap = 3522
steps = 24, shift = 0.00028, angle = 7.61e-05 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99375843 -0.11155353 -0.00000013 -10.76601669
0.11155353 0.99375843 0.00000005 -47.80180248
0.00000013 -0.00000006 1.00000000 -19.31018059
Axis -0.00000049 -0.00000115 1.00000000
Axis point 421.78987926 -120.10967791 0.00000000
Rotation angle (degrees) 6.40487769
Shift along axis -19.31012034
> select clear
> open
> C:/Users/OJS/Desktop/Phenix/220302_Cx43_N55H_CBX/RealSpaceRefine_193/231030_From192-coot-1_real_space_refined_193.pdb
Chain information for 231030_From192-coot-1_real_space_refined_193.pdb #5
---
Chain | Description
A B C D E F | No description available
> color #5 #00aaffff
> hide #!5 atoms
> show #!5 cartoons
> select add #2
2 models selected
> select subtract #2
Nothing selected
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!5 models
> select ::name="6OU"::name="CLR"::name="MC3"::name="PTY"::name="Y01"
7602 atoms, 7560 bonds, 162 residues, 3 models selected
> show sel atoms
> color sel gray
> color sel byhetero
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> select add #5
10512 atoms, 10836 bonds, 6 pseudobonds, 1188 residues, 2 models selected
> view matrix models #5,1,0,0,-26.236,0,1,0,-36.803,0,0,1,-10.901
> fitmap #2 inMap #4
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 59871 points
correlation = 0.4013, correlation about mean = 0.1603, overlap = 3522
steps = 24, shift = 0.000145, angle = 9.39e-05 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99375824 -0.11155515 0.00000006 -10.76574861
0.11155515 0.99375824 -0.00000004 -47.80204382
-0.00000006 0.00000005 1.00000000 -19.31031219
Axis 0.00000039 0.00000053 1.00000000
Axis point 421.78566775 -120.10583262 0.00000000
Rotation angle (degrees) 6.40497078
Shift along axis -19.31034172
> fitmap #2 inMap #4
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 59871 points
correlation = 0.4013, correlation about mean = 0.1603, overlap = 3522
steps = 24, shift = 0.000282, angle = 5.93e-05 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99375836 -0.11155413 0.00000020 -10.76597001
0.11155413 0.99375836 -0.00000010 -47.80188704
-0.00000019 0.00000012 1.00000000 -19.31058408
Axis 0.00000095 0.00000175 1.00000000
Axis point 421.78787119 -120.10850757 0.00000000
Rotation angle (degrees) 6.40491212
Shift along axis -19.31067794
> fitmap #5 inMap #2
Fit molecule 231030_From192-coot-1_real_space_refined_193.pdb (#5) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.06865, steps = 192
shifted from previous position = 3.7
rotated from previous position = 7.95 degrees
atoms outside contour = 9100, contour level = 0.1711
Position of 231030_From192-coot-1_real_space_refined_193.pdb (#5) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.97728566 0.18392584 0.10528070 -42.27920129
-0.18963597 0.98072944 0.04698892 23.16069635
-0.09460941 -0.06588660 0.99333177 35.01544100
Axis -0.25743751 0.45589346 -0.85199007
Axis point 116.28984958 255.97535920 0.00000000
Rotation angle (degrees) 12.66375093
Shift along axis -8.38974578
> fitmap #5 inMap #2
Fit molecule 231030_From192-coot-1_real_space_refined_193.pdb (#5) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.06865, steps = 100
shifted from previous position = 0.0318
rotated from previous position = 0.085 degrees
atoms outside contour = 9100, contour level = 0.1711
Position of 231030_From192-coot-1_real_space_refined_193.pdb (#5) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.97706316 0.18430794 0.10666852 -42.55053272
-0.19013425 0.98062192 0.04721889 23.21443950
-0.09589867 -0.06641718 0.99317280 35.31492447
Axis -0.25789536 0.45972318 -0.84979091
Axis point 116.12425147 257.02215164 0.00000000
Rotation angle (degrees) 12.72749438
Shift along axis -8.36450073
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.98256,0.090989,-0.16215,-12.019,-0.048424,0.96721,0.24931,-62.613,0.17952,-0.23711,0.95475,5.1796
> view matrix models
> #5,0.98066,0.0018608,-0.19572,8.8234,0.10106,0.85155,0.51445,-113.5,0.16762,-0.52427,0.83489,75.289
> view matrix models
> #5,0.99717,0.0040589,-0.075089,-14.878,0.020228,0.94726,0.31983,-82.737,0.072426,-0.32044,0.9445,38.542
> view matrix models
> #5,0.98559,-0.034013,-0.16568,8.8298,0.12321,0.81544,0.56557,-119.91,0.11586,-0.57784,0.80788,97.384
> view matrix models
> #5,0.86475,-0.32392,-0.38378,114.25,0.46311,0.80994,0.35989,-140.3,0.19426,-0.48895,0.85041,62.354
> view matrix models
> #5,0.88847,-0.44116,-0.12648,85.846,0.45887,0.84945,0.26052,-129.19,-0.007496,-0.28951,0.95715,44.513
> fitmap #5 inMap #2
Fit molecule 231030_From192-coot-1_real_space_refined_193.pdb (#5) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.06992, steps = 92
shifted from previous position = 4.84
rotated from previous position = 4.64 degrees
atoms outside contour = 9094, contour level = 0.1711
Position of 231030_From192-coot-1_real_space_refined_193.pdb (#5) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.91043892 -0.38185848 -0.15901280 104.43746875
0.41277205 0.86364911 0.28936041 -100.79796552
0.02683654 -0.32908102 0.94392027 64.13290563
Axis -0.60398373 -0.18150462 0.77605395
Axis point 310.87005563 208.47486879 0.00000000
Rotation angle (degrees) 30.79504738
Shift along axis 4.98735885
> fitmap #5 inMap #2
Fit molecule 231030_From192-coot-1_real_space_refined_193.pdb (#5) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.06991, steps = 44
shifted from previous position = 0.0154
rotated from previous position = 0.0169 degrees
atoms outside contour = 9093, contour level = 0.1711
Position of 231030_From192-coot-1_real_space_refined_193.pdb (#5) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.91038022 -0.38191726 -0.15920759 104.50101007
0.41288607 0.86366680 0.28914486 -100.77220766
0.02707290 -0.32896636 0.94395349 64.07002651
Axis -0.60365354 -0.18192336 0.77621279
Axis point 310.74431490 208.57871672 0.00000000
Rotation angle (degrees) 30.79548338
Shift along axis 4.98238911
> fitmap #5 inMap #2
Fit molecule 231030_From192-coot-1_real_space_refined_193.pdb (#5) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.06991, steps = 48
shifted from previous position = 0.0138
rotated from previous position = 0.0205 degrees
atoms outside contour = 9094, contour level = 0.1711
Position of 231030_From192-coot-1_real_space_refined_193.pdb (#5) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.91042444 -0.38195633 -0.15886064 104.42803069
0.41280706 0.86372108 0.28909555 -100.76087051
0.02678941 -0.32877845 0.94402704 64.07763429
Axis -0.60359205 -0.18135881 0.77639270
Axis point 310.70127763 208.42573583 0.00000000
Rotation angle (degrees) 30.78585529
Shift along axis 4.99134999
> view matrix models
> #5,0.82287,-0.56573,-0.05328,101.74,0.56421,0.8023,0.19488,-130.01,-0.067504,-0.19042,0.97938,31.417
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.82287,-0.56573,-0.05328,104.02,0.56421,0.8023,0.19488,-127.97,-0.067504,-0.19042,0.97938,29.813
> fitmap #5 inMap #2
Fit molecule 231030_From192-coot-1_real_space_refined_193.pdb (#5) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.07186, steps = 100
shifted from previous position = 1.03
rotated from previous position = 4.12 degrees
atoms outside contour = 9062, contour level = 0.1711
Position of 231030_From192-coot-1_real_space_refined_193.pdb (#5) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.91122002 -0.41001852 -0.03953346 91.92108592
0.40836710 0.88661249 0.21715112 -90.22302917
-0.05398512 -0.21401661 0.97533712 51.13334573
Axis -0.46606070 0.01562119 0.88461484
Axis point 267.45257587 167.39449790 0.00000000
Rotation angle (degrees) 27.55281574
Shift along axis 0.98311953
> fitmap #5 inMap #2
Fit molecule 231030_From192-coot-1_real_space_refined_193.pdb (#5) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.07186, steps = 60
shifted from previous position = 0.00168
rotated from previous position = 0.00564 degrees
atoms outside contour = 9064, contour level = 0.1711
Position of 231030_From192-coot-1_real_space_refined_193.pdb (#5) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.91124989 -0.40995505 -0.03950297 91.90073461
0.40829533 0.88663002 0.21721451 -90.22614441
-0.05402367 -0.21406557 0.97532424 51.15104204
Axis -0.46621549 0.01569693 0.88453192
Axis point 267.49643208 167.38090021 0.00000000
Rotation angle (degrees) 27.55067747
Shift along axis 0.98291025
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.84117,-0.53381,0.086452,72.721,0.51066,0.83672,0.1978,-125.65,-0.17793,-0.12224,0.97642,36.978
> view matrix models
> #5,0.81779,-0.52679,0.23174,50.63,0.55127,0.83267,-0.05256,-88.971,-0.16527,0.17073,0.97136,-12.892
> view matrix models
> #5,0.94062,-0.26345,0.21406,-10.455,0.29038,0.95108,-0.10547,-56.287,-0.1758,0.16137,0.97111,-9.5474
> view matrix models
> #5,0.94828,-0.30789,0.07727,19.006,0.25801,0.88937,0.37743,-123.12,-0.18493,-0.33798,0.92281,83.107
> view matrix models
> #5,0.93193,-0.32857,0.15348,12.141,0.28053,0.92135,0.2691,-113.67,-0.22982,-0.20772,0.95081,64.157
> view matrix models
> #5,0.91272,-0.33983,0.22685,4.6717,0.29771,0.93338,0.20043,-106.79,-0.27985,-0.1154,0.95308,56.747
> view matrix models
> #5,0.94739,-0.18769,0.25928,-31.877,0.14703,0.9747,0.16832,-83.159,-0.28432,-0.12134,0.95102,58.827
> view matrix models
> #5,0.96777,-0.176,0.18014,-23.687,0.12951,0.96125,0.24338,-90.831,-0.21599,-0.2122,0.95306,62.22
> fitmap #5 inMap #2
Fit molecule 231030_From192-coot-1_real_space_refined_193.pdb (#5) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.2284, steps = 120
shifted from previous position = 5.42
rotated from previous position = 17.8 degrees
atoms outside contour = 5356, contour level = 0.1711
Position of 231030_From192-coot-1_real_space_refined_193.pdb (#5) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999996 -0.00021060 -0.00018067 0.07478475
0.00021062 0.99999997 0.00012622 -0.06338469
0.00018064 -0.00012626 0.99999998 -0.00121625
Axis -0.41411606 -0.59260886 0.69088540
Axis point 284.80516726 366.36081299 0.00000000
Rotation angle (degrees) 0.01746629
Shift along axis 0.00575248
> fitmap #5 inMap #2
Fit molecule 231030_From192-coot-1_real_space_refined_193.pdb (#5) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.2284, steps = 28
shifted from previous position = 0.0209
rotated from previous position = 0.0293 degrees
atoms outside contour = 5353, contour level = 0.1711
Position of 231030_From192-coot-1_real_space_refined_193.pdb (#5) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999997 -0.00020933 0.00015446 0.00298312
0.00020937 0.99999994 -0.00025947 0.01751335
-0.00015440 0.00025951 0.99999995 -0.00959806
Axis 0.70620700 0.42029007 0.56976128
Axis point 0.00000000 45.77629868 61.00889927
Rotation angle (degrees) 0.02105279
Shift along axis 0.00399879
> fitmap #5 inMap #2
Fit molecule 231030_From192-coot-1_real_space_refined_193.pdb (#5) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.2284, steps = 28
shifted from previous position = 0.0171
rotated from previous position = 0.0293 degrees
atoms outside contour = 5355, contour level = 0.1711
Position of 231030_From192-coot-1_real_space_refined_193.pdb (#5) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999997 -0.00020967 -0.00010238 0.05609251
0.00020969 0.99999996 0.00018212 -0.07207096
0.00010235 -0.00018214 0.99999998 0.02109112
Axis -0.61530483 -0.34583612 0.70837656
Axis point 334.93688900 283.19285435 0.00000000
Rotation angle (degrees) 0.01695925
Shift along axis 0.00535120
> select clear
> hide #!5 models
> hide #!2 models
> show #!5 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!4 models
> hide #!8 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> show #!2 models
> hide #!4 models
> show #!4 models
> fitmap #2 inMap #4
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 59871 points
correlation = 0.4013, correlation about mean = 0.1603, overlap = 3522
steps = 24, shift = 0.000325, angle = 7.49e-05 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99375821 -0.11155543 0.00000016 -10.76569508
0.11155543 0.99375821 -0.00000012 -47.80209716
-0.00000014 0.00000014 1.00000000 -19.31091762
Axis 0.00000115 0.00000134 1.00000000
Axis point 421.78495527 -120.10499944 0.00000000
Rotation angle (degrees) 6.40498698
Shift along axis -19.31099406
> fitmap #2 inMap #4
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 59871 points
correlation = 0.4013, correlation about mean = 0.1603, overlap = 3522
steps = 24, shift = 0.000314, angle = 0.000186 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99375857 -0.11155223 0.00000028 -10.76633014
0.11155223 0.99375857 -0.00000052 -47.80154827
-0.00000022 0.00000055 1.00000000 -19.31128635
Axis 0.00000476 0.00000220 1.00000000
Axis point 421.79193136 -120.11254061 0.00000000
Rotation angle (degrees) 6.40480277
Shift along axis -19.31144274
> ui mousemode right "translate selected models"
> select add #2
2 models selected
> view matrix models
> #2,0.99376,-0.11155,2.7502e-07,-11.795,0.11155,0.99376,-5.1762e-07,-47.624,-2.1556e-07,5.4507e-07,1,-24.513
> fitmap #2 inMap #4
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 59871 points
correlation = 0.7977, correlation about mean = 0.4343, overlap = 9400
steps = 52, shift = 1.05, angle = 2.41 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.98818765 -0.15324874 -0.00001319 -2.91633276
0.15324874 0.98818765 0.00003953 -53.80778401
0.00000698 -0.00004108 1.00000000 -24.56492507
Axis -0.00026301 -0.00006579 0.99999996
Axis point 347.58938165 -45.86426754 0.00000000
Rotation angle (degrees) 8.81524335
Shift along axis -24.56061713
> fitmap #2 inMap #4
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 59871 points
correlation = 0.7978, correlation about mean = 0.4346, overlap = 9399
steps = 28, shift = 0.0128, angle = 0.0117 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.98820444 -0.15314043 0.00002484 -2.94424105
0.15314043 0.98820442 0.00020825 -53.83277594
-0.00005644 -0.00020199 0.99999998 -24.52054178
Axis -0.00133940 0.00026538 0.99999907
Axis point 347.92153726 -46.23879060 0.00000000
Rotation angle (degrees) 8.80897147
Shift along axis -24.53086153
> fitmap #2 inMap #4
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 59871 points
correlation = 0.7977, correlation about mean = 0.4344, overlap = 9399
steps = 28, shift = 0.0249, angle = 0.0175 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.98818765 -0.15324869 -0.00001401 -2.91717649
0.15324869 0.98818765 -0.00007448 -53.77405078
0.00002526 0.00007146 1.00000000 -24.58443557
Axis 0.00047616 -0.00012810 0.99999988
Axis point 347.38927773 -45.73582655 0.00000000
Rotation angle (degrees) 8.81524127
Shift along axis -24.57893292
> fitmap #2 inMap #4
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 59871 points
correlation = 0.7977, correlation about mean = 0.4342, overlap = 9400
steps = 28, shift = 0.0238, angle = 0.0117 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.98819279 -0.15321558 0.00001681 -2.92875908
0.15321558 0.98819278 0.00012401 -53.82757865
-0.00003561 -0.00011997 0.99999999 -24.54710902
Axis -0.00079623 0.00017109 0.99999967
Axis point 347.74376502 -46.04097101 0.00000000
Rotation angle (degrees) 8.81332330
Shift along axis -24.55397823
> fitmap #2 inMap #4
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 59871 points
correlation = 0.7977, correlation about mean = 0.4343, overlap = 9400
steps = 28, shift = 0.0192, angle = 0.0169 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.98817382 -0.15333789 -0.00003155 -2.89687419
0.15333789 0.98817381 -0.00014023 -53.77928061
0.00005268 0.00013373 0.99999999 -24.60237157
Axis 0.00089333 -0.00027464 0.99999956
Axis point 347.25648168 -45.53099217 0.00000000
Rotation angle (degrees) 8.82041603
Shift along axis -24.59017848
> fitmap #2 inMap #4
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 59871 points
correlation = 0.7977, correlation about mean = 0.4343, overlap = 9400
steps = 28, shift = 0.0169, angle = 0.0176 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.98819147 -0.15322408 0.00003637 -2.93189198
0.15322408 0.98819146 0.00013666 -53.82867247
-0.00005688 -0.00012947 0.99999999 -24.54071807
Axis -0.00086845 0.00030429 0.99999958
Axis point 347.70758821 -46.07064477 0.00000000
Rotation angle (degrees) 8.81381691
Shift along axis -24.55454091
> fitmap #2 inMap #4
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 59871 points
correlation = 0.7977, correlation about mean = 0.4343, overlap = 9400
steps = 28, shift = 0.0188, angle = 0.0188 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.98818347 -0.15327568 -0.00005338 -2.90418622
0.15327567 0.98818345 -0.00017497 -53.76265079
0.00007957 0.00016472 0.99999998 -24.61228059
Axis 0.00110808 -0.00043368 0.99999929
Axis point 347.31622728 -45.54545153 0.00000000
Rotation angle (degrees) 8.81681081
Shift along axis -24.59216570
> fitmap #2 inMap #4
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 59871 points
correlation = 0.7977, correlation about mean = 0.4343, overlap = 9400
steps = 28, shift = 0.0181, angle = 0.0203 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.98818815 -0.15324549 0.00005404 -2.93138323
0.15324548 0.98818814 0.00016195 -53.83536495
-0.00007822 -0.00015176 0.99999999 -24.53354912
Axis -0.00102356 0.00043154 0.99999938
Axis point 347.67973248 -46.09112360 0.00000000
Rotation angle (degrees) 8.81505972
Shift along axis -24.55376555
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!5 models
> hide #!4 models
> select add #5
10512 atoms, 10836 bonds, 6 pseudobonds, 1188 residues, 4 models selected
> select subtract #2
10512 atoms, 10836 bonds, 6 pseudobonds, 1188 residues, 2 models selected
> view matrix models
> #5,0.99373,-0.11176,-0.00012186,-11.019,0.11176,0.99373,0.00016946,-47.643,0.00010216,-0.00018202,1,-24.338
> fitmap #5 inMap #2
Fit molecule 231030_From192-coot-1_real_space_refined_193.pdb (#5) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.2284, steps = 60
shifted from previous position = 0.452
rotated from previous position = 2.41 degrees
atoms outside contour = 5356, contour level = 0.1711
Position of 231030_From192-coot-1_real_space_refined_193.pdb (#5) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999996 -0.00021074 -0.00016970 0.07238469
0.00021077 0.99999996 0.00016371 -0.07138205
0.00016966 -0.00016374 0.99999997 0.00694157
Axis -0.51770589 -0.53653725 0.66641458
Axis point 324.86323121 356.81695742 0.00000000
Rotation angle (degrees) 0.01811964
Shift along axis 0.00545111
> fitmap #5 inMap #2
Fit molecule 231030_From192-coot-1_real_space_refined_193.pdb (#5) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.2284, steps = 28
shifted from previous position = 0.0211
rotated from previous position = 0.0294 degrees
atoms outside contour = 5354, contour level = 0.1711
Position of 231030_From192-coot-1_real_space_refined_193.pdb (#5) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999997 -0.00020951 0.00011873 0.01027086
0.00020954 0.99999994 -0.00026022 0.01778974
-0.00011868 0.00026024 0.99999996 -0.01565642
Axis 0.73395412 0.33479756 0.59095004
Axis point 0.00000000 69.80422519 62.89242260
Rotation angle (degrees) 0.02031458
Shift along axis 0.00424214
> fitmap #5 inMap #2
Fit molecule 231030_From192-coot-1_real_space_refined_193.pdb (#5) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.2284, steps = 28
shifted from previous position = 0.0163
rotated from previous position = 0.0283 degrees
atoms outside contour = 5354, contour level = 0.1711
Position of 231030_From192-coot-1_real_space_refined_193.pdb (#5) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999998 -0.00021033 -0.00007050 0.04966735
0.00021034 0.99999996 0.00019580 -0.07470012
0.00007046 -0.00019582 0.99999998 0.02866905
Axis -0.66177070 -0.23819746 0.71085970
Axis point 349.17968536 252.79222498 0.00000000
Rotation angle (degrees) 0.01695312
Shift along axis 0.00530465
> fitmap #5 inMap #2
Fit molecule 231030_From192-coot-1_real_space_refined_193.pdb (#5) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.2284, steps = 28
shifted from previous position = 0.0154
rotated from previous position = 0.0276 degrees
atoms outside contour = 5357, contour level = 0.1711
Position of 231030_From192-coot-1_real_space_refined_193.pdb (#5) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999998 -0.00020991 0.00003113 0.02842084
0.00020992 0.99999994 -0.00027567 0.02057250
-0.00003107 0.00027567 0.99999996 -0.03276678
Axis 0.79241126 0.08939270 0.60340148
Axis point 0.00000000 128.91410776 73.11186893
Rotation angle (degrees) 0.01993256
Shift along axis 0.00458850
> fitmap #5 inMap #2
Fit molecule 231030_From192-coot-1_real_space_refined_193.pdb (#5) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.2284, steps = 28
shifted from previous position = 0.015
rotated from previous position = 0.0273 degrees
atoms outside contour = 5355, contour level = 0.1711
Position of 231030_From192-coot-1_real_space_refined_193.pdb (#5) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999998 -0.00021041 -0.00000490 0.03644027
0.00021041 0.99999996 0.00019976 -0.07532447
0.00000485 -0.00019976 0.99999998 0.04018941
Axis -0.68841918 -0.01680260 0.72511841
Axis point 357.59543022 190.55764034 0.00000000
Rotation angle (degrees) 0.01662598
Shift along axis 0.00532155
> select clear
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> fitmap #1 inMap #4
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 103096 points
correlation = 0.8992, correlation about mean = 0.7269, overlap = 1.915e+04
steps = 40, shift = 0.0125, angle = 0.0131 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.99998895 0.00470055 -0.00013319 304.49497925
0.00470054 0.99998895 0.00005329 -34.72075898
0.00013343 0.00005267 -0.99999999 314.55266232
Axis -0.00234941 -0.99999724 -0.00002632
Axis point 152.27779302 0.00000000 157.28693878
Rotation angle (degrees) 179.99236191
Shift along axis 33.99700250
> fitmap #1 inMap #4
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 103096 points
correlation = 0.8993, correlation about mean = 0.7271, overlap = 1.912e+04
steps = 40, shift = 0.0076, angle = 0.00897 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.99998841 0.00481501 -0.00007573 304.46888613
0.00481501 0.99998841 -0.00003675 -34.73167129
0.00007555 -0.00003712 -1.00000000 314.57608646
Axis -0.00240597 -0.99999711 0.00001877
Axis point 152.27027635 0.00000000 157.29347626
Rotation angle (degrees) 179.99566621
Shift along axis 34.00493175
> fitmap #1 inMap #4
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 103096 points
correlation = 0.8993, correlation about mean = 0.7271, overlap = 1.913e+04
steps = 40, shift = 0.0104, angle = 0.0115 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.99998875 0.00474356 0.00008163 304.46294376
0.00474357 0.99998875 0.00006541 -34.73061521
-0.00008132 0.00006580 -1.00000000 314.58474910
Axis 0.00237322 0.99999718 0.00003308
Axis point 152.27909143 0.00000000 157.28674586
Rotation angle (degrees) 179.99533181
Shift along axis -33.99755239
> show #!1 models
> hide #!1 models
> show #!1 models
> fitmap #1 inMap #4
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 103096 points
correlation = 0.8992, correlation about mean = 0.727, overlap = 1.915e+04
steps = 28, shift = 0.00769, angle = 0.0114 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.99998940 0.00460468 0.00001870 304.49407752
0.00460468 0.99998938 0.00019319 -34.72168970
-0.00001781 0.00019327 -0.99999998 314.55177304
Axis 0.00230873 0.99999733 0.00009787
Axis point 152.28855580 0.00000000 157.27619573
Rotation angle (degrees) 179.99895414
Shift along axis -33.98781751
> fitmap #1 inMap #4
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 103096 points
correlation = 0.8992, correlation about mean = 0.727, overlap = 1.914e+04
steps = 40, shift = 0.0185, angle = 0.0142 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.99998888 0.00471655 0.00001423 304.47872034
0.00471655 0.99998888 -0.00002802 -34.72149125
-0.00001436 -0.00002795 -1.00000000 314.59040507
Axis 0.00236643 0.99999720 -0.00001239
Axis point 152.28156737 0.00000000 157.29389922
Rotation angle (degrees) 179.99918108
Shift along axis -34.00476345
> fitmap #1 inMap #4
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 103096 points
correlation = 0.8993, correlation about mean = 0.7271, overlap = 1.913e+04
steps = 40, shift = 0.00573, angle = 0.00724 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.99998841 0.00481459 -0.00003161 304.46591032
0.00481459 0.99998841 -0.00009315 -34.72283856
0.00003116 -0.00009330 -1.00000000 314.59322984
Axis -0.00240359 -0.99999711 0.00004734
Axis point 152.27221686 0.00000000 157.29818237
Rotation angle (degrees) 179.99820189
Shift along axis 34.00581997
> select clear
> hide #!1 models
> hide #!2 models
> show #!8 models
> morph #5,8
Computed 51 frame morph #6
> coordset #6 1,51
> close #6
> show #!5 models
> show #!8 models
> hide #!8 models
> hide #!5 models
> show #!4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> open C:/Users/OJS/Downloads/cryosparc_P76_J135_008_volume_map_sharp.mrc
Opened cryosparc_P76_J135_008_volume_map_sharp.mrc as #6, grid size
400,400,400, pixel 0.848, shown at level 0.0461, step 2, values float32
> volume #3 level 0.1022
> volume #6 step 1
> volume #6 level 0.07767
> ui mousemode right "translate selected models"
> select add #6
2 models selected
> view matrix models #6,1,0,0,-39.453,0,1,0,-27.667,0,0,1,-33.689
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.99164,0.1112,0.0654,-68.169,-0.097986,0.97899,-0.1788,23.338,-0.083908,0.1709,0.98171,-45.29
> view matrix models
> #6,0.94968,0.11921,0.28966,-101.07,-0.064557,0.97939,-0.1914,19.773,-0.30651,0.16307,0.9378,1.3609
> view matrix models
> #6,0.85961,0.16001,0.48525,-126.43,-0.041873,0.96857,-0.2452,27.036,-0.50924,0.19046,0.83929,48.081
> view matrix models
> #6,0.80071,0.36496,0.47504,-149.44,-0.30761,0.93095,-0.19673,70.128,-0.51404,0.011397,0.85769,76.091
> view matrix models
> #6,0.91093,0.34002,0.23364,-122.29,-0.32518,0.94029,-0.10056,54.946,-0.25388,0.015625,0.96711,12.389
> volume #6 level 0.09737
> fitmap #1 inMap #4
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 103096 points
correlation = 0.8992, correlation about mean = 0.727, overlap = 1.914e+04
steps = 40, shift = 0.000567, angle = 0.00546 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.99998885 0.00472315 -0.00002432 304.48029040
0.00472315 0.99998885 -0.00006736 -34.71120322
0.00002400 -0.00006748 -1.00000000 314.59022304
Axis -0.00235676 -0.99999722 0.00003466
Axis point 152.27914824 0.00000000 157.29634953
Rotation angle (degrees) 179.99861576
Shift along axis 34.00442230
> fitmap #1 inMap #4
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 103096 points
correlation = 0.8992, correlation about mean = 0.7271, overlap = 1.914e+04
steps = 40, shift = 0.00339, angle = 0.00484 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.99998883 0.00472713 0.00005684 304.46930163
0.00472712 0.99998883 -0.00009019 -34.70775778
-0.00005726 -0.00008992 -1.00000000 314.60742556
Axis 0.00236561 0.99999720 -0.00004463
Axis point 152.28019057 0.00000000 157.29859461
Rotation angle (degrees) 179.99673123
Shift along axis -34.00144521
> fitmap #1 inMap #4
Fit map WT_PIP2_P68_J150_009_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 103096 points
correlation = 0.8992, correlation about mean = 0.727, overlap = 1.914e+04
steps = 28, shift = 0.0114, angle = 0.0116 degrees
Position of WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.99998928 0.00462477 0.00023004 304.46844668
0.00462475 0.99998930 -0.00010477 -34.69040278
-0.00023052 -0.00010370 -0.99999997 314.63689599
Axis 0.00231289 0.99999732 -0.00005202
Axis point 152.29245488 0.00000000 157.30001267
Rotation angle (degrees) 179.98680574
Shift along axis -34.00247377
> fitmap #6 inMap #4
Fit map cryosparc_P76_J135_008_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 91413 points
correlation = 0.4511, correlation about mean = 0.094, overlap = 2583
steps = 152, shift = 6.83, angle = 15.3 degrees
Position of cryosparc_P76_J135_008_volume_map_sharp.mrc (#6) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.96270926 0.27053813 -0.00011286 -73.45605821
-0.27053813 0.96270926 -0.00002954 18.28747820
0.00010066 0.00005897 0.99999999 -33.03040016
Axis 0.00016358 -0.00039463 -0.99999991
Axis point 29.65283524 275.62560509 0.00000000
Rotation angle (degrees) 15.69629254
Shift along axis 33.01116459
> fitmap #6 inMap #4
Fit map cryosparc_P76_J135_008_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 91413 points
correlation = 0.4513, correlation about mean = 0.09398, overlap = 2583
steps = 28, shift = 0.0171, angle = 0.0122 degrees
Position of cryosparc_P76_J135_008_volume_map_sharp.mrc (#6) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.96274285 0.27041858 0.00005394 -73.47718548
-0.27041859 0.96274285 0.00001683 18.26922421
-0.00004738 -0.00003079 1.00000000 -32.98864058
Axis -0.00008804 0.00018734 -0.99999998
Axis point 29.54095112 275.77576545 0.00000000
Rotation angle (degrees) 15.68917694
Shift along axis 32.99853146
> fitmap #6 inMap #4
Fit map cryosparc_P76_J135_008_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 91413 points
correlation = 0.4511, correlation about mean = 0.094, overlap = 2583
steps = 28, shift = 0.0129, angle = 0.00847 degrees
Position of cryosparc_P76_J135_008_volume_map_sharp.mrc (#6) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.96274853 0.27039835 -0.00008476 -73.44570568
-0.27039836 0.96274853 -0.00002995 18.26113349
0.00007350 0.00005176 1.00000000 -33.02480113
Axis 0.00015109 -0.00029265 -0.99999995
Axis point 29.58602593 275.71475425 0.00000000
Rotation angle (degrees) 15.68797362
Shift along axis 33.00835839
> select clear
> volume #6 level 0.114
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> transparency 0
> show #!4 models
> hide #!6 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!6 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #6 level 0.1291
> volume #6 level 0.1032
> volume #4 level 0.2084
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!4 models
> show #!5 models
> show #!8 models
> show #!6 models
> hide #!8 models
> hide #!6 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!6 models
> hide #!6 models
> hide #!8 models
> show #!8 models
> show #!6 models
> hide #!6 models
> transparency 50
> hide #!5 models
> show #!4 models
> volume #4 level 0.3736
> volume #4 level 0.2414
> hide #!8 models
> show #!6 models
> hide #!4 models
> show #!8 models
> volume #6 level 0.09835
> hide #!6 models
> show #!2 models
> hide #!2 models
> show #!27 models
> hide #!27 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> rename #5 231030_N55H_Chol_193
> rename #5 id #20
> rename #6 id #5
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!4 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> hide #!4 models
> show #!20 models
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!20 models
> hide #!8 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!4 models
> show #!20 models
> hide #!4 models
> show #!8 models
> hide #!8 models
> view 1
> view 2
Expected an objects specifier or a view name or a keyword
> show #!8 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> view orient
> turn x 90
[Repeated 2 time(s)]
> show #!4 models
> view orient
[Repeated 3 time(s)]
> turn x 90
[Repeated 2 time(s)]
> hide #!8 models
> view name 1
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231011_All_Align_wo_POPE.cxs"
> show #!8 models
> hide #!4 models
> select
46296 atoms, 47094 bonds, 18 pseudobonds, 3702 residues, 16 models selected
> ribbon style thickness 0.6
> select clear
> show #!20 models
> ui tool show "Selection Inspector"
> select add #8
11646 atoms, 11886 bonds, 6 pseudobonds, 1230 residues, 2 models selected
> select add #20
22158 atoms, 22722 bonds, 12 pseudobonds, 2418 residues, 4 models selected
> ui tool show "Selection Inspector"
> setattr =sel p display false
Assigning display attribute to 12 items
> size =sel stickRadius 0.3
Changed 22722 bond radii
> select clear
> hide #!20 models
> select ::name="CLR"
504 atoms, 558 bonds, 18 residues, 1 model selected
> color sel yellow
> select ::name="Y01"
1008 atoms, 1044 bonds, 12 residues, 1 model selected
> select ::name="6OU"
2352 atoms, 2304 bonds, 48 residues, 2 models selected
> select clear
> hide #!8 models
> show #!8 models
> show #!4 models
> clip front 0
> volume #4 level 0.1753
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!3 models
> volume #3 level 0.05069
> close #3
> show #!5 models
> volume #5 level 0.07195
> hide #!5 models
> hide #!8 models
> show #!2 models
> show #!20 models
> volume #2 level 0.146
> volume #2 level 0.1385
> volume #2 level 0.1084
> hide #!2 models
> show #!4 models
> hide #!20 models
> show #!8 models
> select
46296 atoms, 47094 bonds, 18 pseudobonds, 3702 residues, 15 models selected
> style sel stick
Changed 46296 atom styles
> select clear
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!4 models
> show #!2 models
> volume #2 level 0.09581
> surface dust #2 size 8.3
> hide #!2 models
> show #!4 models
> show #!8 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> surface dust #4 size 8.48
> volume #4 level 0.1478
> show #!20 models
> show #!2 models
> hide #!4 models
> hide #!8 models
> hide #!2 models
> hide #!20 models
> show #!27 models
> hide #!27 models
> show #!27 models
> hide #!27 models
> show #!5 models
> volume #5 level 0.07977
> volume #5 level 0.07195
> surface dust #5 size 8.48
> volume #5 level 0.06021
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> clip front 1
[Repeated 28 time(s)]
> ui tool show "Hide Dust"
> surface dust #5 size 0.85
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> volume #5 level 0.06852
> hide #!20 models
> show #!20 models
> hide #!5 models
> show #!5 models
> ~clip
> view 1
> clip front t0
Invalid "front" argument: Expected 'off' or a number
> clip front 0
> clip front -1
[Repeated 7 time(s)]
> hide #!20 models
> clip front -1
[Repeated 2 time(s)]
> volume #5 level 0.06168
> show #!20 models
> hide #!5 models
> select #20/D:166
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/D:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> show #!27 models
> hide #!27 models
> show #!5 models
> clip front -1
[Repeated 14 time(s)]
> clip front 1
[Repeated 30 time(s)]
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> hide #!5 models
> show #!5 models
> show #!20 models
> hide #!5 models
> select #20/D:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/D:33
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!5 models
> hide #!5 models
> show #!27 models
> hide #!27 models
> show #!5 models
> select clear
> close #5
> ~clip
> select clear
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231011_All_Align_wo_POPE.cxs"
——— End of log from Mon Oct 30 21:11:50 2023 ———
opened ChimeraX session
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/N55H_CBX_P52_J662_003_volume_map_sharp.mrc"
Opened N55H_CBX_P52_J662_003_volume_map_sharp.mrc as #3, grid size
400,400,400, pixel 0.83, shown at level 0.0457, step 2, values float32
> volume #3 step 1
> volume #3 level 0.06665
> volume #3 level 0.08886
> hide #!20 models
> color #3 #aa55ffff models
> show #!2 models
> ui mousemode right "rotate selected models"
> select add #3
2 models selected
> view matrix models
> #3,-0.96397,0.26452,0.028123,277.58,0.18689,0.7487,-0.63601,113.02,-0.18929,-0.60784,-0.77117,417.28
> view matrix models
> #3,-0.49517,0.86868,0.014237,101.71,0.86795,0.49535,-0.035848,-54.541,-0.038192,-0.0053939,-0.99926,328.89
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.49517,0.86868,0.014237,74.202,0.86795,0.49535,-0.035848,-86.042,-0.038192,-0.0053939,-0.99926,328.36
> view matrix models
> #3,-0.49517,0.86868,0.014237,71.067,0.86795,0.49535,-0.035848,-80.683,-0.038192,-0.0053939,-0.99926,317.9
> ui tool show "Fit in Map"
> fitmap #3 inMap #4
Fit map N55H_CBX_P52_J662_003_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 134279 points
correlation = 0.2432, correlation about mean = 0.03021, overlap = 1539
steps = 132, shift = 4.26, angle = 7.25 degrees
Position of N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#3) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.44604297 0.89482100 -0.01846751 64.39154222
0.89197825 0.44613399 0.07307023 -91.25133189
0.07362376 0.01611985 -0.99715580 292.00912683
Axis -0.52578281 -0.85021387 -0.02624503
Axis point 55.74258392 0.00000000 148.74132017
Rotation angle (degrees) 176.89547290
Shift along axis 36.06339263
> fitmap #3 inMap #4
Fit map N55H_CBX_P52_J662_003_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 134279 points
correlation = 0.2432, correlation about mean = 0.03011, overlap = 1539
steps = 80, shift = 0.0127, angle = 0.00985 degrees
Position of N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#3) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.44616793 0.89475962 -0.01842279 64.42342060
0.89191112 0.44625383 0.07315792 -91.26458030
0.07367999 0.01620922 -0.99715020 291.98732223
Axis -0.52572327 -0.85024912 -0.02629605
Axis point 55.75838081 0.00000000 148.73372482
Rotation angle (degrees) 176.89521338
Shift along axis 36.05062428
> show #!4 models
> view matrix models
> #3,-0.44617,0.89476,-0.018423,63.377,0.89191,0.44625,0.073158,-98.021,0.07368,0.016209,-0.99715,290.08
> fitmap #3 inMap #4
Fit map N55H_CBX_P52_J662_003_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 134279 points
correlation = 0.418, correlation about mean = 0.1586, overlap = 3516
steps = 160, shift = 1.28, angle = 13.4 degrees
Position of N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#3) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.23929892 0.97094594 -0.00000769 14.23169189
0.97094594 0.23929892 -0.00001506 -65.21440691
-0.00001278 -0.00001107 -1.00000000 306.49998235
Axis 0.61675619 0.78715424 0.00000366
Axis point 32.66476800 -0.00000000 153.25010137
Rotation angle (degrees) 179.99981485
Shift along axis -42.55519001
> fitmap #3 inMap #4
Fit map N55H_CBX_P52_J662_003_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 134279 points
correlation = 0.418, correlation about mean = 0.1586, overlap = 3516
steps = 40, shift = 0.0107, angle = 0.00686 degrees
Position of N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#3) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.23930124 0.97094536 -0.00012351 14.24102859
0.97094537 0.23930124 -0.00004533 -65.21501984
-0.00001446 -0.00013077 -0.99999999 306.52005132
Axis -0.61672329 -0.78718002 0.00005649
Axis point 32.66041922 0.00000000 153.25857649
Rotation angle (degrees) 179.99603111
Shift along axis 42.57050201
> fitmap #3 inMap #4
Fit map N55H_CBX_P52_J662_003_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 134279 points
correlation = 0.418, correlation about mean = 0.1586, overlap = 3516
steps = 28, shift = 0.0173, angle = 0.0103 degrees
Position of N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#3) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.23927644 0.97095148 0.00004723 14.22615967
0.97095148 0.23927644 0.00000312 -65.21953843
-0.00000827 0.00004661 -1.00000000 306.49099554
Axis 0.61673757 0.78716883 0.00001691
Axis point 32.66588431 0.00000000 153.24574506
Rotation angle (degrees) 179.99798008
Shift along axis -42.55979828
> select clear
> volume #3 level 0.1096
> hide #!2 models
> hide #!4 models
> volume #3 level 0.09196
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> open C:/Users/OJS/Downloads/cryosparc_P76_J149_007_volume_map_sharp.mrc
Opened cryosparc_P76_J149_007_volume_map_sharp.mrc as #5, grid size
400,400,400, pixel 0.848, shown at level 0.0458, step 2, values float32
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/Maps/N55H_MBCD_100_P76_J149_007_volume_map_sharp.mrc"
Opened N55H_MBCD_100_P76_J149_007_volume_map_sharp.mrc as #6, grid size
400,400,400, pixel 0.848, shown at level 0.0458, step 2, values float32
> volume #5 step 1
> volume #5 level 0.07407
> close #5
> volume #6 step 1
> volume #6 level 0.08068
> combine #8
> hide #!3 models
> select add #5
11646 atoms, 11886 bonds, 6 pseudobonds, 1230 residues, 2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,-4.9462,0,1,0,-3.9886,0,0,1,42.353
> view matrix models #5,1,0,0,30.084,0,1,0,26.161,0,0,1,65.47
> view matrix models #5,1,0,0,36.794,0,1,0,36.679,0,0,1,37.125
> fitmap #3 inMap #4
Fit map N55H_CBX_P52_J662_003_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 125306 points
correlation = 0.4197, correlation about mean = 0.1503, overlap = 3455
steps = 28, shift = 0.0224, angle = 0.00731 degrees
Position of N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#3) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.23915853 0.97098053 0.00000838 14.18614503
0.97098053 0.23915853 0.00000156 -65.20234225
-0.00000049 0.00000851 -1.00000000 306.49087191
Axis 0.61680007 0.78711986 0.00001024
Axis point 32.64043520 0.00000000 153.24578786
Rotation angle (degrees) 179.99967701
Shift along axis -42.56890343
> fitmap #5 inMap #6
Fit molecule copy of 231026_N55H_MBCD_37_wo_water.pdb (#5) to map
N55H_MBCD_100_P76_J149_007_volume_map_sharp.mrc (#6) using 11646 atoms
average map value = 0.05277, steps = 64
shifted from previous position = 2.77
rotated from previous position = 1.52 degrees
atoms outside contour = 8707, contour level = 0.080676
Position of copy of 231026_N55H_MBCD_37_wo_water.pdb (#5) relative to
N55H_MBCD_100_P76_J149_007_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.99964939 -0.02562452 -0.00666868 44.03985194
0.02560856 0.99966900 -0.00246779 33.65444613
0.00672971 0.00229615 0.99997472 35.80800107
Axis 0.08959827 -0.25199179 0.96357267
Axis point -1587.94456601 1635.59892115 0.00000000
Rotation angle (degrees) 1.52338536
Shift along axis 29.96886153
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.9691,-0.2398,0.057887,68.083,0.24218,0.96947,-0.038392,13.465,-0.046914,0.051225,0.99758,36.787
> view matrix models
> #5,0.93896,-0.30018,-0.16806,112.43,0.28755,0.95298,-0.095592,17.663,0.18885,0.041432,0.98113,8.4619
> fitmap #5 inMap #6
Fit molecule copy of 231026_N55H_MBCD_37_wo_water.pdb (#5) to map
N55H_MBCD_100_P76_J149_007_volume_map_sharp.mrc (#6) using 11646 atoms
average map value = 0.1001, steps = 100
shifted from previous position = 7.45
rotated from previous position = 11.2 degrees
atoms outside contour = 4675, contour level = 0.080676
Position of copy of 231026_N55H_MBCD_37_wo_water.pdb (#5) relative to
N55H_MBCD_100_P76_J149_007_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.96129828 -0.27550972 -0.00010971 76.57346047
0.27550973 0.96129828 0.00001137 1.78781713
0.00010233 -0.00004116 0.99999999 32.69883001
Axis -0.00009533 -0.00038480 0.99999992
Axis point 31.87995845 273.46681803 0.00000000
Rotation angle (degrees) 15.99239409
Shift along axis 32.69083949
> fitmap #5 inMap #6
Fit molecule copy of 231026_N55H_MBCD_37_wo_water.pdb (#5) to map
N55H_MBCD_100_P76_J149_007_volume_map_sharp.mrc (#6) using 11646 atoms
average map value = 0.1001, steps = 28
shifted from previous position = 0.0158
rotated from previous position = 0.00847 degrees
atoms outside contour = 4672, contour level = 0.080676
Position of copy of 231026_N55H_MBCD_37_wo_water.pdb (#5) relative to
N55H_MBCD_100_P76_J149_007_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.96129545 -0.27551960 0.00001678 76.55526910
0.27551961 0.96129545 -0.00006451 1.79606625
0.00000164 0.00006664 1.00000000 32.68225057
Axis 0.00023800 0.00002748 0.99999997
Axis point 31.88426499 273.35049465 0.00000000
Rotation angle (degrees) 15.99298207
Shift along axis 32.70051946
> fitmap #5 inMap #6
Fit molecule copy of 231026_N55H_MBCD_37_wo_water.pdb (#5) to map
N55H_MBCD_100_P76_J149_007_volume_map_sharp.mrc (#6) using 11646 atoms
average map value = 0.1001, steps = 28
shifted from previous position = 0.0127
rotated from previous position = 0.00241 degrees
atoms outside contour = 4673, contour level = 0.080676
Position of copy of 231026_N55H_MBCD_37_wo_water.pdb (#5) relative to
N55H_MBCD_100_P76_J149_007_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.96129634 -0.27551649 0.00003465 76.55119499
0.27551649 0.96129634 -0.00002657 1.79103887
-0.00002599 0.00003509 1.00000000 32.70297024
Axis 0.00011188 0.00011004 0.99999999
Axis point 31.91172062 273.35000767 0.00000000
Rotation angle (degrees) 15.99279622
Shift along axis 32.71173181
> transparency 60
> save
> C:/Users/OJS/Desktop/Phenix/230901_MBCD_Chol_N55H/231030_MBCD_37_Fit_P76_J149.pdb
> models #5
> hide #!5 models
> hide #!6 models
> select subtract #5
Nothing selected
> show #!3 models
> open
> C:/Users/OJS/Desktop/Phenix/220302_Cx43_N55H_CBX/RealSpaceRefine_197/MBCD_37_N55H_CBX_P52_J660_Fit_delLipid_real_space_refined_196-coot-4_real_space_refined_197.pdb
Chain information for
MBCD_37_N55H_CBX_P52_J660_Fit_delLipid_real_space_refined_196-coot-4_real_space_refined_197.pdb
#7
---
Chain | Description
A B C D E F | No description available
> color #7 #aa55ffff
> select add #7
9258 atoms, 9594 bonds, 6 pseudobonds, 1056 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> ui mousemode right "rotate selected models"
> color #7 #aa55ffff
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.90462,0.26174,0.33638,218.87,0.26974,0.96264,-0.023609,-34.793,-0.32999,0.06938,-0.94143,353.77
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.90462,0.26174,0.33638,207.86,0.26974,0.96264,-0.023609,-67.644,-0.32999,0.06938,-0.94143,336.07
> view matrix models
> #7,-0.90462,0.26174,0.33638,192.22,0.26974,0.96264,-0.023609,-74.12,-0.32999,0.06938,-0.94143,337.79
> view matrix models
> #7,-0.90462,0.26174,0.33638,193.31,0.26974,0.96264,-0.023609,-66.927,-0.32999,0.06938,-0.94143,343.5
> fitmap #7 inMap #3
Fit molecule
MBCD_37_N55H_CBX_P52_J660_Fit_delLipid_real_space_refined_196-coot-4_real_space_refined_197.pdb
(#7) to map N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#3) using 9258 atoms
average map value = 0.1253, steps = 152
shifted from previous position = 5.83
rotated from previous position = 19.7 degrees
atoms outside contour = 3250, contour level = 0.091964
Position of
MBCD_37_N55H_CBX_P52_J660_Fit_delLipid_real_space_refined_196-coot-4_real_space_refined_197.pdb
(#7) relative to N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.49990714 0.86607896 -0.00029547 -60.70579268
-0.86607897 0.49990698 -0.00048555 226.85109909
-0.00027282 0.00049863 0.99999984 -0.07794311
Axis 0.00056818 -0.00001308 -0.99999984
Axis point 166.08156441 165.99181723 0.00000000
Rotation angle (degrees) 60.00615418
Shift along axis 0.04048534
> fitmap #7 inMap #3
Fit molecule
MBCD_37_N55H_CBX_P52_J660_Fit_delLipid_real_space_refined_196-coot-4_real_space_refined_197.pdb
(#7) to map N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#3) using 9258 atoms
average map value = 0.1253, steps = 40
shifted from previous position = 0.0181
rotated from previous position = 0.012 degrees
atoms outside contour = 3244, contour level = 0.091964
Position of
MBCD_37_N55H_CBX_P52_J660_Fit_delLipid_real_space_refined_196-coot-4_real_space_refined_197.pdb
(#7) relative to N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.50001920 0.86601422 -0.00040689 -60.70624634
-0.86601426 0.50001894 -0.00060707 226.82632667
-0.00032228 0.00065592 0.99999973 -0.09520959
Axis 0.00072920 -0.00004884 -0.99999973
Axis point 166.08921718 165.98768378 0.00000000
Rotation angle (degrees) 59.99874720
Shift along axis 0.03986346
> hide #!7 models
> show #!7 models
> hide #!3 models
> hide #!7 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!7 models
> show #!3 models
> show #!20 models
> hide #!20 models
> select ::name="CBO"
738 atoms, 810 bonds, 18 residues, 1 model selected
> show sel atoms
> color sel dark green
> color sel byhetero
> select clear
> show #!20 models
> hide #!3 models
> select add #7
9258 atoms, 9594 bonds, 6 pseudobonds, 1056 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.94503,0.28835,0.1542,219.99,0.27573,0.9562,-0.098218,-53.126,-0.17577,-0.0503,-0.98315,341.37
> view matrix models
> #7,-0.96078,0.23433,0.14831,232.52,0.21903,0.96921,-0.11249,-43.593,-0.1701,-0.07559,-0.98252,344.54
> view matrix models
> #7,-0.96206,0.17524,0.20912,232.83,0.18137,0.98336,0.010329,-59.336,-0.20383,0.047864,-0.97784,328.87
> view matrix models
> #7,-0.79271,-0.59951,0.11046,349.26,-0.60848,0.76719,-0.20291,141.81,0.036901,-0.22806,-0.97295,333.98
> view matrix models
> #7,-0.70155,-0.66019,0.26827,318.98,-0.67909,0.73347,0.029129,122.03,-0.216,-0.16175,-0.9629,363.34
> view matrix models
> #7,-0.041437,-0.98909,0.14134,284.36,-0.99116,0.022846,-0.1307,317.5,0.12605,-0.1455,-0.9813,306.8
> view matrix models
> #7,0.085813,-0.97901,0.18485,254.6,-0.98241,-0.052267,0.17925,278.96,-0.16582,-0.19698,-0.96628,361.4
> view matrix models
> #7,0.23113,-0.96447,0.12795,237.16,-0.96683,-0.213,0.14095,309.21,-0.10869,-0.15628,-0.98171,347.62
> view matrix models
> #7,0.16688,-0.9799,0.10931,253.37,-0.9853,-0.16984,-0.018358,330.58,0.036555,-0.10464,-0.99384,316.87
> fitmap #7 inMap #3
Fit molecule
MBCD_37_N55H_CBX_P52_J660_Fit_delLipid_real_space_refined_196-coot-4_real_space_refined_197.pdb
(#7) to map N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#3) using 9258 atoms
average map value = 0.1254, steps = 72
shifted from previous position = 0.281
rotated from previous position = 7.54 degrees
atoms outside contour = 3246, contour level = 0.091964
Position of
MBCD_37_N55H_CBX_P52_J660_Fit_delLipid_real_space_refined_196-coot-4_real_space_refined_197.pdb
(#7) relative to N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.99999999 0.00005252 -0.00016020 332.01092919
-0.00005262 -0.99999980 0.00063043 331.92708862
-0.00016017 0.00063044 0.99999979 -0.11737608
Axis 0.00007931 -0.00031509 -0.99999995
Axis point 166.00982225 165.95919938 0.00000000
Rotation angle (degrees) 179.99698799
Shift along axis 0.03912311
> select clear
> morph #20,7
Computed 51 frame morph #9
> coordset #9 1,51
> hide #!9 models
> show #!7 models
> show #!3 models
> close #9
> show #!5 models
> hide #!3 models
> hide #!7 models
> show #!20 models
> hide #!20 models
> show #!27 models
> hide #!27 models
> show #!27 models
> hide #!27 models
> show #!20 models
> hide #!20 models
> show #!8 models
> hide #!8 models
> show #!6 models
> show #!20 models
> close #5
> hide #!6 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!7 models
> hide #!3 models
> hide #!20 models
> open
> C:/Users/OJS/Desktop/Phenix/220302_Cx43_N55H_CBX/RealSpaceRefine_199/231031_From197_CBX_Re_real_space_refined_199.pdb
Chain information for 231031_From197_CBX_Re_real_space_refined_199.pdb #5
---
Chain | Description
A B C D E F | No description available
> color #5 #aa55ffff
> select add #5
9138 atoms, 9474 bonds, 6 pseudobonds, 1038 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> close #7
> show #!3 models
> ui mousemode right "rotate selected models"
> select add #3
9138 atoms, 9474 bonds, 6 pseudobonds, 1038 residues, 4 models selected
> select subtract #3
9138 atoms, 9474 bonds, 6 pseudobonds, 1038 residues, 2 models selected
> select add #3
9138 atoms, 9474 bonds, 6 pseudobonds, 1038 residues, 4 models selected
> select subtract #3
9138 atoms, 9474 bonds, 6 pseudobonds, 1038 residues, 2 models selected
> select add #3
9138 atoms, 9474 bonds, 6 pseudobonds, 1038 residues, 4 models selected
> select subtract #5
2 models selected
> select add #5
9138 atoms, 9474 bonds, 6 pseudobonds, 1038 residues, 4 models selected
> select subtract #5
2 models selected
> select subtract #3
Nothing selected
> select add #5
9138 atoms, 9474 bonds, 6 pseudobonds, 1038 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.96358,0.1145,0.24166,267.87,0.086972,0.98875,-0.12169,6.9483,-0.25288,-0.09624,-0.9627,372.46
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.96358,0.1145,0.24166,256.79,0.086972,0.98875,-0.12169,-28.917,-0.25288,-0.09624,-0.9627,365.03
> view matrix models
> #5,-0.96358,0.1145,0.24166,242.84,0.086972,0.98875,-0.12169,-26.393,-0.25288,-0.09624,-0.9627,366.4
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!20 models
> view matrix models
> #5,-0.96358,0.1145,0.24166,237.12,0.086972,0.98875,-0.12169,-24.387,-0.25288,-0.09624,-0.9627,367.88
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.79417,0.01023,0.60761,167.71,-0.04077,0.99671,-0.070069,-12.799,-0.60633,-0.080419,-0.79114,396.37
> view matrix models
> #5,-0.72493,-0.66024,0.19636,333.54,-0.49714,0.6988,0.51432,18.728,-0.47679,0.27523,-0.83481,322.79
> view matrix models
> #5,-0.59238,-0.79109,0.15252,340.33,-0.79422,0.6052,0.054284,157.27,-0.13525,-0.088977,-0.98681,351.03
> view matrix models
> #5,-0.12581,-0.9832,-0.13226,340.51,-0.95848,0.086078,0.27188,235.9,-0.25592,0.16097,-0.9532,324.12
> view matrix models
> #5,0.17479,-0.98339,0.048893,261.67,-0.96772,-0.18074,-0.17566,353.48,0.18158,-0.016611,-0.98324,285.89
> view matrix models
> #5,0.15462,-0.96258,-0.22257,305.06,-0.96174,-0.19821,0.18914,296.94,-0.22617,0.18481,-0.9564,315.74
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.15462,-0.96258,-0.22257,305.73,-0.96174,-0.19821,0.18914,294.39,-0.22617,0.18481,-0.9564,312.68
> view matrix models
> #5,0.15462,-0.96258,-0.22257,303.9,-0.96174,-0.19821,0.18914,302.4,-0.22617,0.18481,-0.9564,307.25
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.36632,-0.92449,-0.10553,243.71,-0.93047,-0.36463,-0.035584,360.88,-0.0055839,0.11123,-0.99378,288.89
> ui tool show "Fit in Map"
> fitmap #5 inMap #3
Fit molecule 231031_From197_CBX_Re_real_space_refined_199.pdb (#5) to map
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#3) using 9138 atoms
average map value = 0.1236, steps = 96
shifted from previous position = 4.87
rotated from previous position = 10 degrees
atoms outside contour = 3321, contour level = 0.091964
Position of 231031_From197_CBX_Re_real_space_refined_199.pdb (#5) relative to
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.99999977 0.00060890 0.00030273 331.82330838
-0.00060883 -0.99999979 0.00021698 332.09983698
0.00030286 0.00021679 0.99999993 -0.13959914
Axis -0.00015151 -0.00010807 -0.99999998
Axis point 165.96221555 165.99941734 0.00000000
Rotation angle (degrees) 179.96511475
Shift along axis 0.05343415
> select clear
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!20 models
> show #!3 models
> select
> ::name="6OU"::name="CBO"::name="CLR"::name="MC3"::name="PTY"::name="Y01"
8340 atoms, 8370 bonds, 180 residues, 4 models selected
> show sel atoms
> select ::name="CBO"
738 atoms, 810 bonds, 18 residues, 1 model selected
> color sel green
> color sel byhetero
> hide #!3 models
> select #5:155-140
Nothing selected
> select #5:140-155
324 atoms, 324 bonds, 42 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 0
Assigning ss_type attribute to 42 items
> select clear
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!8 models
> select #5:74-105
1686 atoms, 1740 bonds, 192 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 1
Assigning ss_type attribute to 192 items
> hide #!8 models
> close #5
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> select clear
> open C:/Users/OJS/Downloads/cryosparc_P76_J149_007_volume_map_sharp.mrc
Opened cryosparc_P76_J149_007_volume_map_sharp.mrc as #5, grid size
400,400,400, pixel 0.848, shown at level 0.0458, step 2, values float32
> color #5 #ffaa7fff models
> color #5 #00aa00ff models
> volume #5 step 1
> volume #5 level 0.09652
> fitmap #5 inMap #4
Fit map cryosparc_P76_J149_007_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 98567 points
correlation = 0.2527, correlation about mean = 0.02241, overlap = 561.2
steps = 364, shift = 21, angle = 24.2 degrees
Position of cryosparc_P76_J149_007_volume_map_sharp.mrc (#5) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.95141879 -0.22381088 0.21144970 6.57927021
0.15530454 0.94182046 0.29808510 -76.16410678
-0.26586234 -0.25076466 0.93082453 80.09211685
Axis -0.66913428 0.58191854 0.46220140
Axis point 0.00000000 262.64343872 283.92297177
Rotation angle (degrees) 24.21232904
Shift along axis -11.70503260
> ui mousemode right "translate selected models"
> select add #5
2 models selected
> view matrix models
> #5,0.95142,-0.22381,0.21145,-33.093,0.1553,0.94182,0.29809,-87.97,-0.26586,-0.25076,0.93082,62.631
> view matrix models
> #5,0.95142,-0.22381,0.21145,-32.402,0.1553,0.94182,0.29809,-104.64,-0.26586,-0.25076,0.93082,59.949
> view matrix models
> #5,0.95142,-0.22381,0.21145,-32.306,0.1553,0.94182,0.29809,-110.43,-0.26586,-0.25076,0.93082,62.718
> fitmap #5 inMap #4
Fit map cryosparc_P76_J149_007_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 98567 points
correlation = 0.2402, correlation about mean = 0.01853, overlap = 958
steps = 120, shift = 3.33, angle = 7.92 degrees
Position of cryosparc_P76_J149_007_volume_map_sharp.mrc (#5) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.95532275 -0.26807002 0.12448660 -7.95147118
0.23765672 0.94709986 0.21568760 -108.94953107
-0.17572062 -0.17646619 0.96849468 30.26096746
Axis -0.55477314 0.42469793 0.71544282
Axis point 391.86841253 -136.79522984 -0.00000000
Rotation angle (degrees) 20.69763127
Shift along axis -20.20938612
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.60862,-0.79271,0.034489,155.48,0.77347,0.60242,0.19704,-138.12,-0.17698,-0.093249,0.97979,14.397
> fitmap #5 inMap #4
Fit map cryosparc_P76_J149_007_volume_map_sharp.mrc in map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc using 98567 points
correlation = 0.5725, correlation about mean = 0.2811, overlap = 3552
steps = 132, shift = 7.76, angle = 14.2 degrees
Position of cryosparc_P76_J149_007_volume_map_sharp.mrc (#5) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.71853405 -0.69549178 -0.00001732 131.77493541
0.69549178 0.71853405 0.00000754 -104.14010617
0.00000720 -0.00001747 1.00000000 -32.71666577
Axis -0.00001798 -0.00001763 1.00000000
Axis point 194.55102977 110.73438714 0.00000000
Rotation angle (degrees) 44.06641900
Shift along axis -32.71719860
> select clear
> hide #!5 models
> show #!5 models
> show #!4 models
> select clear
> transparency 30
> select clear
[Repeated 1 time(s)]
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> volume #2 level 0.1542
> volume #2 level 0.1007
> volume #2 level 0.1153
> show #!20 models
> hide #!20 models
> hide #!2 models
> show #!20 models
> show #!8 models
> hide #!20 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!4 models
> show #!2 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> hide #!2 models
> show #!4 models
> show #!2 models
> hide #!2 models
> hide #!8 models
> hide #!4 models
> show #!4 models
> show #!5 models
> hide #!4 models
> open
> C:/Users/OJS/Desktop/Phenix/230901_MBCD_Chol_N55H/RealSpaceRefine_43/231031_From42_100_real_space_refined_043.pdb
Chain information for 231031_From42_100_real_space_refined_043.pdb #7
---
Chain | Description
A B C D E F | No description available
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231011_All_Align_wo_POPE.cxs"
——— End of log from Tue Oct 31 06:40:42 2023 ———
opened ChimeraX session
> color #7 #00aa00ff
> select add #7
9840 atoms, 10116 bonds, 6 pseudobonds, 1194 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,-15.314,0,1,0,-37.392,0,0,1,-28.401
> view matrix models #7,1,0,0,-29.441,0,1,0,-34.915,0,0,1,-37.309
> ui tool show "Fit in Map"
> color #7 #00aa00ff
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> show #!2 models
> hide #!2 models
> close #6
> show #!27 models
> show #!7 models
> hide #!7 models
> show #!2 models
> hide #!2 models
> hide #!5 models
> select subtract #7
Nothing selected
> show #!1 models
> select add #27
24138 atoms, 24372 bonds, 6 pseudobonds, 1284 residues, 2 models selected
> view matrix models
> #27,0.97738,-0.2115,3.8748e-05,34.388,-0.2115,-0.97738,-0.00036461,289.61,0.00011499,0.00034817,-1,243.17
> ui mousemode right "rotate selected models"
> view matrix models
> #27,0.62638,-0.7794,-0.013527,165.93,0.77756,0.6235,0.081532,-85.658,-0.055112,-0.061588,0.99658,62.894
> fitmap #27 inMap #1
Fit molecule Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 24138 atoms
average map value = 0.07242, steps = 108
shifted from previous position = 5.5
rotated from previous position = 3.09 degrees
atoms outside contour = 20290, contour level = 0.18061
Position of Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) relative
to WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.63556945 0.77192317 0.01364193 144.09097523
0.77190158 0.63501421 0.03041234 -44.09645037
0.01481317 0.02985938 -0.99944434 265.84326946
Axis -0.42686646 -0.90416110 -0.01666544
Axis point 82.40721600 0.00000000 133.35183837
Rotation angle (degrees) 179.96288970
Shift along axis -26.06770453
> ui mousemode right "rotate selected models"
> view matrix models
> #27,0.98398,-0.15717,-0.084117,31.663,0.16206,0.98526,0.054716,-43.53,0.074277,-0.067471,0.99495,41.871
> ui mousemode right "translate selected models"
> view matrix models
> #27,0.98398,-0.15717,-0.084117,27.233,0.16206,0.98526,0.054716,-31.429,0.074277,-0.067471,0.99495,40.137
> fitmap #27 inMap #1
Fit molecule Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 24138 atoms
average map value = 0.07706, steps = 100
shifted from previous position = 2.16
rotated from previous position = 1.38 degrees
atoms outside contour = 19450, contour level = 0.18061
Position of Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) relative
to WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.98243372 0.15393199 0.10549374 275.45113856
0.15956975 0.98605686 0.04721614 5.52601659
-0.09675475 0.06322034 -0.99329840 278.16442569
Axis 0.07885433 0.99649907 0.02777782
Axis point 144.58226323 0.00000000 132.04468496
Rotation angle (degrees) 174.17562571
Shift along axis 34.95398635
> fitmap #27 inMap #1
Fit molecule Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 24138 atoms
average map value = 0.07705, steps = 60
shifted from previous position = 0.0133
rotated from previous position = 0.0158 degrees
atoms outside contour = 19454, contour level = 0.18061
Position of Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) relative
to WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.98240200 0.15404638 0.10562214 275.42604932
0.15971223 0.98602422 0.04741572 5.48941627
-0.09684176 0.06345044 -0.99327525 278.15199708
Axis 0.07892003 0.99649084 0.02788628
Axis point 144.57825473 0.00000000 132.03183308
Rotation angle (degrees) 174.16935275
Shift along axis 34.96341000
> fitmap #27 inMap #1
Fit molecule Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 24138 atoms
average map value = 0.07706, steps = 40
shifted from previous position = 0.0115
rotated from previous position = 0.00694 degrees
atoms outside contour = 19458, contour level = 0.18061
Position of Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) relative
to WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.98241835 0.15395951 0.10559672 275.43436205
0.15961670 0.98604300 0.04734686 5.50657099
-0.09683341 0.06336942 -0.99328124 278.15557799
Axis 0.07887370 0.99649556 0.02784843
Axis point 144.58073530 0.00000000 132.03445805
Rotation angle (degrees) 174.17035624
Shift along axis 34.95799743
> ui mousemode right "rotate selected models"
> view matrix models
> #27,0.84569,-0.53058,-0.057287,97.825,0.53246,0.84612,0.023855,-59.229,0.035814,-0.050677,0.99807,42.817
> view matrix models
> #27,0.85363,-0.52067,-0.015064,91.117,0.52072,0.85228,0.049775,-61.007,-0.013078,-0.050334,0.99865,49.67
> view matrix models
> #27,0.89405,-0.44792,-0.0058662,74.171,0.44744,0.8923,0.059964,-57.298,-0.021625,-0.056236,0.99818,51.764
> view matrix models
> #27,0.87229,-0.48887,-0.011097,83.573,0.4887,0.87075,0.054382,-59.541,-0.016923,-0.052859,0.99846,50.592
> fitmap #27 inMap #1
Fit molecule Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 24138 atoms
average map value = 0.2203, steps = 80
shifted from previous position = 3.42
rotated from previous position = 7.17 degrees
atoms outside contour = 12646, contour level = 0.18061
Position of Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) relative
to WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.91978532 0.39242192 0.00008501 244.35224554
0.39242191 0.91978518 0.00052114 -16.45218247
0.00012631 0.00051269 -0.99999986 272.60480377
Axis -0.20026366 -0.97974201 -0.00025195
Axis point 123.85610658 0.00000000 136.30579608
Rotation angle (degrees) 179.99879237
Shift along axis -32.88466289
> fitmap #27 inMap #1
Fit molecule Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 24138 atoms
average map value = 0.2203, steps = 24
shifted from previous position = 0.00208
rotated from previous position = 0.0043 degrees
atoms outside contour = 12641, contour level = 0.18061
Position of Cx43-nano-pope-chs-pH8-rs37-final-for-revision.pdb (#27) relative
to WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.91981231 0.39235866 0.00005484 244.36904832
0.39235863 0.91981218 0.00052031 -16.44875633
0.00015370 0.00050010 -0.99999987 272.60239821
Axis -0.20023259 -0.97974836 -0.00025543
Axis point 123.86184296 0.00000000 136.30640440
Rotation angle (degrees) 179.99710934
Shift along axis -32.88463530
> hide #!1 models
> select clear
> select #27:185,68,189
402 atoms, 390 bonds, 18 residues, 1 model selected
> show sel atoms
> select #27/b,c,e,f
16092 atoms, 16248 bonds, 4 pseudobonds, 856 residues, 2 models selected
> hide sel ribbons
> hide sel atoms
> select clear
> hide #!27 models
> open
> C:/Users/OJS/Desktop/Phenix/220302_Cx43_N55H_CBX/RealSpaceRefine_201/231031_From199_real_space_refined_201.pdb
Chain information for 231031_From199_real_space_refined_201.pdb #6
---
Chain | Description
A B C D E F | No description available
> color #6 #aa55ffff
> select add #6
9138 atoms, 9474 bonds, 6 pseudobonds, 1038 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> select #6:74-110
1686 atoms, 1740 bonds, 192 residues, 1 model selected
> lighting full
> ui tool show "Selection Inspector"
> setattr sel r ss_type 1
Assigning ss_type attribute to 192 items
> close #6
> show #!7 models
> open
> C:/Users/OJS/Desktop/Phenix/230320_Cx43_WT_POPE_PIP2/RealSpaceRefine_104/231026_From103_real_space_refined_104.pdb
Chain information for 231026_From103_real_space_refined_104.pdb #6
---
Chain | Description
A B C D E F | No description available
> select add #6
11616 atoms, 11814 bonds, 6 pseudobonds, 1266 residues, 2 models selected
> color #6 #ff557fff
> hide sel atoms
> show sel cartoons
> color #6 #ff557fff
> rename #7 id #10
> rename #20 id #7
> rename #8 id #9
> select clear
> show #!1 models
> hide #!10 models
> ui tool show "Selection Inspector"
> select add #6
11616 atoms, 11814 bonds, 6 pseudobonds, 1266 residues, 2 models selected
> view matrix models
> #6,-0.47714,0.87235,0.10649,84.213,0.87429,0.48348,-0.043261,-53.22,-0.089226,0.072465,-0.99337,346.53
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.47714,0.87235,0.10649,60.152,0.87429,0.48348,-0.043261,-94.031,-0.089226,0.072465,-0.99337,319.48
> view matrix models
> #6,-0.47714,0.87235,0.10649,53.576,0.87429,0.48348,-0.043261,-88.899,-0.089226,0.072465,-0.99337,314.23
> fitmap #6 inMap #1
Fit molecule 231026_From103_real_space_refined_104.pdb (#6) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11616 atoms
average map value = 0.3596, steps = 80
shifted from previous position = 4.03
rotated from previous position = 6.66 degrees
atoms outside contour = 2608, contour level = 0.18061
Position of 231026_From103_real_space_refined_104.pdb (#6) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.50016724 -0.86592883 0.00006158 231.63096687
0.86592883 0.50016724 -0.00001211 -62.09368508
-0.00002032 0.00005938 1.00000000 -0.00634146
Axis 0.00004128 0.00004729 1.00000000
Axis point 169.60218583 169.59619934 0.00000000
Rotation angle (degrees) 59.98893512
Shift along axis 0.00028380
> fitmap #6 inMap #1
Fit molecule 231026_From103_real_space_refined_104.pdb (#6) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11616 atoms
average map value = 0.3596, steps = 24
shifted from previous position = 0.000245
rotated from previous position = 0.0022 degrees
atoms outside contour = 2612, contour level = 0.18061
Position of 231026_From103_real_space_refined_104.pdb (#6) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.50015622 -0.86593519 0.00006368 231.63358895
0.86593519 0.50015622 -0.00004822 -62.08698308
0.00000991 0.00007926 1.00000000 -0.01491191
Axis 0.00007361 0.00003105 1.00000000
Axis point 169.59690203 169.59887491 0.00000000
Rotation angle (degrees) 59.98966385
Shift along axis 0.00021130
> select clear
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!7 models
> hide #!1 models
> view orient
> turn x 90
[Repeated 2 time(s)]
> hide #!7 models
> show #!7 models
> ui mousemode right "rotate selected models"
> select add #7
10512 atoms, 10836 bonds, 6 pseudobonds, 1188 residues, 2 models selected
> view matrix models
> #7,0.89733,-0.34666,-0.27317,90.911,0.35835,0.93356,-0.007586,-77.497,0.25765,-0.091084,0.96193,-45.715
> view matrix models
> #7,0.59925,-0.78087,0.1765,135.69,0.78974,0.61273,0.029557,-102.19,-0.13123,0.12167,0.98386,-20.222
> view matrix models
> #7,0.50313,-0.8642,-0.0037141,196.25,0.86301,0.5022,0.054821,-100.32,-0.045511,-0.030787,0.99849,-11.64
> view matrix models
> #7,0.41229,-0.90877,0.064485,207.08,0.90887,0.41517,0.039838,-90.928,-0.062976,0.042184,0.99712,-20.621
> fitmap #7 inMap #2
Fit molecule 231030_N55H_Chol_193 (#7) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.2281, steps = 68
shifted from previous position = 0.0364
rotated from previous position = 5.45 degrees
atoms outside contour = 3303, contour level = 0.11528
Position of 231030_N55H_Chol_193 (#7) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.49980992 -0.86613510 0.00014674 226.77994896
0.86613511 0.49980988 -0.00022848 -60.69966605
0.00012456 0.00024129 0.99999996 -0.05309330
Axis 0.00027119 0.00001280 0.99999996
Axis point 165.94411476 165.99759826 0.00000000
Rotation angle (degrees) 60.01257709
Shift along axis 0.00763043
> select clear
> show #!9 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> show #!6 models
> ui mousemode right "rotate selected models"
> select add #9
11646 atoms, 11886 bonds, 6 pseudobonds, 1230 residues, 2 models selected
> view matrix models
> #9,0.92071,-0.25041,0.29931,2.26,0.27164,0.96191,-0.030827,-27.313,-0.28019,0.10969,0.95366,29.71
> view matrix models
> #9,0.70439,-0.68597,-0.18243,159.07,0.70888,0.69303,0.13119,-73.147,0.036434,-0.22173,0.97443,28.77
> view matrix models
> #9,0.53867,-0.84248,0.0076256,175.82,0.84247,0.53852,-0.015423,-49.505,0.0088871,0.014732,0.99985,-3.1837
> fitmap #9 inMap #4
Fit molecule 231026_N55H_MBCD_37_wo_water.pdb (#9) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) using 11646 atoms
average map value = 0.5225, steps = 40
shifted from previous position = 0.022
rotated from previous position = 2.78 degrees
atoms outside contour = 1116, contour level = 0.14776
Position of 231026_N55H_MBCD_37_wo_water.pdb (#9) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.49997719 -0.86603857 -0.00008250 185.35752684
0.86603858 0.49997718 0.00009293 -49.67309697
-0.00003923 -0.00011791 0.99999999 0.02568620
Axis -0.00012172 -0.00002498 0.99999999
Axis point 135.69562015 135.68289622 0.00000000
Rotation angle (degrees) 60.00150983
Shift along axis 0.00436499
> select clear
> show #!10 models
> hide #!9 models
> hide #!7 models
> ui mousemode right "rotate selected models"
> select add #10
9840 atoms, 10116 bonds, 6 pseudobonds, 1194 residues, 2 models selected
> view matrix models
> #10,0.91312,-0.37299,0.1646,19.791,0.36366,0.92767,0.084727,-99.166,-0.18429,-0.017509,0.98272,-0.045392
> view matrix models
> #10,0.90753,-0.4167,0.05243,47.75,0.40949,0.90567,0.10992,-107.62,-0.093288,-0.078287,0.99256,-6.9022
> view matrix models
> #10,0.87796,-0.46757,0.10283,52.59,0.4643,0.88396,0.055205,-103.67,-0.11671,-0.00072516,0.99317,-16.187
> view matrix models
> #10,0.76831,-0.63653,-0.067266,129.57,0.63983,0.76087,0.10812,-121.84,-0.017639,-0.12611,0.99186,-11.509
> view matrix models
> #10,0.78353,-0.61297,-0.10179,129.02,0.62126,0.77571,0.11092,-121.69,0.010971,-0.15014,0.9886,-11.719
> fitmap #10 inMap #5
Fit molecule 231031_From42_100_real_space_refined_043.pdb (#10) to map
cryosparc_P76_J149_007_volume_map_sharp.mrc (#5) using 9840 atoms
average map value = 0.1163, steps = 108
shifted from previous position = 6.36
rotated from previous position = 10.4 degrees
atoms outside contour = 3737, contour level = 0.096521
Position of 231031_From42_100_real_space_refined_043.pdb (#10) relative to
cryosparc_P76_J149_007_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99999952 0.00037653 0.00090192 -0.26705915
-0.00037607 0.99999980 -0.00050736 0.16111479
-0.00090211 0.00050702 0.99999946 0.03662488
Axis 0.46061308 0.81917577 -0.34174063
Axis point 39.08113840 0.00000000 294.31032895
Rotation angle (degrees) 0.06308991
Shift along axis -0.00354582
> fitmap #10 inMap #5
Fit molecule 231031_From42_100_real_space_refined_043.pdb (#10) to map
cryosparc_P76_J149_007_volume_map_sharp.mrc (#5) using 9840 atoms
average map value = 0.1163, steps = 28
shifted from previous position = 0.0163
rotated from previous position = 0.00457 degrees
atoms outside contour = 3729, contour level = 0.096521
Position of 231031_From42_100_real_space_refined_043.pdb (#10) relative to
cryosparc_P76_J149_007_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99999958 0.00036020 0.00084182 -0.25183489
-0.00035974 0.99999978 -0.00055715 0.16397195
-0.00084202 0.00055684 0.99999949 0.00211135
Axis 0.51970540 0.78555578 -0.33586963
Axis point 1.21859449 0.00000000 297.43878773
Rotation angle (degrees) 0.06140700
Shift along axis -0.00277997
> select clear
> hide #!10 models
> hide #!6 models
> show #!6 models
> show #!7 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231011_All_Align_wo_POPE.cxs"
> select ::name="PIO"
258 atoms, 258 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel green
> select clear
> select
67752 atoms, 69024 bonds, 30 pseudobonds, 6162 residues, 20 models selected
> ui tool show "Selection Inspector"
> setattr =sel p display true
Assigning display attribute to 30 items
> setattr =sel p display false
Assigning display attribute to 30 items
> size =sel stickRadius 0.3
Changed 69024 bond radii
> select clear
> hide #!7 models
> select
> ::name="6OU"::name="CLR"::name="MC3"::name="PIO"::name="PTY"::name="Y01"
9756 atoms, 9630 bonds, 252 residues, 5 models selected
> show sel atoms
> select ::name="MC3"
3456 atoms, 3336 bonds, 120 residues, 2 models selected
> color sel gray
> select ::name="6OU"
2940 atoms, 2880 bonds, 60 residues, 3 models selected
> color sel gray
> select ::name="PTY"
1590 atoms, 1554 bonds, 36 residues, 4 models selected
> color sel gray
> select
67752 atoms, 69024 bonds, 30 pseudobonds, 6162 residues, 20 models selected
> color sel byhetero
> select
67752 atoms, 69024 bonds, 30 pseudobonds, 6162 residues, 20 models selected
> style sel stick
Changed 67752 atom styles
> select clear
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231011_All_Align_wo_POPE.cxs"
> show #!7 models
> morph #6,7
Computed 51 frame morph #8
> coordset #8 1,51
> show #!2 models
> hide #!2 models
> morph #7,9
Computed 51 frame morph #11
> coordset #11 1,51
> close #8
> close #11
> morph #9,10
Computed 51 frame morph #8
> coordset #8 1,51
> show #!7 models
> select
> ::name="6OU"::name="CLR"::name="MC3"::name="PIO"::name="PTY"::name="Y01"
9756 atoms, 9630 bonds, 252 residues, 5 models selected
> hide sel atoms
> select clear
> show #!6 models
> morph #8,6
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\morph.py", line 73, in morph
traj = compute_morph(structures, session.logger, method=method, rate=rate,
frames=frames,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\motion.py", line 28, in compute_morph
motion.interpolate(res_groups, atom_map, res_interp)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\motion.py", line 149, in interpolate
coords0[maindices] = matoms.coords
IndexError: index 9705 is out of bounds for axis 0 with size 9684
IndexError: index 9705 is out of bounds for axis 0 with size 9684
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\morph\motion.py", line 149, in interpolate
coords0[maindices] = matoms.coords
See log for complete Python traceback.
> close #8
> morph #9,6
Computed 51 frame morph #8
> coordset #8 1,51
> hide #!7 models
> show #!7 models
> select #6,7,9,10:189
264 atoms, 240 bonds, 24 residues, 4 models selected
> show sel atoms
> select clear
> hide #!8 models
> show #!8 models
> select #6,7,9,10:189,185
552 atoms, 528 bonds, 48 residues, 4 models selected
> show sel atoms
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!9 models
> show #!10 models
> hide #!9 models
> select clear
> select
77358 atoms, 78900 bonds, 42 pseudobonds, 7344 residues, 22 models selected
> ribbon style thickness 0.6
> select clear
> show #!5 models
> hide #!5 models
> hide #!10 models
> show #!9 models
> hide #!7 models
> show #!4 models
> hide #!9 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!7 models
> sel: 74-110
Unknown command: sel: 74-110
> sel:74-110
Unknown command: sel:74-110
> sel:74-110
Unknown command: sel:74-110
> sel: 74-110
Unknown command: sel: 74-110
> sel: 74-110
Unknown command: sel: 74-110
> select #6,7,9,10: 74-110
7566 atoms, 7782 bonds, 864 residues, 4 models selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 1
Assigning ss_type attribute to 864 items
> select clear
> close #8
> morph #7,9
Computed 51 frame morph #8
> coordset #8 1,51
> select #6-10
53034 atoms, 54354 bonds, 30 pseudobonds, 6036 residues, 10 models selected
> select #6-10/b,c,e,f
35356 atoms, 36236 bonds, 20 pseudobonds, 4024 residues, 10 models selected
> hide sel ribbons
> hide sel atoms
> select clear
> hide #!8 models
> show #!9 models
> show #!6 models
> close #8
> morph #7,9,10,6
Computed 151 frame morph #8
> coordset #8 1,151
> hide #!9 models
> show #!6 models
> hide #!8 models
> hide #!6 models
> show #!8 models
> morph #9,10
Computed 51 frame morph #11
> coordset #11 1,51
> hide #!8 models
> select #6-10
53010 atoms, 54324 bonds, 30 pseudobonds, 6036 residues, 10 models selected
> show sel ribbons
> close #11
> show #!9 models
> show #!8 models
> hide #!9 models
> select clear
> close #8
> morph #9,10
Computed 51 frame morph #8
> coordset #8 1,51
> morph #10,6
Computed 51 frame morph #11
> coordset #11 1,51
> hide #!8 models
> close #8,11
> show #!7 models
> morph #7,9,10,6
Computed 151 frame morph #8
> coordset #8 1,151
> select #6-10
53010 atoms, 54324 bonds, 30 pseudobonds, 6036 residues, 10 models selected
> select #6-10:33
330 atoms, 300 bonds, 30 residues, 5 models selected
> hide sel atoms
> select clear
> hide #!8 models
> show #!7 models
> select
> ::name="6OU"::name="CLR"::name="MC3"::name="PIO"::name="PTY"::name="Y01"
9756 atoms, 9630 bonds, 252 residues, 5 models selected
> show sel atoms
> select clear
> hide #!7 models
> show #!9 models
> show #!4 models
> hide #!4 models
> hide #!9 models
> show #!8 models
> select #8
9396 atoms, 9672 bonds, 6 pseudobonds, 1158 residues, 2 models selected
> show sel atoms
> select clear
> hide #!8 models
> show #!6 models
> mlp #!6
Map values for surface "231026_From103_real_space_refined_104.pdb_A SES
surface": minimum -27.83, mean 0.02625, maximum 26.49
Map values for surface "231026_From103_real_space_refined_104.pdb_B SES
surface": minimum -27.45, mean 0.07152, maximum 26.11
Map values for surface "231026_From103_real_space_refined_104.pdb_C SES
surface": minimum -27.25, mean -0.01701, maximum 23.5
Map values for surface "231026_From103_real_space_refined_104.pdb_D SES
surface": minimum -27.72, mean 0.03478, maximum 26.1
Map values for surface "231026_From103_real_space_refined_104.pdb_E SES
surface": minimum -27.16, mean 7.777e-05, maximum 26.13
Map values for surface "231026_From103_real_space_refined_104.pdb_F SES
surface": minimum -28.3, mean -0.06602, maximum 23.46
To also show corresponding color key, enter the above mlp command and add key
true
> show #!7 models
> hide #!6 models
> mlp #!7
Map values for surface "231030_N55H_Chol_193_A SES surface": minimum -25.64,
mean 0.3385, maximum 25.03
Map values for surface "231030_N55H_Chol_193_B SES surface": minimum -25.22,
mean 0.3385, maximum 24.84
Map values for surface "231030_N55H_Chol_193_C SES surface": minimum -25.96,
mean 0.2875, maximum 24.31
Map values for surface "231030_N55H_Chol_193_D SES surface": minimum -26.16,
mean 0.3782, maximum 24.07
Map values for surface "231030_N55H_Chol_193_E SES surface": minimum -25.6,
mean 0.3232, maximum 25.35
Map values for surface "231030_N55H_Chol_193_F SES surface": minimum -25.37,
mean 0.3887, maximum 24.67
To also show corresponding color key, enter the above mlp command and add key
true
> show #!8 models
> hide #!7 models
> hide #!8 models
> show #!9 models
> mlp #!9
Map values for surface "231026_N55H_MBCD_37_wo_water.pdb_A SES surface":
minimum -29.47, mean -0.08969, maximum 24.45
Map values for surface "231026_N55H_MBCD_37_wo_water.pdb_B SES surface":
minimum -29.72, mean -0.01814, maximum 24.81
Map values for surface "231026_N55H_MBCD_37_wo_water.pdb_C SES surface":
minimum -29.24, mean -0.03067, maximum 24.43
Map values for surface "231026_N55H_MBCD_37_wo_water.pdb_D SES surface":
minimum -29.64, mean -0.07075, maximum 24.46
Map values for surface "231026_N55H_MBCD_37_wo_water.pdb_E SES surface":
minimum -28.99, mean -0.05671, maximum 25.01
Map values for surface "231026_N55H_MBCD_37_wo_water.pdb_F SES surface":
minimum -28.91, mean -0.05575, maximum 25.01
To also show corresponding color key, enter the above mlp command and add key
true
> show #!10 models
> hide #!9 models
> mlp #!10
Map values for surface "231031_From42_100_real_space_refined_043.pdb_A SES
surface": minimum -25.08, mean 0.5653, maximum 24.82
Map values for surface "231031_From42_100_real_space_refined_043.pdb_B SES
surface": minimum -25.8, mean 0.4647, maximum 24.1
Map values for surface "231031_From42_100_real_space_refined_043.pdb_C SES
surface": minimum -25.51, mean 0.4946, maximum 23.66
Map values for surface "231031_From42_100_real_space_refined_043.pdb_D SES
surface": minimum -25.66, mean 0.537, maximum 24.14
Map values for surface "231031_From42_100_real_space_refined_043.pdb_E SES
surface": minimum -25.48, mean 0.4144, maximum 23.57
Map values for surface "231031_From42_100_real_space_refined_043.pdb_F SES
surface": minimum -25.12, mean 0.4616, maximum 24.27
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!10 models
> show #!7 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!10 models
> hide #!10 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!6 models
> hide #!9 models
> show #!9 models
> hide #!6 models
> show #!6 models
> hide #!9 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> show #!6 models
> hide #!7 models
> hide #!6 surfaces
> show #!1 models
> volume #1 level 0.1516
> hide #!6 models
> show #!5 models
> hide #!1 models
> hide #!5 models
> show #!4 models
> show #!9 models
> hide #!9 surfaces
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7,9 surfaces
> hide #!9 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> hide #!4 models
> show #!9 models
> show #!4 models
> hide #!4 models
> hide #!9 models
> hide #!7 models
> show #!7 models
> select #7/A:189@NH2
1 atom, 1 residue, 1 model selected
> select add #7/B:301@N29
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #7/A:189@NH2 #7/B:301@N29
Distance between 231030_N55H_Chol_193 #7/A ARG 189 NH2 and /B 6OU 301 N29:
3.9Å
> select clear
> show #!5 models
> hide #!7 models
> show #!10 models
> hide #!10 surfaces
> view orient
> turn x 90
[Repeated 2 time(s)]
> clip front 0
> ui tool show "Map Coordinates"
> ui tool show "Volume Viewer"
> volume #5 level 0.0662
> show #!8 models
> hide #!8 models
> show #!2 models
> hide #!2 models
> select #10
9840 atoms, 10116 bonds, 6 pseudobonds, 1194 residues, 2 models selected
> show sel atoms
> select clear
> hide #!10 models
> hide #!5 models
> show #!2 models
> show #!8 models
> volume #2 level 0.1497
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> volume #2 level 0.1028
> volume #2 level 0.0871
> volume #2 level 0.1247
> ~clip
> volume #2 level 0.1028
> view orient
> view 1
> clip front 0
> volume #2 level 0.08084
> select
> ::name="6OU"::name="CLR"::name="MC3"::name="PIO"::name="PTY"::name="Y01"
9756 atoms, 9630 bonds, 252 residues, 5 models selected
> show sel atoms
> select clear
> hide #!8 models
> show #!7 models
> volume #2 level 0.09649
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!6 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!6 models
> show #!10 models
> close #11
> hide #!10 models
> show #!9 models
> hide #!4 models
> ~clip
> show #!6 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> mlp #!6
Map values for surface "231026_From103_real_space_refined_104.pdb_A SES
surface": minimum -27.83, mean 0.02625, maximum 26.49
Map values for surface "231026_From103_real_space_refined_104.pdb_B SES
surface": minimum -27.45, mean 0.07152, maximum 26.11
Map values for surface "231026_From103_real_space_refined_104.pdb_C SES
surface": minimum -27.25, mean -0.01701, maximum 23.5
Map values for surface "231026_From103_real_space_refined_104.pdb_D SES
surface": minimum -27.72, mean 0.03478, maximum 26.1
Map values for surface "231026_From103_real_space_refined_104.pdb_E SES
surface": minimum -27.16, mean 7.777e-05, maximum 26.13
Map values for surface "231026_From103_real_space_refined_104.pdb_F SES
surface": minimum -28.3, mean -0.06602, maximum 23.46
To also show corresponding color key, enter the above mlp command and add key
true
> select #6:57,54,194,197
198 atoms, 180 bonds, 24 residues, 1 model selected
> color sel magenta
> select clear
> hide #!6 models
> show #!7 models
> mlp #!7
Map values for surface "231030_N55H_Chol_193_A SES surface": minimum -25.39,
mean 0.3403, maximum 25.18
Map values for surface "231030_N55H_Chol_193_B SES surface": minimum -25.2,
mean 0.3412, maximum 24.75
Map values for surface "231030_N55H_Chol_193_C SES surface": minimum -26.3,
mean 0.2841, maximum 24.44
Map values for surface "231030_N55H_Chol_193_D SES surface": minimum -25.84,
mean 0.3776, maximum 24
Map values for surface "231030_N55H_Chol_193_E SES surface": minimum -25.77,
mean 0.3259, maximum 24.92
Map values for surface "231030_N55H_Chol_193_F SES surface": minimum -25.96,
mean 0.385, maximum 24.78
To also show corresponding color key, enter the above mlp command and add key
true
> select #6,7,9,10:57,54,194,197
792 atoms, 720 bonds, 96 residues, 4 models selected
> color sel magenta
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231011_All_Align_wo_POPE.cxs"
> select clear
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> morph #6,7
Computed 51 frame morph #11
> coordset #11 1,51
> close #8
> close #11
> show #!6 models
> show #!7 models
> hide #!6-7 surfaces
> show #!9 models
> hide #!9 models
> show #!1 models
> hide #!1 models
> hide #!6 models
> show #!6 models
> select add #6
11616 atoms, 11814 bonds, 6 pseudobonds, 1266 residues, 2 models selected
> view matrix models
> #6,0.24309,0.9047,0.34989,-119.3,0.93237,-0.31743,0.17299,1.5526,0.26757,0.28417,-0.92068,207.33
> view matrix models
> #6,0.43732,0.89814,0.045849,-98.713,0.88271,-0.43844,0.16908,31.173,0.17196,-0.03347,-0.98454,288.43
> view matrix models
> #6,0.45659,0.88856,0.044585,-100.14,0.88893,-0.45769,0.018212,59.391,0.036589,0.031317,-0.99884,302.86
> ui tool show "Fit in Map"
> fitmap #6 inMap #1
Fit molecule 231026_From103_real_space_refined_104.pdb (#6) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11616 atoms
average map value = 0.3596, steps = 68
shifted from previous position = 0.128
rotated from previous position = 4.08 degrees
atoms outside contour = 1850, contour level = 0.15164
Position of 231026_From103_real_space_refined_104.pdb (#6) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.49985016 -0.86611183 -0.00033606 401.31679808
0.86611186 -0.49985021 0.00008093 107.46889385
-0.00023807 -0.00025061 0.99999994 0.08322749
Axis -0.00019140 -0.00005657 0.99999998
Axis point 169.62861309 169.60776938 0.00000000
Rotation angle (degrees) 119.99009069
Shift along axis 0.00033738
> select clear
> morph #6,7
Computed 51 frame morph #8
> coordset #8 1,51
> mlp #!8
Map values for surface "Morph - 231026_From103_real_space_refined_104.pdb_A
SES surface": minimum -25.8, mean 0.3751, maximum 24.61
Map values for surface "Morph - 231026_From103_real_space_refined_104.pdb_B
SES surface": minimum -25.56, mean 0.2898, maximum 24.95
Map values for surface "Morph - 231026_From103_real_space_refined_104.pdb_C
SES surface": minimum -26.27, mean 0.2309, maximum 24.64
Map values for surface "Morph - 231026_From103_real_space_refined_104.pdb_D
SES surface": minimum -26.69, mean 0.3794, maximum 24.33
Map values for surface "Morph - 231026_From103_real_space_refined_104.pdb_E
SES surface": minimum -25.38, mean 0.239, maximum 25.27
Map values for surface "Morph - 231026_From103_real_space_refined_104.pdb_F
SES surface": minimum -27.35, mean 0.2739, maximum 24.85
To also show corresponding color key, enter the above mlp command and add key
true
> select #8/b,c,e,f
6264 atoms, 6448 bonds, 4 pseudobonds, 772 residues, 2 models selected
> hide sel atoms
> hide sel ribbons
> hide sel surfaces
> close #8
> show #!6 models
> mlp #!6
Map values for surface "231026_From103_real_space_refined_104.pdb_A SES
surface": minimum -27.53, mean 0.03269, maximum 26.46
Map values for surface "231026_From103_real_space_refined_104.pdb_B SES
surface": minimum -27.21, mean 0.06696, maximum 26.08
Map values for surface "231026_From103_real_space_refined_104.pdb_C SES
surface": minimum -27.6, mean -0.01504, maximum 23.57
Map values for surface "231026_From103_real_space_refined_104.pdb_D SES
surface": minimum -27.49, mean 0.03672, maximum 26.33
Map values for surface "231026_From103_real_space_refined_104.pdb_E SES
surface": minimum -27.25, mean -0.005369, maximum 26.02
Map values for surface "231026_From103_real_space_refined_104.pdb_F SES
surface": minimum -28.6, mean -0.0675, maximum 23.74
To also show corresponding color key, enter the above mlp command and add key
true
> show #!7 models
> hide #!6 models
> mlp #!7
Map values for surface "231030_N55H_Chol_193_A SES surface": minimum -25.39,
mean 0.3403, maximum 25.18
Map values for surface "231030_N55H_Chol_193_B SES surface": minimum -25.2,
mean 0.3412, maximum 24.75
Map values for surface "231030_N55H_Chol_193_C SES surface": minimum -26.3,
mean 0.2841, maximum 24.44
Map values for surface "231030_N55H_Chol_193_D SES surface": minimum -25.84,
mean 0.3776, maximum 24
Map values for surface "231030_N55H_Chol_193_E SES surface": minimum -25.77,
mean 0.3259, maximum 24.92
Map values for surface "231030_N55H_Chol_193_F SES surface": minimum -25.96,
mean 0.385, maximum 24.78
To also show corresponding color key, enter the above mlp command and add key
true
> show #!6 models
> hide #!7 models
> show #!27 models
> hide #!27 models
> show #!7 models
> hide #!6 models
> hide #!7 models
> show #!6 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!9 models
> mlp #!9
Map values for surface "231026_N55H_MBCD_37_wo_water.pdb_A SES surface":
minimum -29.57, mean -0.08785, maximum 24.29
Map values for surface "231026_N55H_MBCD_37_wo_water.pdb_B SES surface":
minimum -29.15, mean -0.01704, maximum 25.25
Map values for surface "231026_N55H_MBCD_37_wo_water.pdb_C SES surface":
minimum -29.79, mean -0.03799, maximum 24.31
Map values for surface "231026_N55H_MBCD_37_wo_water.pdb_D SES surface":
minimum -29.73, mean -0.06976, maximum 24.07
Map values for surface "231026_N55H_MBCD_37_wo_water.pdb_E SES surface":
minimum -28.45, mean -0.05459, maximum 25.28
Map values for surface "231026_N55H_MBCD_37_wo_water.pdb_F SES surface":
minimum -29.45, mean -0.06095, maximum 24.67
To also show corresponding color key, enter the above mlp command and add key
true
> show #!6 models
> hide #!9 models
> show #!9 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!9 models
> show #!10 models
> mlp #!10
Map values for surface "231031_From42_100_real_space_refined_043.pdb_A SES
surface": minimum -25.08, mean 0.5653, maximum 24.82
Map values for surface "231031_From42_100_real_space_refined_043.pdb_B SES
surface": minimum -25.8, mean 0.4647, maximum 24.1
Map values for surface "231031_From42_100_real_space_refined_043.pdb_C SES
surface": minimum -25.51, mean 0.4946, maximum 23.66
Map values for surface "231031_From42_100_real_space_refined_043.pdb_D SES
surface": minimum -25.66, mean 0.537, maximum 24.14
Map values for surface "231031_From42_100_real_space_refined_043.pdb_E SES
surface": minimum -25.48, mean 0.4144, maximum 23.57
Map values for surface "231031_From42_100_real_space_refined_043.pdb_F SES
surface": minimum -25.12, mean 0.4616, maximum 24.27
To also show corresponding color key, enter the above mlp command and add key
true
> show #!6 models
> hide #!10 models
> transparency 30
> select clear
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> transparency 10
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!9 models
> hide #!7 models
> hide #!9 models
> show #!7 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!10 models
> hide #!7 models
> hide #!9 models
> show #!2 models
> hide #!2 models
> show #!6 models
> hide #!10 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!10 models
> show #!5 models
> select add #10
9840 atoms, 10116 bonds, 6 pseudobonds, 1194 residues, 2 models selected
> hide sel surfaces
> select clear
> clip front 0
> volume #5 level 0.04884
> transparency 50
> hide #!5 models
> show #!2 models
> hide #!10 models
> show #!7 models
> volume #2 level 0.08321
> select add #7
10512 atoms, 10836 bonds, 6 pseudobonds, 1188 residues, 4 models selected
> hide sel surfaces
> volume #2 level 0.09384
> hide #!2 models
> ~clip
> select clear
> morph #7,9
Computed 51 frame morph #8
> coordset #8 1,51
> morph #9,10
Computed 51 frame morph #11
> coordset #11 1,51
> moreph #10,6
Unknown command: moreph #10,6
> hide #!11 models
> select #8
9420 atoms, 9702 bonds, 6 pseudobonds, 1158 residues, 2 models selected
> show sel atoms
> select clear
> select #8/b,c,e,f
6280 atoms, 6468 bonds, 4 pseudobonds, 772 residues, 2 models selected
> hide sel atoms
> hide sel ribobn
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select #8/b,c,e,f
6280 atoms, 6468 bonds, 4 pseudobonds, 772 residues, 2 models selected
> hide sel ribbons
> close #8
> close #11
> show #!2 models
> hide #!2 models
> show #!7 models
> show #!9 models
> hide #!7 models
> hide #!9 models
> show #!10 models
> show #!9 models
> select
67752 atoms, 69024 bonds, 30 pseudobonds, 6162 residues, 20 models selected
> hide sel atoms
> select clear
> hide #!9-10 surfaces
> ui mousemode right "rotate selected models"
> hide #!10 models
> show #!10 models
> select add #10
9840 atoms, 10116 bonds, 6 pseudobonds, 1194 residues, 2 models selected
> view matrix models
> #10,0.94001,-0.24775,0.23453,-22.755,0.30572,0.91682,-0.25686,-26.761,-0.15139,0.31315,0.93756,-49.266
> view matrix models
> #10,0.99817,-0.039611,0.045649,-34.914,0.039046,0.99915,0.013185,-42.656,-0.046132,-0.011378,0.99887,-22.809
> view matrix models
> #10,0.97412,0.17235,0.14623,-84.352,-0.15872,0.98221,-0.10035,13.617,-0.16092,0.074548,0.98415,-15.327
> view matrix models
> #10,0.97478,0.15251,0.1629,-84.012,-0.13308,0.98329,-0.12426,13.26,-0.17912,0.099445,0.97879,-15.524
> view matrix models
> #10,0.99153,0.080099,0.10225,-63.977,-0.070066,0.9927,-0.09821,-3.5797,-0.10937,0.090213,0.9899,-27.737
> fitmap #10 inMap #5
Fit molecule 231031_From42_100_real_space_refined_043.pdb (#10) to map
cryosparc_P76_J149_007_volume_map_sharp.mrc (#5) using 9840 atoms
average map value = 0.1163, steps = 128
shifted from previous position = 0.237
rotated from previous position = 14.2 degrees
atoms outside contour = 721, contour level = 0.048837
Position of 231031_From42_100_real_space_refined_043.pdb (#10) relative to
cryosparc_P76_J149_007_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.49968009 0.86621003 0.00002669 -62.08172788
-0.86620967 0.49967991 -0.00089492 231.96297696
-0.00078853 0.00042405 0.99999960 0.02925669
Axis 0.00076135 0.00047057 -0.99999960
Axis point 169.75931584 169.72294757 0.00000000
Rotation angle (degrees) 60.02118225
Shift along axis 0.03263136
> fitmap #10 inMap #5
Fit molecule 231031_From42_100_real_space_refined_043.pdb (#10) to map
cryosparc_P76_J149_007_volume_map_sharp.mrc (#5) using 9840 atoms
average map value = 0.1163, steps = 40
shifted from previous position = 0.0123
rotated from previous position = 0.00102 degrees
atoms outside contour = 722, contour level = 0.048837
Position of 231031_From42_100_real_space_refined_043.pdb (#10) relative to
cryosparc_P76_J149_007_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.49968790 0.86620552 0.00002068 -62.07361016
-0.86620517 0.49968772 -0.00088082 231.96257952
-0.00077331 0.00042222 0.99999961 0.01823033
Axis 0.00075216 0.00045831 -0.99999961
Axis point 169.76511387 169.71628389 0.00000000
Rotation angle (degrees) 60.02066491
Shift along axis 0.04139216
> select clear
> morph #9,10
Computed 51 frame morph #8
> coordset #8 1,51
> morph #9,10,6
Computed 101 frame morph #11
> coordset #11 1,101
> hide #!8 models
> morph #9,6
Computed 51 frame morph #12
> coordset #12 1,51
> hide #!11 models
> hide #!12 models
> show #!10 models
> ui mousemode right rotate
> mlp #!10
Map values for surface "231031_From42_100_real_space_refined_043.pdb_A SES
surface": minimum -24.91, mean 0.5673, maximum 24.64
Map values for surface "231031_From42_100_real_space_refined_043.pdb_B SES
surface": minimum -25.68, mean 0.4686, maximum 24.05
Map values for surface "231031_From42_100_real_space_refined_043.pdb_C SES
surface": minimum -26.02, mean 0.493, maximum 23.61
Map values for surface "231031_From42_100_real_space_refined_043.pdb_D SES
surface": minimum -25.49, mean 0.5434, maximum 24.11
Map values for surface "231031_From42_100_real_space_refined_043.pdb_E SES
surface": minimum -25.57, mean 0.4128, maximum 23.69
Map values for surface "231031_From42_100_real_space_refined_043.pdb_F SES
surface": minimum -24.9, mean 0.4645, maximum 24
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!10 models
> show #!6 models
> transparency 0
> select clear
> show #!7 models
> hide #!6 models
> mlp #!7
Map values for surface "231030_N55H_Chol_193_A SES surface": minimum -25.39,
mean 0.3403, maximum 25.18
Map values for surface "231030_N55H_Chol_193_B SES surface": minimum -25.2,
mean 0.3412, maximum 24.75
Map values for surface "231030_N55H_Chol_193_C SES surface": minimum -26.3,
mean 0.2841, maximum 24.44
Map values for surface "231030_N55H_Chol_193_D SES surface": minimum -25.84,
mean 0.3776, maximum 24
Map values for surface "231030_N55H_Chol_193_E SES surface": minimum -25.77,
mean 0.3259, maximum 24.92
Map values for surface "231030_N55H_Chol_193_F SES surface": minimum -25.96,
mean 0.385, maximum 24.78
To also show corresponding color key, enter the above mlp command and add key
true
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!10 models
> hide #!7 models
> hide #!10 surfaces
> show #!5 models
> transparency 50
> volume #5 level 0.1053
> volume #5 level 0.09421
> volume #5 level 0.08379
> show #!11 models
> hide #!11 models
> hide #!10 models
> show #!9 models
> show #!10 models
> hide #!5 models
> close #12
> close #11
> morph #9,10
Computed 51 frame morph #11
> coordset #11 1,51
> view orient
> turn x 90
> select #11/b,c,e,f
6456 atoms, 6644 bonds, 4 pseudobonds, 792 residues, 2 models selected
> hide sel ribbons
> select #11/b
1614 atoms, 1661 bonds, 1 pseudobond, 198 residues, 2 models selected
> show sel ribbons
> select clear
> show #!7 models
> hide #!11 models
> select add #7
10512 atoms, 10836 bonds, 6 pseudobonds, 1188 residues, 2 models selected
> hide sel surfaces
> select clear
> select #7
10512 atoms, 10836 bonds, 6 pseudobonds, 1188 residues, 2 models selected
> show sel atoms
> select #7/c-f
7008 atoms, 7224 bonds, 4 pseudobonds, 792 residues, 2 models selected
> hide sel ribbons
> hide sel atoms
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> select
> ::name="6OU"::name="CLR"::name="MC3"::name="PIO"::name="PTY"::name="Y01"
9756 atoms, 9630 bonds, 252 residues, 5 models selected
> show sel atoms
> select clear
> show #!8 models
> hide #!7 models
> select
> ::name="6OU"::name="CLR"::name="MC3"::name="PIO"::name="PTY"::name="Y01"
9756 atoms, 9630 bonds, 252 residues, 5 models selected
> show sel atoms
> show #!9 models
> hide #!8 models
> select add #7
19176 atoms, 19332 bonds, 6 pseudobonds, 1410 residues, 6 models selected
> select subtract #7
8664 atoms, 8496 bonds, 222 residues, 10 models selected
> select add #6
18282 atoms, 18390 bonds, 6 pseudobonds, 1404 residues, 5 models selected
> select subtract #6
6666 atoms, 6576 bonds, 138 residues, 9 models selected
> select add #10
16350 atoms, 16542 bonds, 6 pseudobonds, 1326 residues, 4 models selected
> select subtract #10
6510 atoms, 6426 bonds, 132 residues, 8 models selected
> select add #27
26100 atoms, 26292 bonds, 6 pseudobonds, 1326 residues, 3 models selected
> select subtract #27
1962 atoms, 1920 bonds, 42 residues, 1 model selected
> select clear
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!9 models
> show #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!7 models
> show #!7 models
> select #7,9/c-f
14772 atoms, 15148 bonds, 8 pseudobonds, 1612 residues, 4 models selected
> hide sel atoms
> hide sel ribbons
> select clear
> select #9
11646 atoms, 11886 bonds, 6 pseudobonds, 1230 residues, 2 models selected
> show sel atoms
> select #9/c-f
7764 atoms, 7924 bonds, 4 pseudobonds, 820 residues, 2 models selected
> hide sel atoms
> select clear
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!9 models
> show #!9 models
> show #!7 models
> hide #!7 models
> show #!4 models
> volume #4 level 0.309
> volume #4 level 0.22
> hide #!4 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!7 models
> show #!7 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!7 models
> show #!9 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!9 models
> clip front 0
> show #!9 models
> show #!11 models
> hide #!11 models
> hide #!9 models
> show #!9 models
> show #!9 atoms
> volume #4 level 0.1589
> show #!2 models
> show #!7 models
> hide #!9 models
> show #!7 cartoons
> show #!7 atoms
> hide #!7 models
> show #!7 models
> hide #!4 models
> volume #2 level 0.109
> volume #2 level 0.1065
> volume #2 level 0.09384
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231011_All_Align_wo_POPE.cxs"
——— End of log from Tue Oct 31 21:23:00 2023 ———
opened ChimeraX session
> open
> C:/Users/OJS/Desktop/Phenix/220302_Cx43_N55H_CBX/RealSpaceRefine_204/231106_From203_real_space_refined_204.pdb
Chain information for 231106_From203_real_space_refined_204.pdb #12
---
Chain | Description
A B C D E F | No description available
> color #12 #00aa00ff
> select add #12
10512 atoms, 10836 bonds, 6 pseudobonds, 1188 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> ui mousemode right "translate selected models"
> view matrix models #12,1,0,0,-31.962,0,1,0,-32.831,0,0,1,-26.213
> ui tool show "Fit in Map"
> fitmap #12 inMap #2
Fit molecule 231106_From203_real_space_refined_204.pdb (#12) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.2279, steps = 84
shifted from previous position = 3.41
rotated from previous position = 8.83 degrees
atoms outside contour = 2334, contour level = 0.093838
Position of 231106_From203_real_space_refined_204.pdb (#12) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999994 -0.00024794 -0.00023259 0.08348348
0.00024801 0.99999992 0.00029823 -0.09746148
0.00023251 -0.00029829 0.99999993 0.01987940
Axis -0.65950004 -0.51420733 0.54831608
Axis point 0.00000000 55.61692139 316.54203033
Rotation angle (degrees) 0.02591189
Shift along axis 0.00595824
> select clear
> select
> ::name="6OU"::name="CLR"::name="MC3"::name="PIO"::name="PTY"::name="Y01"
10848 atoms, 10764 bonds, 282 residues, 6 models selected
> show sel atoms
> select clear
> select ::name="6OU"
3528 atoms, 3456 bonds, 72 residues, 4 models selected
> color sel gray
> color sel byhetero
> select ::name="CLR"
1008 atoms, 1116 bonds, 36 residues, 2 models selected
> color sel yellow
> color sel byhetero
> select clear
> hide #!7 models
> volume #2 level 0.07333
> select add #12
10512 atoms, 10836 bonds, 6 pseudobonds, 1188 residues, 2 models selected
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.3
Changed 10836 bond radii
> select clear
> close #8
> close #11
> volume #2 level 0.1015
> select #12
10512 atoms, 10836 bonds, 6 pseudobonds, 1188 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 10512 atom styles
> color sequential lbyhetero
Expected one of 'chains', 'polymers', 'residues', or 'structures' or a keyword
> color sel byhetero
> select clear
> volume #2 level 0.08615
> mlp #!12
Map values for surface "231106_From203_real_space_refined_204.pdb_A SES
surface": minimum -25.04, mean 0.3091, maximum 25.3
Map values for surface "231106_From203_real_space_refined_204.pdb_B SES
surface": minimum -25, mean 0.3561, maximum 25.35
Map values for surface "231106_From203_real_space_refined_204.pdb_C SES
surface": minimum -25.7, mean 0.3617, maximum 25.14
Map values for surface "231106_From203_real_space_refined_204.pdb_D SES
surface": minimum -25.81, mean 0.2966, maximum 24.44
Map values for surface "231106_From203_real_space_refined_204.pdb_E SES
surface": minimum -25.23, mean 0.3748, maximum 25.49
Map values for surface "231106_From203_real_space_refined_204.pdb_F SES
surface": minimum -26.28, mean 0.3046, maximum 24.61
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!12 models
> hide #!2 models
> show #!4 models
> show #!9 models
> color #4 #00ff7f80 models
> color #4 #00ff0080 models
> color #4 #ff000080 models
> color #4 #ffff7f80 models
> lighting full
[Repeated 1 time(s)]
> lighting soft
> lighting full
> hide #!9 models
> hide #!4 models
> show #!2 models
> show #!12 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!12 models
> mlp #!9
Map values for surface "231026_N55H_MBCD_37_wo_water.pdb_A SES surface":
minimum -29.57, mean -0.08785, maximum 24.29
Map values for surface "231026_N55H_MBCD_37_wo_water.pdb_B SES surface":
minimum -29.15, mean -0.01704, maximum 25.25
Map values for surface "231026_N55H_MBCD_37_wo_water.pdb_C SES surface":
minimum -29.79, mean -0.03799, maximum 24.31
Map values for surface "231026_N55H_MBCD_37_wo_water.pdb_D SES surface":
minimum -29.73, mean -0.06976, maximum 24.07
Map values for surface "231026_N55H_MBCD_37_wo_water.pdb_E SES surface":
minimum -28.45, mean -0.05459, maximum 25.28
Map values for surface "231026_N55H_MBCD_37_wo_water.pdb_F SES surface":
minimum -29.45, mean -0.06095, maximum 24.67
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!2 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!9 models
> close #9
> show #!7 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!12 models
> hide #!7,12 atoms
> show #!7,12 atoms
> hide #!7 models
> hide #!12 models
> show #!12 models
> show #!2 models
> show #!7 models
> hide #!7 models
> hide #!12 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!10 models
> hide #!10 models
> show #!5 models
> hide #!5 models
> show #!4 models
> color #4 #aaff7f80 models
> color #4 #aaff0080 models
> open
> C:/Users/OJS/Desktop/Phenix/230901_MBCD_Chol_N55H/RealSpaceRefine_44/231106_From39-coot-1_real_space_refined_044.pdb
Chain information for 231106_From39-coot-1_real_space_refined_044.pdb #8
---
Chain | Description
A B C D E F | No description available
> volume #4 level 0.1926
> volume #4 level 0.142
> volume #4 level 0.1251
> close #10
> close #8
> hide #!4 models
> color #2 #00aa0080 models
> color #4 #00ff0080 models
> color #5 #aaff0080 models
> color #5 #aaff7f80 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231011_All_Align_wo_POPE.cxs"
——— End of log from Tue Nov 7 00:43:02 2023 ———
opened ChimeraX session
> show #!2 models
> hide #!2 models
> show #!4 models
> open
> C:/Users/OJS/Desktop/Phenix/230901_MBCD_Chol_N55H/RealSpaceRefine_45/231106_From44-coot-2_real_space_refined_045.pdb
Chain information for 231106_From44-coot-2_real_space_refined_045.pdb #8
---
Chain | Description
A B C D E F | No description available
> color #8 lime
> hide #!8 atoms
> show #!8 cartoons
> select #8
11718 atoms, 11976 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> color #8 lime
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.3
Changed 11976 bond radii
> ui tool show "Selection Inspector"
> setattr =sel p display false
Assigning display attribute to 6 items
> setattr =sel p display true
Assigning display attribute to 6 items
> setattr =sel p display false
Assigning display attribute to 6 items
> hide #!8 models
> show #!8 models
> select clear
> select
> ::name="6OU"::name="CLR"::name="MC3"::name="PIO"::name="PTY"::name="Y01"
10764 atoms, 10704 bonds, 282 residues, 5 models selected
> show sel atoms
> color sel yellow
> color sel byhetero
> select clear
> volume #4 level 0.1663
> volume #4 level 0.1457
> volume #4 level 0.1251
> close #8
> rename #3 id #30
> rename #4 id #3
> rename #5 id #4
> rename #4 N55H_MBCD_P76_J149_007_volume_map_sharp
> select clear
> rename #30 id #5
> color #2 #00aaff80 models
> color #3 #00ffff80 models
> color #4 #aaffff80 models
> show #!4 models
> hide #!4 models
> show #!12 models
> hide #!3 models
> show #!2 models
> volume #2 level 0.06737
> volume #2 level 0.0705
> close #7
> close #12
> show #!6 models
> hide #!6 models
> show #!6 models
> close #6
> show #!3 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!2 models
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231106_N55H_MBCD10_45.pdb"
Chain information for 231106_N55H_MBCD10_45.pdb #6
---
Chain | Description
A B C D E F | No description available
> rename #5 id #8
> rename #8 id #5
> rename #6 id #8
> color #8 cyan
> hide #!8 atoms
> show #!8 cartoons
> select clear
> color #8 cyan
> select clear
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231106_N55H_Chol_204.pdb"
Chain information for 231106_N55H_Chol_204.pdb #6
---
Chain | Description
A B C D E F | No description available
> color #6 #00aaffff
> rename #6 id #7
> hide #!7-8 atoms
> show #!7-8 cartoons
> hide #!2 models
> hide #!8 models
> show #!2 models
> ui mousemode right "translate selected models"
> select add #2
3 models selected
> view matrix models
> #2,0.98819,-0.15325,5.4041e-05,1.1662,0.15325,0.98819,0.00016195,-58.513,-7.8221e-05,-0.00015176,1,-30.584
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc using 271891 points
correlation = 0.348, correlation about mean = 0.05369, overlap = 2731
steps = 120, shift = 3.5, angle = 3.12 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.98835637 0.14298832 -0.05201950 312.93290407
0.14280008 0.98972436 0.00733679 -25.78332157
0.05253404 -0.00017703 -0.99861912 338.99681230
Axis -0.07168074 -0.99742601 -0.00179579
Axis point 152.93648426 0.00000000 173.63788206
Rotation angle (degrees) 176.99565563
Shift along axis 2.67692744
> fitmap #2 inMap #1
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc using 271891 points
correlation = 0.3481, correlation about mean = 0.05382, overlap = 2731
steps = 48, shift = 0.017, angle = 0.00844 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.98835260 0.14298090 -0.05211132 312.94449589
0.14278663 0.98972544 0.00745119 -25.79570256
0.05264128 -0.00007640 -0.99861348 338.97708414
Axis -0.07167567 -0.99742628 -0.00184973
Axis point 152.93442310 0.00000000 173.63672014
Rotation angle (degrees) 176.98993098
Shift along axis 2.67178853
> fitmap #2 inMap #1
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc using 271891 points
correlation = 0.348, correlation about mean = 0.05372, overlap = 2731
steps = 40, shift = 0.0132, angle = 0.00563 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.98835718 0.14296677 -0.05206314 312.94331226
0.14277695 0.98972747 0.00736629 -25.78425381
0.05258146 -0.00015289 -0.99861662 338.98826644
Axis -0.07166956 -0.99742679 -0.00180925
Axis point 152.93780867 0.00000000 173.63750346
Rotation angle (degrees) 176.99303874
Shift along axis 2.67608216
> fitmap #2 inMap #1
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc using 271891 points
correlation = 0.3481, correlation about mean = 0.05379, overlap = 2731
steps = 44, shift = 0.00958, angle = 0.0191 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.98836985 0.14285829 -0.05212050 312.97467309
0.14265229 0.98974314 0.00767047 -25.81854445
0.05268170 0.00014615 -0.99861134 338.93045550
Axis -0.07161095 -0.99743071 -0.00196054
Axis point 152.94802402 0.00000000 173.61717846
Rotation angle (degrees) 176.98851788
Shift along axis 2.67530786
> show #!1 models
> view matrix models
> #2,0.98903,-0.13828,0.051926,-14.26,0.13807,0.99039,0.007534,-58.041,-0.052469,-0.00028172,0.99862,-16.641
> fitmap #2 inMap #1
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc using 271891 points
correlation = 0.8523, correlation about mean = 0.7042, overlap = 1.013e+04
steps = 300, shift = 5.21, angle = 3.15 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.98734240 0.15860323 -0.00001552 307.17409740
0.15860322 0.98734239 0.00011356 -20.65671480
0.00003333 0.00010966 -0.99999999 339.16336740
Axis -0.07954955 -0.99683091 -0.00005347
Axis point 154.40919289 0.00000000 169.58412329
Rotation angle (degrees) 179.99859620
Shift along axis -3.86244374
> fitmap #2 inMap #1
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc using 271891 points
correlation = 0.8523, correlation about mean = 0.7042, overlap = 1.013e+04
steps = 28, shift = 0.0184, angle = 0.0101 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.98734242 0.15860309 0.00000896 307.16852403
0.15860309 0.98734242 -0.00006158 -20.60892362
-0.00001861 -0.00005938 -1.00000000 339.19999708
Axis 0.07956113 0.99682999 -0.00002588
Axis point 154.40788038 0.00000000 169.59866656
Rotation angle (degrees) 179.99920752
Shift along axis 3.88630187
> fitmap #2 inMap #1
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc using 271891 points
correlation = 0.8523, correlation about mean = 0.7042, overlap = 1.013e+04
steps = 28, shift = 0.0149, angle = 8.02e-05 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.98734237 0.15860337 0.00001031 307.16957946
0.15860337 0.98734237 -0.00006132 -20.62382759
-0.00001990 -0.00005891 -1.00000000 339.20005486
Axis 0.07956062 0.99683003 -0.00002609
Axis point 154.40910999 0.00000000 169.59859144
Rotation angle (degrees) 179.99913182
Shift along axis 3.87130268
> fitmap #2 inMap #1
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc using 271891 points
correlation = 0.8523, correlation about mean = 0.7042, overlap = 1.013e+04
steps = 28, shift = 0.0167, angle = 6.98e-06 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.98734239 0.15860326 0.00001034 307.16794444
0.15860326 0.98734239 -0.00006134 -20.60719415
-0.00001994 -0.00005892 -1.00000000 339.20016961
Axis 0.07956055 0.99683004 -0.00002610
Axis point 154.40763113 0.00000000 169.59864596
Rotation angle (degrees) 179.99912966
Shift along axis 3.88772456
> fitmap #2 inMap #1
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc using 271891 points
correlation = 0.8523, correlation about mean = 0.7042, overlap = 1.013e+04
steps = 28, shift = 0.0175, angle = 5.09e-05 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.98734235 0.15860352 0.00001117 307.16961111
0.15860352 0.98734235 -0.00006114 -20.62471232
-0.00002072 -0.00005860 -1.00000000 339.20016224
Axis 0.07956034 0.99683005 -0.00002618
Axis point 154.40922992 0.00000000 169.59857927
Rotation angle (degrees) 179.99908350
Shift along axis 3.87030513
> hide #!2 models
> show #!2 models
> hide #!1 models
> select add #2
3 models selected
> select subtract #2
Nothing selected
> select add #7
10512 atoms, 10836 bonds, 6 pseudobonds, 1188 residues, 2 models selected
> view matrix models #7,1,0,0,-31.253,0,1,0,-31.648,0,0,1,-24.36
> fitmap #7 inMap #2
Fit molecule 231106_N55H_Chol_204.pdb (#7) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.2279, steps = 84
shifted from previous position = 1.64
rotated from previous position = 8.88 degrees
atoms outside contour = 1328, contour level = 0.070496
Position of 231106_N55H_Chol_204.pdb (#7) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999996 -0.00025799 -0.00014421 0.06780241
0.00025798 0.99999997 -0.00004992 -0.02957928
0.00014422 0.00004989 0.99999999 -0.02328160
Axis 0.16649299 -0.48112773 0.86069518
Axis point 104.46909328 259.25863117 0.00000000
Rotation angle (degrees) 0.01717370
Shift along axis 0.00548167
> fitmap #7 inMap #2
Fit molecule 231106_N55H_Chol_204.pdb (#7) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.2279, steps = 28
shifted from previous position = 0.0149
rotated from previous position = 0.0267 degrees
atoms outside contour = 1329, contour level = 0.070496
Position of 231106_N55H_Chol_204.pdb (#7) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999996 -0.00024732 -0.00009620 0.05646554
0.00024736 0.99999988 0.00041352 -0.12155893
0.00009609 -0.00041354 0.99999991 0.06175906
Axis -0.84161578 -0.19567378 0.50338320
Axis point 0.00000000 140.32889418 290.52280633
Rotation angle (degrees) 0.02815246
Shift along axis 0.00735208
> fitmap #7 inMap #2
Fit molecule 231106_N55H_Chol_204.pdb (#7) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.2279, steps = 28
shifted from previous position = 0.017
rotated from previous position = 0.0275 degrees
atoms outside contour = 1331, contour level = 0.070496
Position of 231106_N55H_Chol_204.pdb (#7) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999996 -0.00024835 -0.00009275 0.05549170
0.00024834 0.99999997 -0.00006693 -0.02291039
0.00009276 0.00006691 0.99999999 -0.01756373
Axis 0.24475044 -0.33924523 0.90830055
Axis point 84.90455329 218.10784854 0.00000000
Rotation angle (degrees) 0.01566571
Shift along axis 0.00540071
> select clear
> hide #!7 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!8 models
> fitmap #8 inMap #3
Fit molecule 231106_N55H_MBCD10_45.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5177, steps = 40
shifted from previous position = 0.00869
rotated from previous position = 0.0108 degrees
atoms outside contour = 925, contour level = 0.12512
Position of 231106_N55H_MBCD10_45.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00006288 0.00012727 -0.01526767
0.00006286 0.99999999 0.00012447 -0.03196747
-0.00012728 -0.00012446 0.99999998 0.03769369
Axis -0.65926622 0.67414923 0.33300281
Axis point 293.34893546 0.00000000 114.46091765
Rotation angle (degrees) 0.01081693
Shift along axis 0.00106672
> fitmap #8 inMap #3
Fit molecule 231106_N55H_MBCD10_45.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5177, steps = 24
shifted from previous position = 0.00493
rotated from previous position = 0.00603 degrees
atoms outside contour = 923, contour level = 0.12512
Position of 231106_N55H_MBCD10_45.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
1.00000000 -0.00008633 0.00004328 0.00391074
0.00008632 0.99999998 0.00018329 -0.04646977
-0.00004329 -0.00018329 0.99999998 0.03435429
Axis -0.88471097 0.20893837 0.41669083
Axis point 0.00000000 184.80317413 254.85541308
Rotation angle (degrees) 0.01187027
Shift along axis 0.00114592
> fitmap #8 inMap #3
Fit molecule 231106_N55H_MBCD10_45.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5176, steps = 24
shifted from previous position = 0.00631
rotated from previous position = 0.0067 degrees
atoms outside contour = 925, contour level = 0.12512
Position of 231106_N55H_MBCD10_45.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00008564 -0.00007185 0.02659363
0.00008565 0.99999998 0.00016305 -0.04334834
0.00007184 -0.00016306 0.99999998 0.01612981
Axis -0.82477402 -0.36341905 0.43321406
Axis point 0.00000000 96.74892212 264.06480695
Rotation angle (degrees) 0.01132724
Shift along axis 0.00080754
> fitmap #8 inMap #3
Fit molecule 231106_N55H_MBCD10_45.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5176, steps = 24
shifted from previous position = 0.00606
rotated from previous position = 0.00578 degrees
atoms outside contour = 928, contour level = 0.12512
Position of 231106_N55H_MBCD10_45.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00008718 -0.00014443 0.04170876
0.00008719 0.99999999 0.00009290 -0.02948309
0.00014442 -0.00009291 0.99999999 -0.00316916
Axis -0.48239008 -0.74990770 0.45270106
Axis point 23.71335425 0.00000000 290.63541470
Rotation angle (degrees) 0.01103461
Shift along axis 0.00055502
> fitmap #8 inMap #3
Fit molecule 231106_N55H_MBCD10_45.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5176, steps = 24
shifted from previous position = 0.0084
rotated from previous position = 0.00796 degrees
atoms outside contour = 926, contour level = 0.12512
Position of 231106_N55H_MBCD10_45.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999998 -0.00009096 -0.00016115 0.04577422
0.00009095 0.99999999 -0.00004499 -0.00194818
0.00016116 0.00004498 0.99999999 -0.02433268
Axis 0.23621831 -0.84622718 0.47759864
Axis point 153.49974540 0.00000000 282.79119049
Rotation angle (degrees) 0.01091150
Shift along axis 0.00084005
> fitmap #8 inMap #3
Fit molecule 231106_N55H_MBCD10_45.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5176, steps = 24
shifted from previous position = 0.00429
rotated from previous position = 0.00396 degrees
atoms outside contour = 927, contour level = 0.12512
Position of 231106_N55H_MBCD10_45.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00008963 -0.00012710 0.03864581
0.00008962 0.99999999 -0.00010507 0.01058368
0.00012711 0.00010506 0.99999999 -0.02783017
Axis 0.55979164 -0.67721272 0.47751047
Axis point 223.40305062 0.00000000 298.85697430
Rotation angle (degrees) 0.01075359
Shift along axis 0.00117701
> fitmap #8 inMap #3
Fit molecule 231106_N55H_MBCD10_45.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5176, steps = 24
shifted from previous position = 0.00495
rotated from previous position = 0.00428 degrees
atoms outside contour = 922, contour level = 0.12512
Position of 231106_N55H_MBCD10_45.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00008758 -0.00007074 0.02645884
0.00008757 0.99999998 -0.00015411 0.02099520
0.00007075 0.00015410 0.99999999 -0.02685333
Axis 0.80748568 -0.37070285 0.45885321
Axis point 0.00000000 178.02059677 139.24871691
Rotation angle (degrees) 0.01093479
Shift along axis 0.00126042
> hide #!2 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select clear
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231011_All_Align_wo_POPE.cxs"
> show #!2 models
> hide #!2 models
> ~clip
> show #!4 models
> volume #3 level 0.1061
> volume #4 level 0.05646
> view orient
> turn x 90
[Repeated 2 time(s)]
> clip front 0
> volume #4 level 0.08309
> volume #4 level 0.07468
> volume #4 level 0.06627
> hide #!8 models
> hide #!7 models
> hide #!4 models
> show #!8 models
> show #!3 models
> hide #!3 models
> show #!4 models
> select #8/b
1953 atoms, 1996 bonds, 1 pseudobond, 206 residues, 2 models selected
> select #8/d
1953 atoms, 1996 bonds, 1 pseudobond, 206 residues, 2 models selected
> select #8/e
1953 atoms, 1996 bonds, 1 pseudobond, 206 residues, 2 models selected
> select #8/e:33
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/e:31
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/e:30
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> hide sel atoms
> volume #4 level 0.04665
> hide #!8 models
> volume #4 level 0.06417
> select clear
> open
> C:/Users/OJS/Desktop/Phenix/230901_MBCD_Chol_N55H/RealSpaceRefine_46/231107_From43_real_space_refined_046.pdb
Chain information for 231107_From43_real_space_refined_046.pdb #6
---
Chain | Description
A B C D E F | No description available
> select add #6
10164 atoms, 10428 bonds, 6 pseudobonds, 1206 residues, 2 models selected
> view matrix models #6,1,0,0,8.2564,0,1,0,-35.975,0,0,1,-0.34924
> view matrix models #6,1,0,0,-17.359,0,1,0,-37.252,0,0,1,-40.744
> view matrix models #6,1,0,0,-30.083,0,1,0,-37.062,0,0,1,-38.68
> fitmap #6 inMap #4
Fit molecule 231107_From43_real_space_refined_046.pdb (#6) to map
N55H_MBCD_P76_J149_007_volume_map_sharp (#4) using 10164 atoms
average map value = 0.07039, steps = 112
shifted from previous position = 5.12
rotated from previous position = 13.8 degrees
atoms outside contour = 5249, contour level = 0.064171
Position of 231107_From43_real_space_refined_046.pdb (#6) relative to
N55H_MBCD_P76_J149_007_volume_map_sharp (#4) coordinates:
Matrix rotation and translation
0.53125879 0.84720919 -0.00083081 -64.02973600
-0.84720944 0.53125903 0.00008376 223.21308758
0.00051234 0.00065937 0.99999965 -5.07318578
Axis 0.00033971 -0.00079269 -0.99999963
Axis point 169.70709224 169.47420038 0.00000000
Rotation angle (degrees) 57.90945793
Shift along axis 4.87449420
> hide sel atoms
> show sel cartoons
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.97095,0.23926,-0.00067254,-69.824,-0.23926,0.97095,-0.00051009,10.463,0.00053096,0.00065619,1,-28.165
> fitmap #6 inMap #4
Fit molecule 231107_From43_real_space_refined_046.pdb (#6) to map
N55H_MBCD_P76_J149_007_volume_map_sharp (#4) using 10164 atoms
average map value = 0.1139, steps = 64
shifted from previous position = 4.96
rotated from previous position = 2.09 degrees
atoms outside contour = 1724, contour level = 0.064171
Position of 231107_From43_real_space_refined_046.pdb (#6) relative to
N55H_MBCD_P76_J149_007_volume_map_sharp (#4) coordinates:
Matrix rotation and translation
0.49996032 0.86604831 -0.00004680 -62.05792169
-0.86604796 0.49996006 -0.00093131 231.88463004
-0.00078316 0.00050615 0.99999957 0.00753382
Axis 0.00082989 0.00042513 -0.99999957
Axis point 169.77837853 169.68323700 0.00000000
Rotation angle (degrees) 60.00264811
Shift along axis 0.03954545
> select clear
> select ::name="6OU"::name="CLR"::name="MC3"::name="PTY"::name="Y01"
8154 atoms, 8112 bonds, 186 residues, 4 models selected
> show sel atoms
> color sel byhetero
> select clear
> close #6
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231107_N55H_MBCD100_46.pdb"
Chain information for 231107_N55H_MBCD100_46.pdb #6
---
Chain | Description
A B C D E F | No description available
> rename #6 id #9
> color #9 cyan
> color #9 #aaffffff
> select add #9
10164 atoms, 10428 bonds, 6 pseudobonds, 1206 residues, 2 models selected
> view matrix models #9,1,0,0,-35.89,0,1,0,2.2782,0,0,1,-30.318
> view matrix models #9,1,0,0,-35.48,0,1,0,-24.726,0,0,1,-28.732
> hide sel atoms
> show sel cartoons
> select clear
> hide #!4 models
> show #!8 models
> fitmap #9 inMap #4
Fit molecule 231107_N55H_MBCD100_46.pdb (#9) to map
N55H_MBCD_P76_J149_007_volume_map_sharp (#4) using 10164 atoms
average map value = 0.1139, steps = 128
shifted from previous position = 10.1
rotated from previous position = 15.9 degrees
atoms outside contour = 1730, contour level = 0.064171
Position of 231107_N55H_MBCD100_46.pdb (#9) relative to
N55H_MBCD_P76_J149_007_volume_map_sharp (#4) coordinates:
Matrix rotation and translation
0.50002530 0.86601078 -0.00017841 -62.03875912
-0.86601064 0.50002508 -0.00070034 231.82881648
-0.00051730 0.00050469 0.99999974 -0.02049358
Axis 0.00069574 0.00019566 -0.99999974
Axis point 169.75701519 169.64337069 0.00000000
Rotation angle (degrees) 59.99834196
Shift along axis 0.02269054
> select ::name="6OU"
2058 atoms, 2016 bonds, 42 residues, 2 models selected
> color sel gray
> select ::name="MC3"
2784 atoms, 2712 bonds, 72 residues, 2 models selected
> color sel dark gray
> color sel gray
> select ::name="6OU"
2058 atoms, 2016 bonds, 42 residues, 2 models selected
> color sel dark gray
> select ::name="PTY"
1632 atoms, 1596 bonds, 36 residues, 3 models selected
> color sel dark gray
> select ::name="CLR"
672 atoms, 744 bonds, 24 residues, 2 models selected
> color sel yellow
> select
56532 atoms, 57612 bonds, 24 pseudobonds, 4914 residues, 18 models selected
> color sel byhetero
> ribbon style thickness 0.6
> select clear
> show #!7 models
> select add #7
10512 atoms, 10836 bonds, 6 pseudobonds, 1188 residues, 2 models selected
> select add #8
22230 atoms, 22812 bonds, 12 pseudobonds, 2424 residues, 4 models selected
> hide #!8 models
> hide #!7 models
> hide #!9 models
> select add #9
32394 atoms, 33240 bonds, 18 pseudobonds, 3630 residues, 6 models selected
> ui tool show "Selection Inspector"
> setattr =sel p display false
Assigning display attribute to 18 items
> size =sel stickRadius 0.3
Changed 33240 bond radii
> show #!8 models
> select subtract #8
20676 atoms, 21264 bonds, 12 pseudobonds, 2394 residues, 4 models selected
> show #!7 models
> select subtract #9
10512 atoms, 10836 bonds, 6 pseudobonds, 1188 residues, 2 models selected
> hide #!8 models
> select clear
> ~clip
> select clear
> show #!9 models
> hide #!9 models
> select #7: 74-103
1578 atoms, 1632 bonds, 180 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 1
Assigning ss_type attribute to 180 items
> select clear
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> select ::name="6OU"::name="CLR"::name="MC3"::name="PTY"::name="Y01"
8154 atoms, 8112 bonds, 186 residues, 4 models selected
> show sel atoms
> select clear
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231011_All_Align_wo_POPE.cxs"
> morph #7,8,9
Computed 101 frame morph #6
> coordset #6 1,101
> close #6
> show #!9 models
> show #!8 models
> hide #!9 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231011_All_Align_wo_POPE.cxs"
——— End of log from Tue Nov 7 22:27:07 2023 ———
opened ChimeraX session
> show #!1 models
> hide #!8 models
> open
> C:/Users/OJS/Desktop/Phenix/230320_Cx43_WT_POPE_PIP2/RealSpaceRefine_107/231109_From104_real_space_refined_107.pdb
Chain information for 231109_From104_real_space_refined_107.pdb #6
---
Chain | Description
A B C D E F | No description available
> ui mousemode right "rotate selected models"
> select add #1
2 models selected
> select subtract #1
Nothing selected
> select add #6
11532 atoms, 11736 bonds, 6 pseudobonds, 1260 residues, 2 models selected
> view matrix models
> #6,0.13237,-0.68327,0.71806,140.72,0.26252,0.72273,0.63933,-106.4,-0.9558,0.10388,0.27504,267.98
> view matrix models
> #6,0.77882,-0.080654,0.62205,-54.769,-0.25429,-0.94715,0.19557,340.05,0.5734,-0.31049,-0.75816,254.9
> view matrix models
> #6,0.74151,-0.66956,-0.042972,164.72,-0.64662,-0.69608,-0.31202,450.47,0.17901,0.25916,-0.9491,257.7
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.74151,-0.66956,-0.042972,122.47,-0.64662,-0.69608,-0.31202,442.06,0.17901,0.25916,-0.9491,261.11
> view matrix models
> #6,0.74151,-0.66956,-0.042972,123.55,-0.64662,-0.69608,-0.31202,417.94,0.17901,0.25916,-0.9491,254.71
> view matrix models
> #6,0.74151,-0.66956,-0.042972,132.96,-0.64662,-0.69608,-0.31202,415.62,0.17901,0.25916,-0.9491,223.09
> view matrix models
> #6,0.74151,-0.66956,-0.042972,132.51,-0.64662,-0.69608,-0.31202,407.23,0.17901,0.25916,-0.9491,230.03
> hide sel atoms
> show sel cartoons
> ui tool show "Fit in Map"
> fitmap #6 inMap #1
Fit molecule 231109_From104_real_space_refined_107.pdb (#6) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11532 atoms
average map value = 0.07971, steps = 188
shifted from previous position = 2.87
rotated from previous position = 8.36 degrees
atoms outside contour = 8809, contour level = 0.15164
Position of 231109_From104_real_space_refined_107.pdb (#6) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.71748529 0.69480870 -0.04955538 181.17614317
-0.67278798 -0.70966171 -0.20913295 432.88561805
-0.18047496 -0.11670955 0.97663078 55.00374919
Axis 0.06712163 0.09507911 -0.99320423
Axis point 179.43580819 182.66068980 0.00000000
Rotation angle (degrees) 136.49032364
Shift along axis -1.31074062
> view matrix models
> #6,0.71432,-0.69811,0.048812,122.56,-0.67608,-0.70643,-0.20946,399.92,0.18071,0.11662,-0.9766,258.75
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.61384,-0.78772,0.051964,154.26,-0.76535,-0.60996,-0.20541,398,0.1935,0.086317,-0.9773,261.84
> view matrix models
> #6,0.61891,-0.78013,0.091404,145.31,-0.77448,-0.6255,-0.094467,383.05,0.13087,-0.012324,-0.99132,291.61
> view matrix models
> #6,0.60681,-0.79445,0.025187,161.21,-0.76988,-0.59533,-0.22992,400.51,0.19766,0.12013,-0.97288,254.64
> view matrix models
> #6,0.62666,-0.77592,0.072482,146.54,-0.75147,-0.6263,-0.20748,398.77,0.20638,0.075548,-0.97555,261.18
> fitmap #6 inMap #1
Fit molecule 231109_From104_real_space_refined_107.pdb (#6) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11532 atoms
average map value = 0.3568, steps = 176
shifted from previous position = 6.43
rotated from previous position = 15.9 degrees
atoms outside contour = 1929, contour level = 0.15164
Position of 231109_From104_real_space_refined_107.pdb (#6) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.50028589 0.86586026 0.00020476 107.56608506
-0.86586028 -0.50028590 -0.00001700 401.30148644
0.00008772 -0.00018580 0.99999998 0.01309877
Axis -0.00009748 0.00006758 -0.99999999
Axis point 169.58464230 169.61092630 0.00000000
Rotation angle (degrees) 120.01891703
Shift along axis 0.00353785
> fitmap #6 inMap #1
Fit molecule 231109_From104_real_space_refined_107.pdb (#6) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11532 atoms
average map value = 0.3568, steps = 24
shifted from previous position = 0.00614
rotated from previous position = 0.00953 degrees
atoms outside contour = 1932, contour level = 0.15164
Position of 231109_From104_real_space_refined_107.pdb (#6) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.50020698 0.86590587 0.00011095 107.56389557
-0.86590588 -0.50020696 -0.00011983 401.30796047
-0.00004827 -0.00015602 0.99999999 0.03112354
Axis -0.00002089 0.00009194 -1.00000000
Axis point 169.59760743 169.61152849 0.00000000
Rotation angle (degrees) 120.01369424
Shift along axis 0.00352389
> fitmap #6 inMap #1
Fit molecule 231109_From104_real_space_refined_107.pdb (#6) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11532 atoms
average map value = 0.3568, steps = 24
shifted from previous position = 0.000462
rotated from previous position = 0.00141 degrees
atoms outside contour = 1931, contour level = 0.15164
Position of 231109_From104_real_space_refined_107.pdb (#6) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.50018665 0.86591761 0.00011759 107.55777922
-0.86591762 -0.50018663 -0.00011681 401.30600788
-0.00004233 -0.00016025 0.99999999 0.03075263
Axis -0.00002509 0.00009234 -1.00000000
Axis point 169.59712637 169.61147556 0.00000000
Rotation angle (degrees) 120.01234886
Shift along axis 0.00360584
> select clear
> color #6 #ff5500ff
> color #6 #ff557fff
> mlp #!6
Map values for surface "231109_From104_real_space_refined_107.pdb_A SES
surface": minimum -26.99, mean 0.04315, maximum 26.26
Map values for surface "231109_From104_real_space_refined_107.pdb_B SES
surface": minimum -27.29, mean 0.03899, maximum 25.53
Map values for surface "231109_From104_real_space_refined_107.pdb_C SES
surface": minimum -26.49, mean 0.01245, maximum 23.7
Map values for surface "231109_From104_real_space_refined_107.pdb_D SES
surface": minimum -26.66, mean 0.07194, maximum 26.22
Map values for surface "231109_From104_real_space_refined_107.pdb_E SES
surface": minimum -28.05, mean -0.02388, maximum 25.33
Map values for surface "231109_From104_real_space_refined_107.pdb_F SES
surface": minimum -26.49, mean 0.05334, maximum 23.73
To also show corresponding color key, enter the above mlp command and add key
true
> select
> ::name="6OU"::name="CLR"::name="MC3"::name="PIO"::name="PTY"::name="Y01"
10068 atoms, 9954 bonds, 264 residues, 5 models selected
> show sel atoms
> color sel byhetero
> select clear
> select ::name="6OU"
2646 atoms, 2592 bonds, 54 residues, 3 models selected
> color sel gray
> color sel byhetero
> select clear
> hide #!1 models
> open
> C:/Users/OJS/Desktop/Phenix/230320_Cx43_WT_POPE_PIP2/RealSpaceRefine_108/231109_From104_plus6OU_real_space_refined_108.pdb
Chain information for 231109_From104_plus6OU_real_space_refined_108.pdb #10
---
Chain | Description
A B C D E F | No description available
> select add #10
11658 atoms, 11868 bonds, 6 pseudobonds, 1254 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> color #10 springgreen
> hide #!6 models
> show #!1 models
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.4459,-0.86958,-0.21212,429.28,-0.87295,0.37012,0.31775,200.1,-0.1978,0.32686,-0.92414,309.86
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.4459,-0.86958,-0.21212,387.11,-0.87295,0.37012,0.31775,180.43,-0.1978,0.32686,-0.92414,279.45
> view matrix models
> #10,-0.4459,-0.86958,-0.21212,390.28,-0.87295,0.37012,0.31775,173.95,-0.1978,0.32686,-0.92414,282.7
> ui tool show "Fit in Map"
> fitmap #10 inMap #1
Fit molecule 231109_From104_plus6OU_real_space_refined_108.pdb (#10) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11658 atoms
average map value = 0.07802, steps = 96
shifted from previous position = 2.75
rotated from previous position = 4.34 degrees
atoms outside contour = 9059, contour level = 0.15164
Position of 231109_From104_plus6OU_real_space_refined_108.pdb (#10) relative
to WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.38069495 0.90299489 0.19917720 -78.95055282
-0.90547157 0.32032996 0.27840604 227.36619818
0.18759681 -0.28633707 0.93958421 26.01609916
Axis -0.29807580 0.00611222 -0.95452263
Axis point 122.45512037 171.38612659 0.00000000
Rotation angle (degrees) 71.31865537
Shift along axis 0.09000606
> view matrix models
> #10,-0.38484,-0.90157,-0.19767,383.78,-0.90372,0.32453,0.27923,190.14,-0.18759,0.2861,-0.93966,291.92
> fitmap #10 inMap #1
Fit molecule 231109_From104_plus6OU_real_space_refined_108.pdb (#10) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11658 atoms
average map value = 0.3546, steps = 252
shifted from previous position = 6.91
rotated from previous position = 21.8 degrees
atoms outside contour = 2009, contour level = 0.15164
Position of 231109_From104_plus6OU_real_space_refined_108.pdb (#10) relative
to WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.49970300 0.86619679 0.00003886 -62.05998605
-0.86619679 0.49970300 0.00000325 231.75675355
-0.00001660 -0.00003529 0.99999999 0.00551060
Axis -0.00002225 0.00003202 -1.00000000
Axis point 169.59779534 169.60262675 0.00000000
Rotation angle (degrees) 60.01964719
Shift along axis 0.00329037
> fitmap #10 inMap #1
Fit molecule 231109_From104_plus6OU_real_space_refined_108.pdb (#10) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11658 atoms
average map value = 0.3546, steps = 24
shifted from previous position = 0.00432
rotated from previous position = 0.00495 degrees
atoms outside contour = 2016, contour level = 0.15164
Position of 231109_From104_plus6OU_real_space_refined_108.pdb (#10) relative
to WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.49977604 0.86615465 0.00004490 -62.06237052
-0.86615465 0.49977604 -0.00001452 231.73836261
-0.00003501 -0.00003164 0.99999999 0.00804593
Axis -0.00000988 0.00004613 -1.00000000
Axis point 169.60021437 169.60072652 0.00000000
Rotation angle (degrees) 60.01481554
Shift along axis 0.00325777
> fitmap #10 inMap #1
Fit molecule 231109_From104_plus6OU_real_space_refined_108.pdb (#10) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11658 atoms
average map value = 0.3546, steps = 24
shifted from previous position = 0.000227
rotated from previous position = 0.00209 degrees
atoms outside contour = 2018, contour level = 0.15164
Position of 231109_From104_plus6OU_real_space_refined_108.pdb (#10) relative
to WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.49979520 0.86614359 0.00007336 -62.06845979
-0.86614359 0.49979520 -0.00002054 231.73443048
-0.00005446 -0.00005328 0.99999998 0.01494287
Axis -0.00001890 0.00007379 -1.00000000
Axis point 169.59888920 169.60540510 0.00000000
Rotation angle (degrees) 60.01354820
Shift along axis 0.00332953
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> select
> ::name="6OU"::name="CLR"::name="MC3"::name="PIO"::name="PTY"::name="Y01"
12108 atoms, 11928 bonds, 336 residues, 6 models selected
> show sel atoms
> select ::name="6OU"
3528 atoms, 3456 bonds, 72 residues, 4 models selected
> color sel gray
> color sel byhetero
> select clear
> select add #10
11658 atoms, 11868 bonds, 6 pseudobonds, 1254 residues, 2 models selected
> ui tool show "Selection Inspector"
> setattr =sel p display false
Assigning display attribute to 6 items
> size =sel stickRadius 0.3
Changed 11868 bond radii
> show #!1 models
> mlp sel
Map values for surface "231109_From104_plus6OU_real_space_refined_108.pdb_A
SES surface": minimum -27.13, mean 0.04459, maximum 26.25
Map values for surface "231109_From104_plus6OU_real_space_refined_108.pdb_B
SES surface": minimum -27.26, mean 0.01529, maximum 25.51
Map values for surface "231109_From104_plus6OU_real_space_refined_108.pdb_C
SES surface": minimum -26.61, mean 0.0247, maximum 23.59
Map values for surface "231109_From104_plus6OU_real_space_refined_108.pdb_D
SES surface": minimum -26.58, mean 0.06535, maximum 26.34
Map values for surface "231109_From104_plus6OU_real_space_refined_108.pdb_E
SES surface": minimum -26.27, mean 0.001931, maximum 25.13
Map values for surface "231109_From104_plus6OU_real_space_refined_108.pdb_F
SES surface": minimum -26.63, mean 0.08962, maximum 23.51
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> select
79722 atoms, 81216 bonds, 36 pseudobonds, 7428 residues, 22 models selected
> hide sel surfaces
> select clear
> mlp #!10
Map values for surface "231109_From104_plus6OU_real_space_refined_108.pdb_A
SES surface": minimum -27.13, mean 0.04459, maximum 26.25
Map values for surface "231109_From104_plus6OU_real_space_refined_108.pdb_B
SES surface": minimum -27.26, mean 0.01529, maximum 25.51
Map values for surface "231109_From104_plus6OU_real_space_refined_108.pdb_C
SES surface": minimum -26.61, mean 0.0247, maximum 23.59
Map values for surface "231109_From104_plus6OU_real_space_refined_108.pdb_D
SES surface": minimum -26.58, mean 0.06535, maximum 26.34
Map values for surface "231109_From104_plus6OU_real_space_refined_108.pdb_E
SES surface": minimum -26.27, mean 0.001931, maximum 25.13
Map values for surface "231109_From104_plus6OU_real_space_refined_108.pdb_F
SES surface": minimum -26.63, mean 0.08962, maximum 23.51
To also show corresponding color key, enter the above mlp command and add key
true
> volume #1 level 0.198
> volume #1 level 0.164
> surface dust #1 size 8.48
> show #!6 models
> select add #6
11532 atoms, 11736 bonds, 6 pseudobonds, 1260 residues, 2 models selected
> select add #10
23190 atoms, 23604 bonds, 12 pseudobonds, 2514 residues, 10 models selected
> close #6
> close #10
> hide #!1 models
> show #!8 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231011_All_Align_wo_POPE.cxs"
> show #!9 models
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!8 models
> show #!8 models
> show #!7 models
> hide #!8 models
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231109_WT_PIP2_109.pdb"
Chain information for 231109_WT_PIP2_109.pdb #6
---
Chain | Description
A B C D E F | No description available
> color #6 #ff557fff
> color #6 #ff007fff
> color #6 #ff557fff
> select add #6
11658 atoms, 11868 bonds, 6 pseudobonds, 1254 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> ui mousemode right "rotate selected models"
> color #6 #ff557fff
> view matrix models
> #6,0.26097,0.9267,-0.27041,14.791,0.94973,-0.19629,0.24389,-0.23198,0.17293,-0.32046,-0.93134,357.98
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.26097,0.9267,-0.27041,-28.919,0.94973,-0.19629,0.24389,-16.343,0.17293,-0.32046,-0.93134,338.77
> view matrix models
> #6,0.26097,0.9267,-0.27041,-23.946,0.94973,-0.19629,0.24389,-30.565,0.17293,-0.32046,-0.93134,342.72
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.10939,0.97803,0.17743,-84.151,0.9828,-0.079712,-0.16656,14.814,-0.14875,0.1926,-0.96994,316.92
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.10939,0.97803,0.17743,-79.462,0.9828,-0.079712,-0.16656,20.055,-0.14875,0.1926,-0.96994,303.89
> view matrix models
> #6,0.10939,0.97803,0.17743,-80.805,0.9828,-0.079712,-0.16656,14.15,-0.14875,0.1926,-0.96994,308.76
> view matrix models
> #6,0.10939,0.97803,0.17743,-81.122,0.9828,-0.079712,-0.16656,14.141,-0.14875,0.1926,-0.96994,308.59
> fitmap #6 inMap #1
Fit molecule 231109_WT_PIP2_109.pdb (#6) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11658 atoms
average map value = 0.07403, steps = 76
shifted from previous position = 2.43
rotated from previous position = 3.87 degrees
atoms outside contour = 9248, contour level = 0.16402
Position of 231109_WT_PIP2_109.pdb (#6) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.11341985 -0.98690128 -0.11472486 377.23606203
0.97790726 -0.09048019 -0.18844286 54.62798157
0.17559417 -0.13356344 0.97536018 -7.17037806
Axis 0.02762063 -0.14611662 0.98888171
Axis point 164.39853407 196.89912116 0.00000000
Rotation angle (degrees) 96.56151736
Shift along axis -4.65321313
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.36336,0.91529,0.17379,-112.36,0.93147,-0.35328,-0.086948,55.657,-0.018187,0.19347,-0.98094,285.85
> fitmap #6 inMap #1
Fit molecule 231109_WT_PIP2_109.pdb (#6) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11658 atoms
average map value = 0.3534, steps = 140
shifted from previous position = 5.55
rotated from previous position = 14.4 degrees
atoms outside contour = 2342, contour level = 0.16402
Position of 231109_WT_PIP2_109.pdb (#6) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.49983934 -0.86611812 0.00015051 401.24689018
0.86611813 -0.49983935 0.00000125 107.47907192
0.00007415 0.00013098 0.99999998 -0.03909655
Axis 0.00007489 0.00004408 1.00000000
Axis point 169.59026523 169.59434710 0.00000000
Rotation angle (degrees) 119.98937251
Shift along axis -0.00430798
> select clear
> hide #!7 models
> show #!9 models
> select clear
> select add #6
11658 atoms, 11868 bonds, 6 pseudobonds, 1254 residues, 2 models selected
> ui tool show "Selection Inspector"
> setattr =sel p display false
Assigning display attribute to 6 items
> size =sel stickRadius 0.3
Changed 11868 bond radii
> select clear
> select
68190 atoms, 69480 bonds, 30 pseudobonds, 6168 residues, 20 models selected
> ribbon style thickness 0.6
> select clear
> graphics silhouettes true width 2.5
> graphics silhouettes true width 2
> select clear
> lighting soft
> graphics silhouettes true width 1
> graphics silhouettes true width 1.5
> graphics silhouettes true width 2
> select clear
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231011_All_Align_wo_POPE.cxs"
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/MBCD/MBCD_Align.cxs"
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 38395 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> view orient
> turn x 90
[Repeated 2 time(s)]
> select #7,8,9
32394 atoms, 33240 bonds, 18 pseudobonds, 3630 residues, 6 models selected
> select #7,8,9/b,c,e,f
21596 atoms, 22160 bonds, 12 pseudobonds, 2420 residues, 6 models selected
> hide sel ribbons
> turn y 10
[Repeated 13 time(s)]
> select clear
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/MBCD/a_Align.cxs"
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> hide #!9 models
> show #!8 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> select #7,8,0/b,c,e,f
14820 atoms, 15208 bonds, 8 pseudobonds, 1616 residues, 4 models selected
> hide sel atoms
> hide #!8 models
> show #!7 models
> show #!8 models
> show #!9 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> hide #!9 models
> lighting soft
[Repeated 1 time(s)]
> show #!8 models
> show #!9 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> show #!8 models
> select add #7
18324 atoms, 18820 bonds, 10 pseudobonds, 2012 residues, 4 models selected
> select add #8
22230 atoms, 22812 bonds, 12 pseudobonds, 2424 residues, 4 models selected
> select subtract #8
10512 atoms, 10836 bonds, 6 pseudobonds, 1188 residues, 2 models selected
> select subtract #7
Nothing selected
> view name 1
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/MBCD/a_Align.cxs"
> hide #!8 models
> show #!9 models
> select ::name="MC3"
3288 atoms, 3180 bonds, 108 residues, 3 models selected
> color sel black
> select clear
> select ::name="MC3"
3288 atoms, 3180 bonds, 108 residues, 3 models selected
> color sel dark gray
> color sel light gray
> select clear
> color sel white
> select ::name="MC3"
3288 atoms, 3180 bonds, 108 residues, 3 models selected
> color sel white
> select clear
> select ::name="MC3"
3288 atoms, 3180 bonds, 108 residues, 3 models selected
> color sel cyan
> color sel orange
> select clear
> select ::name="6OU"
2940 atoms, 2880 bonds, 60 residues, 3 models selected
> color sel orange
> color sel byhetero
> select ::name="PTY"
2028 atoms, 1980 bonds, 48 residues, 4 models selected
> color sel orange
> color sel byhetero
> select ::name="MC3"
3288 atoms, 3180 bonds, 108 residues, 3 models selected
> color sel gray
> select clear
> show #!7 models
> hide #!9 models
> show #!8 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!1 models
> hide #!1 models
> show #!6 models
> select #6/b,c,e,f
7772 atoms, 7912 bonds, 4 pseudobonds, 836 residues, 2 models selected
> hide sel ribbons
> select
> ::name="6OU"::name="CLR"::name="MC3"::name="PIO"::name="PTY"::name="Y01"
10194 atoms, 10086 bonds, 258 residues, 5 models selected
> show sel atoms
> select #6/b,c,e,f
7772 atoms, 7912 bonds, 4 pseudobonds, 836 residues, 2 models selected
> hide sel atoms
> select ::name="PIO"
258 atoms, 258 bonds, 6 residues, 1 model selected
> color sel dark green
> color sel byhetero
> select clear
> view 1
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/MBCD/1a_Align.cxs"
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!7 models
> view 1
> turn x 90
[Repeated 5 time(s)]
> show #!8 models
> hide #!8 models
> select #6,7,8,9/b,c,e,f
29368 atoms, 30072 bonds, 16 pseudobonds, 3256 residues, 8 models selected
> hide sel atoms
> turn x 90
[Repeated 4 time(s)]
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/MBCD/a_Align.cxs"
——— End of log from Thu Nov 9 05:24:54 2023 ———
opened ChimeraX session
> show #!9 models
> show #!8 models
> show #!6 models
> show #!7 models
> select add #6
33254 atoms, 34028 bonds, 18 pseudobonds, 3674 residues, 8 models selected
> select add #7
36758 atoms, 37640 bonds, 20 pseudobonds, 4070 residues, 8 models selected
> select add #8
40664 atoms, 41632 bonds, 22 pseudobonds, 4482 residues, 8 models selected
> select add #9
44052 atoms, 45108 bonds, 24 pseudobonds, 4884 residues, 8 models selected
> select subtract #8
32334 atoms, 33132 bonds, 18 pseudobonds, 3648 residues, 6 models selected
> select subtract #7
21822 atoms, 22296 bonds, 12 pseudobonds, 2460 residues, 4 models selected
> select subtract #6
10164 atoms, 10428 bonds, 6 pseudobonds, 1206 residues, 2 models selected
> select subtract #9
Nothing selected
> turn x 90
> select clear
> hide #!7 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> hide #!9 models
> view 1
> show #!2 models
> hide #!2 models
> show #!2 models
> clip front 0
> clip back 0
clip back plane is in front of front plane
> clip back 1
[Repeated 1 time(s)]
> clip front -1
[Repeated 5 time(s)]
> hide #!7 models
> show #!7 models
> ~clip
> view 1
> volume zone #4 nearAtoms #7/a,d
> volume zone #2 nearAtoms #7/a,d
> transparency 50
> transparency 80
> transparency 90
> view 1
> transparency 50
> transparency 20
> transparency 75
> ~clip
> ~zone
Unknown command: ~zone
> unzone
Unknown command: unzone
> ~zone
Unknown command: ~zone
> ~volume zome
Unknown command: ~volume zome
> ~volume zone
Unknown command: ~volume zone
> zone clear
> clear zone
Unknown command: clear zone
> volume #2 level 0.1237
> volume #2 level 0.09867
> view 1
> hide #!2 models
> show #!2 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!3 models
> show #!2 models
> volume zone #2 nearAtoms #7/a,d:300-360
[Repeated 1 time(s)]
> select clear
> volume #2 level 0.09867
> select clear
> view 1
> select clear
> view 1
[Repeated 1 time(s)]
> hide #!2 models
> hide #!7 models
> show #!3 models
> show #!8 models
> volume zone #3 nearAtoms #8/a,d:300-360
> volume #3 level 0.1267
> select clear
> view 1
> hide #!8 models
> hide #!3 models
> show #!4 models
> show #!9 models
> volume zone #4 nearAtoms #9/a,d:300-360
[Repeated 1 time(s)]
> volume #4 level 0.05053
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/MBCD/b_lipids_position.cxs"
> select #7,8,9/a,d:30
66 atoms, 66 bonds, 6 residues, 3 models selected
> show sel atoms
> select clear
> select #7,8,9/a,d:30
66 atoms, 66 bonds, 6 residues, 3 models selected
> color sel magenta
> select clear
> view 1
> volume zone #4 nearAtoms #9/a,d:300-360
> volume zone #4 nearAtoms #9/a,d:300-360 range 3
> volume zone #4 nearAtoms #9/a,d:300-360 range 5
> volume zone #4 nearAtoms #9/a,d:300-360 range 4
> volume zone #4 nearAtoms #9/a,d:300-360 range 2
> volume zone #4 nearAtoms #9/a,d:300-360 range 3
> volume zone #4 nearAtoms #9/a,d:300-360 range 2.5
[Repeated 2 time(s)]
> hide #!9 models
> show #!8 models
> hide #!4 models
> show #!3 models
> volume zone #3 nearAtoms #8/a,d:300-360 range 2.5
[Repeated 1 time(s)]
> hide #!3 models
> show #!2 models
> hide #!8 models
> show #!7 models
> volume zone #2 nearAtoms #7/a,d:300-360 range 2.5
[Repeated 1 time(s)]
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> hide #!7 models
> hide #!2 models
> show #!7 models
> show #!8 models
> show #!9 models
> view name 1
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/MBCD/b_lipids_position.cxs"
——— End of log from Thu Nov 9 07:14:57 2023 ———
opened ChimeraX session
> show #!2 models
> hide #!8 models
> hide #!9 models
> volume #2 level 0.0705
> show #!8 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!2 models
> show #!3 models
> volume #3 level 0.1335
> hide #!3 models
> show #!4 models
> hide #!8 models
> show #!9 models
> volume #4 level 0.05053
> volume #4 level 0.07251
> volume #4 level 0.0672
> volume #4 level 0.05129
> volume #4 level 0.05735
> volume #4 level 0.06569
> volume #4 level 0.06341
> volume zone #4 nearAtoms #7/a,d:300-360 range 3
> volume zone #4 nearAtoms #9/a,d:300-360 range 3
[Repeated 1 time(s)]
> volume zone #4 nearAtoms #9/a,d:300-360 range 3.5
> volume zone #4 nearAtoms #9/a,d:300-360 range 3
> volume zone #4 nearAtoms #9/a,d:300-360 range 2.5
[Repeated 2 time(s)]
> volume #4 level 0.06
> volume #4 level 0.07
> volume #4 level 0.05
> volume #4 level 0.04
> volume #4 level 0.055
> volume #4 level 0.052
> volume #4 level 0.053
> volume #4 level 0.056
> volume #4 level 0.057
> volume #4 level 0.058
> volume #4 level 0.056
> volume #4 level 0.054
> volume #4 level 0.055
> volume zone #4 nearAtoms #9/a,d:300-360 range 3
[Repeated 1 time(s)]
> volume zone #4 nearAtoms #9/a,d:300-360 range 4
> volume zone #4 nearAtoms #9/a,d:300-360 range 3
[Repeated 2 time(s)]
> volume zone #4 nearAtoms #9/a,d:300-360 range 1
> volume zone #4 nearAtoms #9/a,d:300-360 range 2
> volume zone #4 nearAtoms #9/a,d:300-360 range 3
> volume zone #4 nearAtoms #9/a,d:300-360 range 2
> volume #4 level 0.0459
> volume zone #4 nearAtoms #9/a,d:300-360 range 2.5
> volume #4 level 0.05348
> volume #4 level 0.04894
> volume #4 level 0.05197
> volume #4 level 0.05348
> view 1
[Repeated 1 time(s)]
> hide #!4 models
> show #!3 models
> show #!8 models
> hide #!9 models
> show #!7 models
> hide #!8 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> hide #!7 models
> show #!8 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/MBCD/b_lipids_position.cxs"
> volume #3 level 0.1542
> volume #3 level 0.09919
> volume #3 level 0.08545
> volume zone #3 nearAtoms #8/a,d:300-360 range 1
> volume zone #3 nearAtoms #8/a,d:300-360 range 2
> volume #3 level 0.08545
> volume zone #3 nearAtoms #8/a,d:300-360 range 2.2
> volume zone #3 nearAtoms #8/a,d:300-360 range 2.3
> volume zone #3 nearAtoms #8/a,d:300-360 range 2.1
> volume #3 level 0.09919
> volume zone #3 nearAtoms #8/a,d:300-360 range 2
[Repeated 2 time(s)]
> select clear
> volume #3 level 0.0717
> volume zone #3 nearAtoms #8/a,d:300-360 range 1.5
> volume zone #3 nearAtoms #8/a,d:300-360 range 1.8
> volume zone #3 nearAtoms #8/a,d:300-360 range 2.2
> volume zone #3 nearAtoms #8/a,d:300-360 range 2
> volume zone #3 nearAtoms #8/a,d:300-360 range 2.5
> volume #3 level 0.1198
> volume zone #3 nearAtoms #8/a,d:300-360 range 2.2
> volume zone #3 nearAtoms #8/a,d:300-360 range 2.3
> volume zone #3 nearAtoms #8/a,d:300-360 range 2.1
> volume #3 level 0.09919
> hide #!8 models
> hide #!3 models
> show #!2 models
> show #!7 models
> volume zone #2 nearAtoms #7/a,d:300-360 range 2.1
[Repeated 1 time(s)]
> volume zone #2 nearAtoms #7/a,d:300-360 range 2.2
[Repeated 1 time(s)]
> volume zone #2 nearAtoms #7/a,d:300-360 range 2.5
> volume zone #2 nearAtoms #7/a,d:300-360 range 2.3
> volume zone #2 nearAtoms #7/a,d:300-360 range 2.5
[Repeated 2 time(s)]
> volume zone #2 nearAtoms #7/a,d:300-360 range 2.2
> volume zone #2 nearAtoms #7/a,d:300-360 range 2.1
> volume zone #2 nearAtoms #7/a,d:300-360 range 2
[Repeated 2 time(s)]
> volume zone #2 nearAtoms #7/a,d:300-360 range 2.5
> volume zone #2 nearAtoms #7/a,d:300-360 range 3
> volume zone #2 nearAtoms #7/a,d:300-360 range 2
> volume #2 level 0.07989
> volume #2 level 0.0705
> volume zone #2 nearAtoms #7/a,d:300-360 range 2.5
> volume #2 level 0.0705
> volume #2 level 0.07989
> volume #2 level 0.09241
> volume zone #2 nearAtoms #7/a,d:30,300-360 range 2.5
> volume #2 level 0.07989
> volume zone #2 nearAtoms #7/a,d:30,300-360 range 2
> volume #2 level 0.05171
> volume zone #2 nearAtoms #7/a,d:30,300-360 range 1.5
> volume #2 level 0.07676
> volume zone #2 nearAtoms #7/a,d:30,300-360 range 2
> volume #2 level 0.07989
> volume zone #2 nearAtoms #7/a,d:30,300-360 range 2.5
> volume zone #2 nearAtoms #7/a,d:30,300-360 range 2.6
> volume zone #2 nearAtoms #7/a,d:30,300-360 range 2.7
> volume zone #2 nearAtoms #7/a,d:30,300-360 range 2.8
> volume zone #2 nearAtoms #7/a,d:30,300-360 range 2.9
> volume zone #2 nearAtoms #7/a,d:30,300-360 range 3
[Repeated 1 time(s)]
> volume #2 level 0.09554
> volume zone #2 nearAtoms #7/a,d:30,300-360 range 2
[Repeated 2 time(s)]
> volume #2 level 0.07989
> volume zone #2 nearAtoms #7/a,d:30,300-360 range 2.5
> hide #!2 models
> show #!3 models
> hide #!7 models
> show #!8 models
> volume zone #3 nearAtoms #8/a,d:30,300-360 range 2.5
[Repeated 1 time(s)]
> volume #3 level 0.1198
> volume zone #3 nearAtoms #8/a,d:30,300-360 range 2
[Repeated 1 time(s)]
> volume zone #3 nearAtoms #8/a,d:30,300-360 range 2.2
> volume zone #3 nearAtoms #8/a,d:30,300-360 range 2.3
> volume zone #3 nearAtoms #8/a,d:30,300-360 range 2.5
> volume zone #3 nearAtoms #8/a,d:30,300-360 range 3
> volume zone #3 nearAtoms #8/a,d:30,300-360 range 2.5
> volume #3 level 0.1542
> hide #!3 models
> show #!4 models
> hide #!8 models
> show #!9 models
> volume zone #4 nearAtoms #9/a,d:30,300-360 range 2.5
> volume #4 level 0.04211
> volume zone #4 nearAtoms #9/a,d:30,300-360 range 2
> volume zone #4 nearAtoms #9/a,d:30,300-360 range 3
> volume zone #4 nearAtoms #9/a,d:30,300-360 range 2
> .5
Unknown command: .5
> volume zone #4 nearAtoms #9/a,d:30,300-360 range 2.5
[Repeated 1 time(s)]
> volume #4 level 0.04894
> volume #4 level 0.04969
> volume #4 level 0.05197
> volume #4 level 0.07622
> volume #4 level 0.05652
> volume zone #4 nearAtoms #9/a,d:2-5,30,300-360 range 2.5
> volume zone #4 nearAtoms #9/a,d:30,300-360 range 2.5
> view 1
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/MBCD/b_lipids_position.cxs"
> hide #!4 models
> show #!3 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!3 models
> show #!2 models
> show #!8 models
> hide #!7 models
> show #!3 models
> hide #!2 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/MBCD/b_lipids_position.cxs"
> turn x 180
> save "C:/Users/OJS/OneDrive - korea.ac.kr/MCSB/논문/230801_Re/MBCD/c_F30.cxs"
——— End of log from Thu Nov 9 08:38:33 2023 ———
opened ChimeraX session
> hide #!3 models
> show #!2 models
> hide #!2 models
> view 1
> turn y 10
[Repeated 2 time(s)]
> select #7,8,9/d
5399 atoms, 5540 bonds, 3 pseudobonds, 605 residues, 6 models selected
> hide sel ribbons
> hide sel atoms
> select clear
> turn y 10
[Repeated 5 time(s)]
> view 1
> turn y 90
> show #!3 models
> hide #!3 models
> volume zone #3 nearAtoms #8/d:30,306 range 2.5
> show #!3 models
> volume zone #3 nearAtoms #8/a:30,306 range 2.5
> select clear
> volume zone #3 nearAtoms #8/a:30,306 range 2.4
> volume zone #3 nearAtoms #8/a:30,306 range 2.3
[Repeated 1 time(s)]
> volume zone #3 nearAtoms #8/a:30,306 range 2.2
> volume zone #3 nearAtoms #8/a:30,306 range 2.1
> volume zone #3 nearAtoms #8/a:30,306 range 2.
> volume zone #3 nearAtoms #8/a:30,306 range 2.2
> volume zone #3 nearAtoms #8/a:30,306 range 2.4
> volume zone #3 nearAtoms #8/a:30,306 range 2.5
> save "C:/Users/OJS/OneDrive - korea.ac.kr/MCSB/논문/230801_Re/MBCD/c_F30.cxs"
——— End of log from Thu Nov 9 16:49:07 2023 ———
opened ChimeraX session
> view 2
Expected an objects specifier or a view name or a keyword
> view 1
> turn y 90
> view 2
Expected an objects specifier or a view name or a keyword
> view 1
> turn x 90
[Repeated 1 time(s)]
> view 1
> turn y 90
> show #!7 models
> hide #!8 models
> hide #!3 models
> show #!2 models
> volume zone #2 nearAtoms #7/a:30,305 range 2.5
> volume #2 level 0.0705
> volume zone #2 nearAtoms #7/a:30,305 range 2.4
> volume zone #2 nearAtoms #7/a:30,305 range 2.3
> volume zone #2 nearAtoms #7/a:30,305 range 2.2
> hide #!7 models
> show #!8 models
> hide #!2 models
> show #!3 models
> volume #3 level 0.1816
> volume zone #3 nearAtoms #8/a:30,306 range 2.2
[Repeated 1 time(s)]
> volume #3 level 0.1679
> hide #!8 models
> show #!9 models
> hide #!3 models
> show #!4 models
> volume zone #4 nearAtoms #9/a:30,302 range 2.2
> volume zone #4 nearAtoms #9/a:30,302 range 2.5
> volume zone #4 nearAtoms #9/a:30,302 range 3
> volume zone #4 nearAtoms #9/a:30,302 range 2.7
> volume zone #4 nearAtoms #9/a:30,302 range 2.6
> volume zone #4 nearAtoms #9/a:30,302 range 2.5
> select clear
> save "C:/Users/OJS/OneDrive - korea.ac.kr/MCSB/논문/230801_Re/MBCD/c_F30.cxs"
> view 2
Expected an objects specifier or a view name or a keyword
> view 1
> turn y 90
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!9 models
> show #!8 models
> select #8/d
1953 atoms, 1996 bonds, 1 pseudobond, 206 residues, 2 models selected
> select #8/a
1953 atoms, 1996 bonds, 1 pseudobond, 206 residues, 2 models selected
> select #8/a:227
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231109_N55H_MBCD10_49.pdb"
Chain information for 231109_N55H_MBCD10_49.pdb #10
---
Chain | Description
A B C D E F | No description available
> color #10 cyan
> select add #10
11730 atoms, 11976 bonds, 6 pseudobonds, 1248 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 9684 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> close #8
> show #!10 models
> rename #10 id #8
> ui tool show "Selection Inspector"
> setattr =sel p display false
Assigning display attribute to 6 items
> size =sel stickRadius 0.3
Changed 11976 bond radii
> select clear
> view 1
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/MBCD/a_Align.cxs"
> show #!7 models
> hide #!8 models
> view 1
> show #!9 models
> hide #!7 models
> show #!4 models
> show #!2 models
> show #!1 models
> show #!6 models
> show #!7 models
> show #!8 models
> view orient
> turn x 90
[Repeated 2 time(s)]
> hide #!1 models
> hide #!2 models
> hide #!4 models
> hide #!3 models
> hide #!6 models
> hide #!8 models
> hide #!9 models
> hide #!7 models
> show #!7 models
> select #6,7,8,9/a,b,c,d,e
36720 atoms, 37590 bonds, 20 pseudobonds, 4080 residues, 8 models selected
> select #6,7,8,9/a,b,c,e,f
36720 atoms, 37590 bonds, 20 pseudobonds, 4080 residues, 8 models selected
> hide sel ribbons
> hide sel atoms
> select
> ::name="6OU"::name="CLR"::name="HOH"::name="MC3"::name="PIO"::name="PTY"::name="Y01"
10206 atoms, 10086 bonds, 270 residues, 5 models selected
> show sel atoms
> select #6,7,8,9/d:30
44 atoms, 44 bonds, 4 residues, 4 models selected
> show sel atoms
> select clear
> select #6,7,8,9/a,b,c,e,f
36720 atoms, 37590 bonds, 20 pseudobonds, 4080 residues, 8 models selected
> hide sel atoms
> select clear
> save "C:/Users/OJS/OneDrive - korea.ac.kr/MCSB/논문/230801_Re/MBCD/c_F30.cxs"
> hide #!7 models
> show #!7 models
> show #!6 models
> hide #!7 models
> show #!7 models
> show #!6-7 atoms
> view 1
> hide #!6-7 atoms
> select #6,7,8,9
44064 atoms, 45108 bonds, 24 pseudobonds, 4896 residues, 8 models selected
> select #6,7,8,9/a,d
14688 atoms, 15036 bonds, 8 pseudobonds, 1632 residues, 8 models selected
> show sel ribbons
> select clear
> select
> ::name="6OU"::name="CLR"::name="HOH"::name="MC3"::name="PIO"::name="PTY"::name="Y01"
10206 atoms, 10086 bonds, 270 residues, 5 models selected
> show sel atoms
> select clear
> hide #!7 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!8 models
> select ::name="HOH"
12 atoms, 12 residues, 1 model selected
> color sel red
> view 1
> select ::name="HOH"
12 atoms, 12 residues, 1 model selected
> hide sel atoms
> select ::name="MC3"
3288 atoms, 3180 bonds, 108 residues, 3 models selected
> select ::name="6OU"
2940 atoms, 2880 bonds, 60 residues, 3 models selected
> color sel orange
> color sel byhetero
> select #8
11730 atoms, 11976 bonds, 6 pseudobonds, 1248 residues, 2 models selected
> color sel byhetero
> select ::name="PTY"
2028 atoms, 1980 bonds, 48 residues, 4 models selected
> color sel orange
> color sel byhetero
> select ::name="CLR"
672 atoms, 744 bonds, 24 residues, 2 models selected
> color sel yellow
> color sel byhetero
> select clear
> ui tool show "Model Panel"
> view 1
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/MBCD/a_Align.cxs"
[Repeated 1 time(s)]
> save "C:/Users/OJS/OneDrive - korea.ac.kr/MCSB/논문/230801_Re/MBCD/c_F30.cxs"
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> select #7,8,9/b,c,e,f
21604 atoms, 22160 bonds, 12 pseudobonds, 2428 residues, 6 models selected
> hide sel atoms
> select clear
> save "C:/Users/OJS/OneDrive - korea.ac.kr/MCSB/논문/230801_Re/MBCD/c_F30.cxs"
> select #7,8,9:30
198 atoms, 198 bonds, 18 residues, 3 models selected
> color sel magenta
> select clear
> select #7,8,9:30
198 atoms, 198 bonds, 18 residues, 3 models selected
> show sel atoms
> select #7,8,9/b,c,e,f
21604 atoms, 22160 bonds, 12 pseudobonds, 2428 residues, 6 models selected
> hide sel atoms
> save "C:/Users/OJS/OneDrive - korea.ac.kr/MCSB/논문/230801_Re/MBCD/c_F30.cxs"
> view 1
[Repeated 1 time(s)]
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!7 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume zone #2 nearAtoms #7/a:30,305 range 2.2
[Repeated 1 time(s)]
> hide #!2 models
> show #!3 models
> hide #!7 models
> show #!4 models
> hide #!3 models
> show #!9 models
> hide #!4 models
> show #!3 models
> show #!8 models
> hide #!9 models
> hide #!3 models
> volume zone #3 nearAtoms #8/a:30,227,306 range 2.2
> show #!3 models
> select #8/a,d:227
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> close #8
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!7 models
> view 1
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/MBCD/a_Align.cxs"
> view 1
> show #!1 models
> hide #!1 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> turn y 10
> turn y -10
[Repeated 1 time(s)]
> turn x 90
> turn z 1
[Repeated 2 time(s)]
> turn x 90
[Repeated 2 time(s)]
> view 1
> turn x 90
> view 1
> select clear
> turn z 1
[Repeated 2 time(s)]
> turn z -1
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!7 models
> show #!2 models
> hide #!2 models
> show #!1 models
> turn x 90
[Repeated 2 time(s)]
> view orient
[Repeated 2 time(s)]
> show #!2 models
> show #!3 models
> show #!4 models
> view orient
[Repeated 3 time(s)]
> show #!5 models
> view orient
[Repeated 4 time(s)]
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!5 models
> show #!6 models
> show #!7 models
> show #!9 models
> show #!27 models
> hide #!1 models
> hide #!27 models
> view orient
[Repeated 2 time(s)]
> turn x 90
[Repeated 2 time(s)]
> hide #!9 models
> hide #!7 models
> turn y 10
[Repeated 12 time(s)]
> view 1
> hide #!6 models
> show #!6 models
> turn x 90
> turn z 1
> turn z -1
[Repeated 8 time(s)]
> turn z 1
> turn x 90
[Repeated 2 time(s)]
> view name 2
> view 1
> view 2
> view 1
> view 2
> view 1
> view 2
> view 1
> view name 3
> view 2
> view 3
> view 2
> view 3
> view 2
> turn x 90
> view 3
> turn x 90
> view 1
> turn x 90
> view orient
[Repeated 6 time(s)]
> view 1
> hide #!6 models
> show #!7 models
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231109_N55H_MBCD10_52.pdb"
Chain information for 231109_N55H_MBCD10_52.pdb #8
---
Chain | Description
A B C D E F | No description available
> color #8 cyan
> hide #!7-8 atoms
> show #!7-8 cartoons
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 9684 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select clear
> select add #8
11718 atoms, 11976 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> ui tool show "Selection Inspector"
> setattr =sel p display false
Assigning display attribute to 6 items
> size =sel stickRadius 0.3
Changed 11976 bond radii
> hide #!8 models
> hide #!7 models
> show #!7 models
> show #!8 models
> select clear
> hide #!7 models
> select ::name="6OU"
2940 atoms, 2880 bonds, 60 residues, 3 models selected
> color sel orange
> select ::name="CLR"
672 atoms, 744 bonds, 24 residues, 2 models selected
> color sel yellow
> select ::name="PTY"
2028 atoms, 1980 bonds, 48 residues, 4 models selected
> color sel orange
> select
68190 atoms, 69480 bonds, 30 pseudobonds, 6168 residues, 20 models selected
> color sel byhetero
> select #8
11718 atoms, 11976 bonds, 6 pseudobonds, 1236 residues, 2 models selected
> style sel stick
Changed 11718 atom styles
> select clear
> ui tool show "Fit in Map"
> fitmap #8 inMap #3
Fit molecule 231109_N55H_MBCD10_52.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5192, steps = 36
shifted from previous position = 0.00599
rotated from previous position = 0.00869 degrees
atoms outside contour = 1479, contour level = 0.1679
Position of 231109_N55H_MBCD10_52.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00013403 0.00001380 0.01643959
0.00013403 0.99999999 -0.00006972 -0.00243968
-0.00001379 0.00006972 1.00000000 -0.00600491
Axis 0.45955465 0.09094620 0.88348079
Axis point 19.58852543 115.70431409 0.00000000
Rotation angle (degrees) 0.00869201
Shift along axis 0.00202779
> fitmap #8 inMap #3
Fit molecule 231109_N55H_MBCD10_52.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5192, steps = 24
shifted from previous position = 0.00605
rotated from previous position = 0.00409 degrees
atoms outside contour = 1484, contour level = 0.1679
Position of 231109_N55H_MBCD10_52.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00012403 0.00008097 -0.00036396
0.00012403 0.99999999 -0.00004795 -0.00567708
-0.00008096 0.00004796 1.00000000 0.00664741
Axis 0.30801939 0.52004570 0.79666588
Axis point 55.12496475 -8.48062774 0.00000000
Rotation angle (degrees) 0.00892034
Shift along axis 0.00223132
> fitmap #8 inMap #3
Fit molecule 231109_N55H_MBCD10_52.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5192, steps = 24
shifted from previous position = 0.00645
rotated from previous position = 0.00454 degrees
atoms outside contour = 1478, contour level = 0.1679
Position of 231109_N55H_MBCD10_52.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00012747 0.00010201 -0.00502389
0.00012747 0.99999999 0.00002828 -0.02314497
-0.00010201 -0.00002827 0.99999999 0.01979076
Axis -0.17063233 0.61564565 0.76932766
Axis point 190.42711939 -36.97704378 0.00000000
Rotation angle (degrees) 0.00949339
Shift along axis 0.00183371
> fitmap #8 inMap #3
Fit molecule 231109_N55H_MBCD10_52.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5192, steps = 24
shifted from previous position = 0.00178
rotated from previous position = 0.00118 degrees
atoms outside contour = 1477, contour level = 0.1679
Position of 231109_N55H_MBCD10_52.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00012766 0.00009664 -0.00370260
0.00012766 0.99999999 0.00004820 -0.02771583
-0.00009665 -0.00004819 0.99999999 0.02171490
Axis -0.28820347 0.57799200 0.76345531
Axis point 224.47142815 -25.35513328 0.00000000
Rotation angle (degrees) 0.00958058
Shift along axis 0.00162593
> show #!7 models
> hide #!7 models
> fitmap #8 inMap #3
Fit molecule 231109_N55H_MBCD10_52.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5192, steps = 24
shifted from previous position = 0.00097
rotated from previous position = 0.00061 degrees
atoms outside contour = 1476, contour level = 0.1679
Position of 231109_N55H_MBCD10_52.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00012720 0.00009194 -0.00265577
0.00012719 0.99999999 0.00005773 -0.02988222
-0.00009194 -0.00005772 0.99999999 0.02240136
Axis -0.34520647 0.54979793 0.76062786
Axis point 241.53609750 -16.75914610 0.00000000
Rotation angle (degrees) 0.00958118
Shift along axis 0.00152670
> fitmap #8 inMap #3
Fit molecule 231109_N55H_MBCD10_52.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5192, steps = 24
shifted from previous position = 0.000903
rotated from previous position = 0.000568 degrees
atoms outside contour = 1474, contour level = 0.1679
Position of 231109_N55H_MBCD10_52.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00012697 0.00008713 -0.00153069
0.00012696 0.99999999 0.00006639 -0.03186105
-0.00008714 -0.00006638 0.99999999 0.02292445
Axis -0.39589018 0.51962851 0.75713749
Axis point 256.71218612 -7.69262556 0.00000000
Rotation angle (degrees) 0.00960780
Shift along axis 0.00140704
> select clear
> view 1
> select #8/b,c,e,f
7812 atoms, 7984 bonds, 4 pseudobonds, 824 residues, 2 models selected
> hide sel ribbons
> select clear
> turn y 1
[Repeated 156 time(s)]
> view 1
> turn y -1
[Repeated 25 time(s)]
> view name 1
> show #!9 models
> hide #!9 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/MBCD/a_Align.cxs"
> hide #!8 models
> show #!6 models
> select #6,7,8,9
44052 atoms, 45108 bonds, 24 pseudobonds, 4884 residues, 8 models selected
> select #6,7,8,9/b,c,e,f
29368 atoms, 30072 bonds, 16 pseudobonds, 3256 residues, 8 models selected
> hide sel ribbons
> hide sel atoms
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/MBCD/a_Align.cxs"
> select add #6
33254 atoms, 34028 bonds, 18 pseudobonds, 3674 residues, 8 models selected
> select add #8
37160 atoms, 38020 bonds, 20 pseudobonds, 4086 residues, 8 models selected
> select add #7
40664 atoms, 41632 bonds, 22 pseudobonds, 4482 residues, 8 models selected
> show #!8 models
> hide #!6 models
> select
> ::name="6OU"::name="CLR"::name="MC3"::name="PIO"::name="PTY"::name="Y01"
10194 atoms, 10086 bonds, 258 residues, 5 models selected
> show sel atoms
> select #6,7,8,9
44052 atoms, 45108 bonds, 24 pseudobonds, 4884 residues, 8 models selected
> select #6,7,8,9/b,c,e,f
29368 atoms, 30072 bonds, 16 pseudobonds, 3256 residues, 8 models selected
> hide sel atoms
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/MBCD/a_Align.cxs"
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!7 models
> show #!6 models
> show #!9 models
> view name 1
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/MBCD/a_Align.cxs"
> hide #!9 models
> hide #!8 models
> hide #!7 models
> turn x 90
[Repeated 3 time(s)]
> turn y 1
> turn y -1
[Repeated 2 time(s)]
> turn y 3
> view 1
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/MBCD/a_Align.cxs"
> view name 1
> hide #!6 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!6 models
> show #!7 models
> hide #!6 models
> show #!9 models
> show #!6 models
> view orient
> turn x 90
> turn y 10
[Repeated 5 time(s)]
> turn x 90
[Repeated 1 time(s)]
> select clear
> hide #!7 models
> hide #!6 models
> show #!7 models
> hide #!9 models
> show #!6 models
> hide #!7 models
> view name 1
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> show #!8 models
> hide #!9 models
> hide #!8 models
> show #!8 models
> show #!9 models
> hide #!8 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/MBCD/a_Align.cxs"
> show #!8 models
> hide #!9 models
> show #!7 models
> hide #!8 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> turn x 90
> turn z 10
> turn x 90
[Repeated 2 time(s)]
> view 1
> view 2
> view 1
> show #!1 models
> hide #!7 models
> show #!6 models
> fitmap #6 inMap #1
Fit molecule 231109_WT_PIP2_109.pdb (#6) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11658 atoms
average map value = 0.3534, steps = 24
shifted from previous position = 0.00141
rotated from previous position = 0.00355 degrees
atoms outside contour = 2345, contour level = 0.16402
Position of 231109_WT_PIP2_109.pdb (#6) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.49988470 -0.86609194 0.00015450 401.24999334
0.86609195 -0.49988471 -0.00003153 107.49548405
0.00010454 0.00011805 0.99999998 -0.04210626
Axis 0.00008635 0.00002884 1.00000000
Axis point 169.58895505 169.59644392 0.00000000
Rotation angle (degrees) 119.99237305
Shift along axis -0.00435630
> fitmap #6 inMap #1
Fit molecule 231109_WT_PIP2_109.pdb (#6) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11658 atoms
average map value = 0.3534, steps = 24
shifted from previous position = 0.000958
rotated from previous position = 0.00131 degrees
atoms outside contour = 2345, contour level = 0.16402
Position of 231109_WT_PIP2_109.pdb (#6) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.49989583 -0.86608551 0.00017315 401.24856324
0.86608552 -0.49989584 -0.00002849 107.49805669
0.00011123 0.00013572 0.99999998 -0.04619046
Axis 0.00009480 0.00003575 0.99999999
Axis point 169.58795831 169.59559787 0.00000000
Rotation angle (degrees) 119.99310973
Shift along axis -0.00431031
> fitmap #6 inMap #1
Fit molecule 231109_WT_PIP2_109.pdb (#6) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11658 atoms
average map value = 0.3534, steps = 24
shifted from previous position = 0.000242
rotated from previous position = 0.0013 degrees
atoms outside contour = 2345, contour level = 0.16402
Position of 231109_WT_PIP2_109.pdb (#6) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.49989858 -0.86608392 0.00019517 401.24523516
0.86608394 -0.49989859 -0.00003276 107.49944636
0.00012594 0.00015265 0.99999997 -0.05157584
Axis 0.00010704 0.00003997 0.99999999
Axis point 169.58600734 169.59490757 0.00000000
Rotation angle (degrees) 119.99329163
Shift along axis -0.00432936
> fitmap #6 inMap #1
Fit molecule 231109_WT_PIP2_109.pdb (#6) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11658 atoms
average map value = 0.3534, steps = 24
shifted from previous position = 0.000324
rotated from previous position = 0.00132 degrees
atoms outside contour = 2345, contour level = 0.16402
Position of 231109_WT_PIP2_109.pdb (#6) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.49989845 -0.86608399 0.00021796 401.24165959
0.86608401 -0.49989847 -0.00003651 107.50000939
0.00014058 0.00017052 0.99999997 -0.05705838
Axis 0.00011952 0.00004467 0.99999999
Axis point 169.58405263 169.59417576 0.00000000
Rotation angle (degrees) 119.99328369
Shift along axis -0.00429959
> fitmap #6 inMap #1
Fit molecule 231109_WT_PIP2_109.pdb (#6) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11658 atoms
average map value = 0.3534, steps = 24
shifted from previous position = 0.000138
rotated from previous position = 0.00139 degrees
atoms outside contour = 2348, contour level = 0.16402
Position of 231109_WT_PIP2_109.pdb (#6) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.49989523 -0.86608584 0.00024149 401.23754192
0.86608586 -0.49989525 -0.00004142 107.49993442
0.00015660 0.00018845 0.99999996 -0.06283297
Axis 0.00013271 0.00004901 0.99999999
Axis point 169.58188294 169.59344707 0.00000000
Rotation angle (degrees) 119.99307074
Shift along axis -0.00431744
> fitmap #6 inMap #1
Fit molecule 231109_WT_PIP2_109.pdb (#6) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11658 atoms
average map value = 0.3534, steps = 24
shifted from previous position = 0.00023
rotated from previous position = 0.00161 degrees
atoms outside contour = 2346, contour level = 0.16402
Position of 231109_WT_PIP2_109.pdb (#6) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.49988537 -0.86609152 0.00026722 401.23266934
0.86609155 -0.49988540 -0.00004261 107.49755502
0.00017048 0.00021014 0.99999996 -0.06889645
Axis 0.00014591 0.00005585 0.99999999
Axis point 169.57972683 169.59237252 0.00000000
Rotation angle (degrees) 119.99241907
Shift along axis -0.00434834
> fitmap #6 inMap #1
Fit molecule 231109_WT_PIP2_109.pdb (#6) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11658 atoms
average map value = 0.3534, steps = 24
shifted from previous position = 0.000371
rotated from previous position = 0.0025 degrees
atoms outside contour = 2349, contour level = 0.16402
Position of 231109_WT_PIP2_109.pdb (#6) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.49985838 -0.86610709 0.00029744 401.22594907
0.86610713 -0.49985841 -0.00004634 107.49093485
0.00018881 0.00023445 0.99999995 -0.07611221
Axis 0.00016210 0.00006271 0.99999998
Axis point 169.57716254 169.59129070 0.00000000
Rotation angle (degrees) 119.99063375
Shift along axis -0.00433253
> fitmap #6 inMap #1
Fit molecule 231109_WT_PIP2_109.pdb (#6) to map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) using 11658 atoms
average map value = 0.3534, steps = 24
shifted from previous position = 0.000249
rotated from previous position = 0.0115 degrees
atoms outside contour = 2345, contour level = 0.16402
Position of 231109_WT_PIP2_109.pdb (#6) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.49968995 -0.86620429 0.00025086 401.22205217
0.86620432 -0.49968997 -0.00003279 107.44352132
0.00015376 0.00020091 0.99999996 -0.06447214
Axis 0.00013490 0.00005605 0.99999999
Axis point 169.58193617 169.59247030 0.00000000
Rotation angle (degrees) 119.97949137
Shift along axis -0.00432436
> hide #!1 models
> show #!1 models
> hide #!6 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> fitmap #2 inMap #1
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc using 271891 points
correlation = 0.8523, correlation about mean = 0.7042, overlap = 1.013e+04
steps = 28, shift = 0.0178, angle = 4.97e-05 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.98734238 0.15860331 0.00001034 307.16792534
0.15860331 0.98734238 -0.00006130 -20.60698729
-0.00001993 -0.00005889 -1.00000000 339.20014011
Axis 0.07956057 0.99683003 -0.00002609
Axis point 154.40761331 0.00000000 169.59863167
Rotation angle (degrees) 179.99912986
Shift along axis 3.88794379
> fitmap #2 inMap #1
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc using 271891 points
correlation = 0.8523, correlation about mean = 0.7042, overlap = 1.013e+04
steps = 28, shift = 0.018, angle = 3.13e-05 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.98734234 0.15860359 0.00001079 307.16963607
0.15860359 0.98734234 -0.00006117 -20.62500257
-0.00002035 -0.00005868 -1.00000000 339.20012561
Axis 0.07956053 0.99683004 -0.00002611
Axis point 154.40922394 0.00000000 169.59859059
Rotation angle (degrees) 179.99910507
Shift along axis 3.87009853
> fitmap #2 inMap #1
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc using 271891 points
correlation = 0.8523, correlation about mean = 0.7042, overlap = 1.013e+04
steps = 28, shift = 0.0181, angle = 3.86e-05 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.98734239 0.15860329 0.00001020 307.16797982
0.15860329 0.98734239 -0.00006128 -20.60696427
-0.00001979 -0.00005889 -1.00000000 339.20014738
Axis 0.07956063 0.99683003 -0.00002604
Axis point 154.40762777 0.00000000 169.59864701
Rotation angle (degrees) 179.99913825
Shift along axis 3.88800315
> fitmap #2 inMap #1
Fit map N55H_Chol_P52_J694_007_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc using 271891 points
correlation = 0.8523, correlation about mean = 0.7042, overlap = 1.013e+04
steps = 28, shift = 0.0179, angle = 4.7e-05 degrees
Position of N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.98734235 0.15860351 0.00001097 307.16963007
0.15860351 0.98734235 -0.00006112 -20.62482499
-0.00002052 -0.00005861 -1.00000000 339.20016084
Axis 0.07956041 0.99683005 -0.00002613
Axis point 154.40922767 0.00000000 169.59859451
Rotation angle (degrees) 179.99909497
Shift along axis 3.87023557
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!2 models
> fitmap #3 inMap #1
Fit map N55H_MBCD_P74_J90_011_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc using 140403 points
correlation = 0.9043, correlation about mean = 0.7568, overlap = 2.036e+04
steps = 28, shift = 0.0163, angle = 0.0184 degrees
Position of N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99998844 0.00480713 0.00002027 304.62121878
0.00480713 0.99998844 -0.00001914 33.27435494
-0.00002036 -0.00001904 -1.00000000 314.58917128
Axis 0.00240930 0.99999710 -0.00000841
Axis point 152.27212323 0.00000000 157.29317872
Rotation angle (degrees) 179.99883586
Shift along axis 34.00553625
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> fitmap #5 inMap #1
Fit map N55H_CBX_P52_J662_003_volume_map_sharp.mrc in map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc using 125306 points
correlation = 0.6267, correlation about mean = 0.2509, overlap = 3741
steps = 52, shift = 0.276, angle = 0.0835 degrees
Position of N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.24505586 -0.96950895 0.00011868 289.85316834
0.96950895 0.24505586 0.00005219 -32.01759960
-0.00007969 0.00010227 0.99999999 8.35986617
Axis 0.00002583 0.00010230 0.99999999
Axis point 165.48573196 170.10721464 0.00000000
Rotation angle (degrees) 75.81486542
Shift along axis 8.36407656
> show #!4 models
> hide #!5 models
> fitmap #4 inMap #1
Fit map N55H_MBCD_P76_J149_007_volume_map_sharp in map
WT_PIP2_P68_J150_009_volume_map_sharp.mrc using 439920 points
correlation = 0.723, correlation about mean = 0.5277, overlap = 5275
steps = 48, shift = 0.0163, angle = 0.0137 degrees
Position of N55H_MBCD_P76_J149_007_volume_map_sharp (#4) relative to
WT_PIP2_P68_J150_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.71520638 0.69891332 -0.00004519 172.37039957
0.69891332 0.71520638 -0.00001187 -70.23268393
0.00002402 -0.00004007 -1.00000000 347.30147338
Axis -0.37735395 -0.92606911 0.00001917
Axis point 100.49087762 0.00000000 173.65174841
Rotation angle (degrees) 179.99785921
Shift along axis 0.00232522
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #!7 models
> fitmap #7 inMap #2
Fit molecule 231106_N55H_Chol_204.pdb (#7) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.2279, steps = 28
shifted from previous position = 0.0148
rotated from previous position = 0.0275 degrees
atoms outside contour = 1329, contour level = 0.070496
Position of 231106_N55H_Chol_204.pdb (#7) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999996 -0.00024998 -0.00010119 0.05775415
0.00025002 0.99999988 0.00041232 -0.11944318
0.00010108 -0.00041234 0.99999991 0.06066809
Axis -0.83689197 -0.20527269 0.50741991
Axis point 0.00000000 138.49201027 286.25667487
Rotation angle (degrees) 0.02822923
Shift along axis 0.00696863
> fitmap #7 inMap #2
Fit molecule 231106_N55H_Chol_204.pdb (#7) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.2279, steps = 28
shifted from previous position = 0.0149
rotated from previous position = 0.0275 degrees
atoms outside contour = 1331, contour level = 0.070496
Position of 231106_N55H_Chol_204.pdb (#7) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999996 -0.00024832 -0.00009300 0.05553911
0.00024832 0.99999997 -0.00006746 -0.02252126
0.00009301 0.00006744 0.99999999 -0.01768566
Axis 0.24653048 -0.33991958 0.90756675
Axis point 83.47458033 218.38715308 0.00000000
Rotation angle (degrees) 0.01567669
Shift along axis 0.00529658
> fitmap #7 inMap #2
Fit molecule 231106_N55H_Chol_204.pdb (#7) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.2279, steps = 28
shifted from previous position = 0.0149
rotated from previous position = 0.0275 degrees
atoms outside contour = 1329, contour level = 0.070496
Position of 231106_N55H_Chol_204.pdb (#7) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999996 -0.00024813 -0.00010501 0.05812458
0.00024818 0.99999988 0.00041172 -0.11897775
0.00010491 -0.00041175 0.99999991 0.05994352
Axis -0.83676017 -0.21330005 0.50431686
Axis point 0.00000000 136.98048713 285.40162883
Rotation angle (degrees) 0.02819295
Shift along axis 0.00697215
> fitmap #7 inMap #2
Fit molecule 231106_N55H_Chol_204.pdb (#7) to map
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) using 10512 atoms
average map value = 0.2279, steps = 28
shifted from previous position = 0.0149
rotated from previous position = 0.0275 degrees
atoms outside contour = 1331, contour level = 0.070496
Position of 231106_N55H_Chol_204.pdb (#7) relative to
N55H_Chol_P52_J694_007_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999996 -0.00024830 -0.00009287 0.05551174
0.00024830 0.99999997 -0.00006741 -0.02249422
0.00009289 0.00006739 0.99999999 -0.01766191
Axis 0.24640590 -0.33954546 0.90774061
Axis point 83.39743478 218.30883530 0.00000000
Rotation angle (degrees) 0.01567250
Shift along axis 0.00528380
> hide #!7 models
> show #!8 models
> fitmap #8 inMap #3
Fit molecule 231109_N55H_MBCD10_52.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5192, steps = 28
shifted from previous position = 0.0261
rotated from previous position = 0.029 degrees
atoms outside contour = 1475, contour level = 0.1679
Position of 231109_N55H_MBCD10_52.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999998 -0.00013063 -0.00013229 0.03982865
0.00013062 0.99999999 -0.00004325 -0.01019724
0.00013230 0.00004323 0.99999999 -0.02201892
Axis 0.22653616 -0.69308777 0.68433231
Axis point 171.74089953 0.00000000 299.29036213
Rotation angle (degrees) 0.01093660
Shift along axis 0.00102195
> fitmap #8 inMap #3
Fit molecule 231109_N55H_MBCD10_52.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5192, steps = 24
shifted from previous position = 0.00215
rotated from previous position = 0.00477 degrees
atoms outside contour = 1477, contour level = 0.1679
Position of 231109_N55H_MBCD10_52.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00012898 -0.00007689 0.03138221
0.00012898 0.99999999 -0.00010535 0.00103765
0.00007690 0.00010534 0.99999999 -0.02284708
Axis 0.57430657 -0.41921073 0.70316024
Axis point -12.96954274 236.52290766 0.00000000
Rotation angle (degrees) 0.01050974
Shift along axis 0.00152286
> fitmap #8 inMap #3
Fit molecule 231109_N55H_MBCD10_52.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5192, steps = 24
shifted from previous position = 0.00467
rotated from previous position = 0.00738 degrees
atoms outside contour = 1482, contour level = 0.1679
Position of 231109_N55H_MBCD10_52.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00012443 0.00004758 0.00862741
0.00012444 0.99999998 -0.00013837 0.00812041
-0.00004756 0.00013837 0.99999999 -0.01035449
Axis 0.72039363 0.24766963 0.64783699
Axis point 0.00000000 81.94413518 55.96033429
Rotation angle (degrees) 0.01100496
Shift along axis 0.00151829
> fitmap #8 inMap #3
Fit molecule 231109_N55H_MBCD10_52.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5192, steps = 24
shifted from previous position = 0.00721
rotated from previous position = 0.00995 degrees
atoms outside contour = 1481, contour level = 0.1679
Position of 231109_N55H_MBCD10_52.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999998 -0.00012429 0.00015262 -0.01140834
0.00012429 0.99999999 -0.00000005 -0.01685912
-0.00015262 0.00000007 0.99999999 0.02272563
Axis 0.00032438 0.77539907 0.63147144
Axis point 143.62375916 0.00000000 74.77023465
Rotation angle (degrees) 0.01127749
Shift along axis 0.00127434
> fitmap #8 inMap #3
Fit molecule 231109_N55H_MBCD10_52.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5192, steps = 24
shifted from previous position = 0.00352
rotated from previous position = 0.00474 degrees
atoms outside contour = 1477, contour level = 0.1679
Position of 231109_N55H_MBCD10_52.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999998 -0.00012757 0.00013472 -0.00782614
0.00012756 0.99999999 0.00008069 -0.03233082
-0.00013473 -0.00008067 0.99999999 0.03130024
Axis -0.39878455 0.66588634 0.63052856
Axis point 226.10426485 0.00000000 54.19131175
Rotation angle (degrees) 0.01159202
Shift along axis 0.00132799
> fitmap #8 inMap #3
Fit molecule 231109_N55H_MBCD10_52.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5192, steps = 24
shifted from previous position = 0.00109
rotated from previous position = 0.00124 degrees
atoms outside contour = 1476, contour level = 0.1679
Position of 231109_N55H_MBCD10_52.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999998 -0.00012698 0.00012149 -0.00544808
0.00012697 0.99999999 0.00009774 -0.03562280
-0.00012150 -0.00009773 0.99999999 0.03179502
Axis -0.48604991 0.60419044 0.63143440
Axis point 286.28496774 -38.34141355 0.00000000
Rotation angle (degrees) 0.01152126
Shift along axis 0.00120156
> fitmap #8 inMap #3
Fit molecule 231109_N55H_MBCD10_52.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5192, steps = 24
shifted from previous position = 0.00162
rotated from previous position = 0.00174 degrees
atoms outside contour = 1474, contour level = 0.1679
Position of 231109_N55H_MBCD10_52.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00012651 0.00010009 -0.00140154
0.00012649 0.99999998 0.00011938 -0.03988496
-0.00010011 -0.00011937 0.99999999 0.03182110
Axis -0.59484355 0.49880708 0.63035914
Axis point 319.24330215 -6.42126255 0.00000000
Rotation angle (degrees) 0.01149809
Shift along axis 0.00099751
> fitmap #8 inMap #3
Fit molecule 231109_N55H_MBCD10_52.pdb (#8) to map
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) using 11718 atoms
average map value = 0.5192, steps = 24
shifted from previous position = 0.00347
rotated from previous position = 0.00345 degrees
atoms outside contour = 1479, contour level = 0.1679
Position of 231109_N55H_MBCD10_52.pdb (#8) relative to
N55H_MBCD_P74_J90_011_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00012532 0.00004860 0.00882473
0.00012531 0.99999998 0.00015048 -0.04588033
-0.00004862 -0.00015047 0.99999999 0.02919503
Axis -0.74578739 0.24092702 0.62109205
Axis point 0.00000000 191.94584300 305.72176310
Rotation angle (degrees) 0.01156025
Shift along axis 0.00049762
> hide #!8 models
> show #!9 models
> fitmap #9 inMap #4
Fit molecule 231107_N55H_MBCD100_46.pdb (#9) to map
N55H_MBCD_P76_J149_007_volume_map_sharp (#4) using 10164 atoms
average map value = 0.1139, steps = 40
shifted from previous position = 0.0206
rotated from previous position = 0.0142 degrees
atoms outside contour = 1240, contour level = 0.056516
Position of 231107_N55H_MBCD100_46.pdb (#9) relative to
N55H_MBCD_P76_J149_007_volume_map_sharp (#4) coordinates:
Matrix rotation and translation
0.50005290 0.86599486 0.00002981 -62.07798969
-0.86599457 0.50005276 -0.00079472 231.83874839
-0.00070313 0.00037159 0.99999968 0.01986024
Axis 0.00067339 0.00042318 -0.99999968
Axis point 169.75340955 169.68430872 0.00000000
Rotation angle (degrees) 59.99651510
Shift along axis 0.03644650
> fitmap #9 inMap #4
Fit molecule 231107_N55H_MBCD100_46.pdb (#9) to map
N55H_MBCD_P76_J149_007_volume_map_sharp (#4) using 10164 atoms
average map value = 0.1139, steps = 40
shifted from previous position = 0.0105
rotated from previous position = 0.00569 degrees
atoms outside contour = 1243, contour level = 0.056516
Position of 231107_N55H_MBCD100_46.pdb (#9) relative to
N55H_MBCD_P76_J149_007_volume_map_sharp (#4) coordinates:
Matrix rotation and translation
0.50005024 0.86599639 -0.00003488 -62.06232893
-0.86599608 0.50005003 -0.00086997 231.85077406
-0.00073595 0.00046524 0.99999962 0.01909110
Axis 0.00077091 0.00040477 -0.99999962
Axis point 169.77094221 169.67656226 0.00000000
Rotation angle (degrees) 59.99669553
Shift along axis 0.02691118
> fitmap #9 inMap #4
Fit molecule 231107_N55H_MBCD100_46.pdb (#9) to map
N55H_MBCD_P76_J149_007_volume_map_sharp (#4) using 10164 atoms
average map value = 0.1139, steps = 40
shifted from previous position = 0.00942
rotated from previous position = 0.00352 degrees
atoms outside contour = 1240, contour level = 0.056516
Position of 231107_N55H_MBCD100_46.pdb (#9) relative to
N55H_MBCD_P76_J149_007_volume_map_sharp (#4) coordinates:
Matrix rotation and translation
0.50006364 0.86598866 0.00002291 -62.07738423
-0.86598831 0.50006346 -0.00088376 231.85214555
-0.00077678 0.00042210 0.99999961 0.02514406
Axis 0.00075397 0.00046172 -0.99999961
Axis point 169.76819315 169.69125613 0.00000000
Rotation angle (degrees) 59.99580824
Shift along axis 0.03510213
> fitmap #9 inMap #4
Fit molecule 231107_N55H_MBCD100_46.pdb (#9) to map
N55H_MBCD_P76_J149_007_volume_map_sharp (#4) using 10164 atoms
average map value = 0.1139, steps = 40
shifted from previous position = 0.00767
rotated from previous position = 0.00141 degrees
atoms outside contour = 1242, contour level = 0.056516
Position of 231107_N55H_MBCD100_46.pdb (#9) relative to
N55H_MBCD_P76_J149_007_volume_map_sharp (#4) coordinates:
Matrix rotation and translation
0.50004387 0.86600007 0.00002064 -62.07530718
-0.86599972 0.50004369 -0.00089279 231.85827620
-0.00078348 0.00042856 0.99999960 0.03281239
Axis 0.00076291 0.00046427 -0.99999960
Axis point 169.76925350 169.69110222 0.00000000
Rotation angle (degrees) 59.99711671
Shift along axis 0.02747439
> fitmap #9 inMap #4
Fit molecule 231107_N55H_MBCD100_46.pdb (#9) to map
N55H_MBCD_P76_J149_007_volume_map_sharp (#4) using 10164 atoms
average map value = 0.1139, steps = 40
shifted from previous position = 0.005
rotated from previous position = 0.0127 degrees
atoms outside contour = 1245, contour level = 0.056516
Position of 231107_N55H_MBCD100_46.pdb (#9) relative to
N55H_MBCD_P76_J149_007_volume_map_sharp (#4) coordinates:
Matrix rotation and translation
0.50004182 0.86600125 -0.00011416 -62.04944727
-0.86600108 0.50004162 -0.00071621 231.82313141
-0.00056315 0.00045700 0.99999974 -0.00867578
Axis 0.00067737 0.00025923 -0.99999974
Axis point 169.75117402 169.65097181 0.00000000
Rotation angle (degrees) 59.99724861
Shift along axis 0.02674074
> hide #!9 models
> show #!8 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> view orient
> show #!1 models
> hide #!8 models
> ui tool show "Side View"
> view orient
[Repeated 2 time(s)]
> turn x 90
[Repeated 2 time(s)]
> hide #!1 models
> show #!7 models
> turn y 15
> turn y -15
[Repeated 3 time(s)]
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!7 models
> view orient
> turn x 90
[Repeated 2 time(s)]
> view name 5
> hide #!1 models
> show #!6 models
> turn y 5
> turn y -5
[Repeated 12 time(s)]
> turn y 5
[Repeated 1 time(s)]
> turn y -5
[Repeated 1 time(s)]
> turn y 5
> view orient
> turn z 5
> turn z -5
[Repeated 10 time(s)]
> turn z 5
> turn z 1
> turn z -1
[Repeated 4 time(s)]
> turn x 90
[Repeated 2 time(s)]
> view 1
> view 5
> turn y -10
[Repeated 6 time(s)]
> turn y 10
> show #!1 models
> hide #!6 models
> show #!6 models
> hide #!1 models
> select #6
11658 atoms, 11868 bonds, 6 pseudobonds, 1254 residues, 2 models selected
> show sel ribbons
> select clear
> view orient
[Repeated 2 time(s)]
> turn x 90
[Repeated 2 time(s)]
> turn y -10
[Repeated 1 time(s)]
> view orient
[Repeated 3 time(s)]
> select #6/b,e,
Expected an objects specifier or a keyword
> select #6/b,e
3886 atoms, 3956 bonds, 2 pseudobonds, 418 residues, 2 models selected
> hide sel ribbons
> turn x 90
[Repeated 2 time(s)]
> turn y -10
[Repeated 4 time(s)]
> select #6/b,c,e,f,
Expected an objects specifier or a keyword
> select #6/b,c,e,f
7772 atoms, 7912 bonds, 4 pseudobonds, 836 residues, 2 models selected
> hide sel ribbons
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!8 models
> hide #!7 models
> hide #!6 models
> view orient
> show #!1 models
> hide #!8 models
> view orient
[Repeated 2 time(s)]
> turn x 90
[Repeated 2 time(s)]
> show #!6 models
> hide #!1 models
> turn y -1
[Repeated 64 time(s)]
> view name 1
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/MBCD/a_Align.cxs"
——— End of log from Fri Nov 10 19:29:33 2023 ———
opened ChimeraX session
> view 1
> show #!5 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> show #!5 models
> hide #!6 models
> select add #6
11658 atoms, 11868 bonds, 6 pseudobonds, 1254 residues, 2 models selected
> select subtract #6
Nothing selected
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231112_N55H_CBX_208.pdb"
Chain information for 231112_N55H_CBX_208.pdb #10
---
Chain | Description
A B C D E F | No description available
> color #10 #aa55ffff
> select add #10
8988 atoms, 9324 bonds, 6 pseudobonds, 1014 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.98905,0.12482,-0.078724,-6.4068,0.13112,-0.98808,0.080631,295.55,-0.067721,-0.09007,-0.99363,342.82
> view matrix models
> #10,0.99409,0.036615,-0.10223,11.139,0.049049,-0.99133,0.1219,303.16,-0.096885,-0.12619,-0.98726,352.65
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.99409,0.036615,-0.10223,-6.2414,0.049049,-0.99133,0.1219,265.88,-0.096885,-0.12619,-0.98726,340.63
> view matrix models
> #10,0.99409,0.036615,-0.10223,-18.488,0.049049,-0.99133,0.1219,273.42,-0.096885,-0.12619,-0.98726,344.84
> ui tool show "Fit in Map"
> color #10 #aa55ffff
> fitmap #10 inMap #5
Fit molecule 231112_N55H_CBX_208.pdb (#10) to map
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) using 8988 atoms
average map value = 0.05229, steps = 76
shifted from previous position = 1.36
rotated from previous position = 2.86 degrees
atoms outside contour = 6633, contour level = 0.091964
Position of 231112_N55H_CBX_208.pdb (#10) relative to
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.20886552 -0.97214860 0.10631230 345.77099049
0.97604318 -0.21399935 -0.03929376 45.41569438
0.06095014 0.09555828 0.99355609 -29.24683860
Axis 0.06903523 0.02322239 0.99734390
Axis point 155.55023014 162.55197586 0.00000000
Rotation angle (degrees) 102.39525192
Shift along axis -4.24411640
> fitmap #10 inMap #5
Fit molecule 231112_N55H_CBX_208.pdb (#10) to map
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) using 8988 atoms
average map value = 0.05229, steps = 44
shifted from previous position = 0.00754
rotated from previous position = 0.0101 degrees
atoms outside contour = 6629, contour level = 0.091964
Position of 231112_N55H_CBX_208.pdb (#10) relative to
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.20876335 -0.97217049 0.10631280 345.76233444
0.97607359 -0.21388435 -0.03916422 45.37666669
0.06081294 0.09559306 0.99356115 -29.22904621
Axis 0.06898499 0.02329230 0.99734575
Axis point 155.55807858 162.54563981 0.00000000
Rotation angle (degrees) 102.38873353
Shift along axis -4.24212614
> fitmap #10 inMap #5
Fit molecule 231112_N55H_CBX_208.pdb (#10) to map
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) using 8988 atoms
average map value = 0.05229, steps = 44
shifted from previous position = 0.0157
rotated from previous position = 0.0149 degrees
atoms outside contour = 6627, contour level = 0.091964
Position of 231112_N55H_CBX_208.pdb (#10) relative to
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.20894586 -0.97214903 0.10615033 345.80229822
0.97604204 -0.21404751 -0.03905901 45.40142730
0.06069240 0.09544597 0.99358266 -29.18522003
Axis 0.06885834 0.02327169 0.99735498
Axis point 155.56804057 162.54804527 0.00000000
Rotation angle (degrees) 102.39824161
Shift along axis -4.24008321
> fitmap #10 inMap #5
Fit molecule 231112_N55H_CBX_208.pdb (#10) to map
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) using 8988 atoms
average map value = 0.05229, steps = 60
shifted from previous position = 0.00856
rotated from previous position = 0.00707 degrees
atoms outside contour = 6629, contour level = 0.091964
Position of 231112_N55H_CBX_208.pdb (#10) relative to
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.20892026 -0.97214689 0.10622037 345.78741076
0.97604062 -0.21403570 -0.03915901 45.40736979
0.06080327 0.09549428 0.99357124 -29.21223306
Axis 0.06893407 0.02325072 0.99735024
Axis point 155.55992351 162.54778672 0.00000000
Rotation angle (degrees) 102.39747922
Shift along axis -4.24253983
> fitmap #10 inMap #5
Fit molecule 231112_N55H_CBX_208.pdb (#10) to map
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) using 8988 atoms
average map value = 0.05229, steps = 44
shifted from previous position = 0.0143
rotated from previous position = 0.00423 degrees
atoms outside contour = 6629, contour level = 0.091964
Position of 231112_N55H_CBX_208.pdb (#10) relative to
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.20885622 -0.97216162 0.10621142 345.79404554
0.97605242 -0.21397465 -0.03919846 45.40640276
0.06083379 0.09548107 0.99357064 -29.21538882
Axis 0.06894654 0.02323019 0.99734986
Axis point 155.56276026 162.55887267 0.00000000
Rotation angle (degrees) 102.39382798
Shift along axis -4.24186313
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.97421,-0.020718,0.22471,-58.74,-0.032877,-0.99818,0.050507,299.33,0.22325,-0.056592,-0.97312,278.59
> view matrix models
> #10,0.9316,-0.329,0.15452,10.666,-0.33043,-0.94368,-0.017052,350.39,0.15142,-0.035172,-0.98784,289.29
> view matrix models
> #10,0.95087,-0.30658,-0.043102,35.133,-0.29884,-0.94528,0.13092,321.91,-0.080881,-0.11161,-0.99046,340.94
> fitmap #10 inMap #5
Fit molecule 231112_N55H_CBX_208.pdb (#10) to map
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) using 8988 atoms
average map value = 0.1271, steps = 80
shifted from previous position = 4.32
rotated from previous position = 8.09 degrees
atoms outside contour = 3166, contour level = 0.091964
Position of 231112_N55H_CBX_208.pdb (#10) relative to
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.50014920 -0.86593925 -0.00000175 392.77434310
0.86593922 -0.50014919 -0.00023536 105.32271213
0.00020293 -0.00011923 0.99999998 -0.02430150
Axis 0.00006705 -0.00011819 0.99999999
Axis point 165.98917305 166.02298510 0.00000000
Rotation angle (degrees) 120.00987203
Shift along axis -0.01041286
> fitmap #10 inMap #5
Fit molecule 231112_N55H_CBX_208.pdb (#10) to map
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) using 8988 atoms
average map value = 0.1271, steps = 40
shifted from previous position = 0.0131
rotated from previous position = 0.00413 degrees
atoms outside contour = 3168, contour level = 0.091964
Position of 231112_N55H_CBX_208.pdb (#10) relative to
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.50009278 -0.86597183 -0.00000380 392.76558392
0.86597182 -0.50009277 -0.00020451 105.31511180
0.00017520 -0.00010557 0.99999998 -0.02176748
Axis 0.00005713 -0.00010335 0.99999999
Axis point 165.98469976 166.02518658 0.00000000
Rotation angle (degrees) 120.00613886
Shift along axis -0.01021414
> fitmap #10 inMap #5
Fit molecule 231112_N55H_CBX_208.pdb (#10) to map
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) using 8988 atoms
average map value = 0.1271, steps = 44
shifted from previous position = 0.0145
rotated from previous position = 0.00552 degrees
atoms outside contour = 3162, contour level = 0.091964
Position of 231112_N55H_CBX_208.pdb (#10) relative to
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.50001554 -0.86601644 0.00000746 392.76758969
0.86601642 -0.50001553 -0.00017002 105.27823512
0.00015097 -0.00007855 0.99999999 -0.02334997
Axis 0.00005281 -0.00008285 1.00000000
Axis point 165.99321652 166.01900515 0.00000000
Rotation angle (degrees) 120.00102799
Shift along axis -0.01133017
> fitmap #10 inMap #5
Fit molecule 231112_N55H_CBX_208.pdb (#10) to map
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) using 8988 atoms
average map value = 0.1271, steps = 28
shifted from previous position = 0.0189
rotated from previous position = 0.00582 degrees
atoms outside contour = 3165, contour level = 0.091964
Position of 231112_N55H_CBX_208.pdb (#10) relative to
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.49998350 -0.86603493 -0.00005049 392.76003543
0.86603493 -0.49998349 -0.00009527 105.27017299
0.00005726 -0.00009136 1.00000000 -0.00574925
Axis 0.00000226 -0.00006221 1.00000000
Axis point 165.99046786 166.01763736 0.00000000
Rotation angle (degrees) 119.99890821
Shift along axis -0.01141067
> fitmap #10 inMap #5
Fit molecule 231112_N55H_CBX_208.pdb (#10) to map
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) using 8988 atoms
average map value = 0.1271, steps = 28
shifted from previous position = 0.0169
rotated from previous position = 0.0132 degrees
atoms outside contour = 3161, contour level = 0.091964
Position of 231112_N55H_CBX_208.pdb (#10) relative to
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.49992679 -0.86606766 0.00010304 392.74586862
0.86606763 -0.49992680 -0.00025351 105.27116414
0.00027107 -0.00003750 0.99999997 -0.04922031
Axis 0.00012471 -0.00009701 0.99999999
Axis point 165.98080440 166.02261131 0.00000000
Rotation angle (degrees) 119.99515818
Shift along axis -0.01045285
> select clear
> hide #!5 models
> open
> C:/Users/OJS/Desktop/Phenix/220302_Cx43_N55H_CBX/RealSpaceRefine_209/231112_From208_real_space_refined_209.pdb
Chain information for 231112_From208_real_space_refined_209.pdb #11
---
Chain | Description
A B C D E F | No description available
> close #10
> color #11 #aa55ffff
> show #!11 atoms
> hide #!11 atoms
> show #!11 cartoons
> close #11
> open
> C:/Users/OJS/Desktop/Phenix/220302_Cx43_N55H_CBX/RealSpaceRefine_211/231112_From208_real_space_refined_209-coot-0_real_space_refined_211.pdb
Chain information for
231112_From208_real_space_refined_209-coot-0_real_space_refined_211.pdb #10
---
Chain | Description
A B C D E F | No description available
> color #10 #aa55ffff
> hide #!10 atoms
> show #!10 cartoons
> color #10 #aa55ffff
> select ::name="CBO"
738 atoms, 810 bonds, 18 residues, 1 model selected
> show sel atoms
> color sel green
> color sel yellow
> color sel byhetero
> color sel lime
> color sel byhetero
> select clear
> select #10:74-110
1632 atoms, 1686 bonds, 186 residues, 1 model selected
> select #10:74-103
1578 atoms, 1632 bonds, 180 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 1
Assigning ss_type attribute to 180 items
> select clear
> ui tool show "Selection Inspector"
> select add #10
8988 atoms, 9324 bonds, 6 pseudobonds, 1014 residues, 2 models selected
> ui tool show "Selection Inspector"
> hide #!10 models
> show #!9 models
> show #!10 models
> hide #!9 models
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 8250 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select clear
> select add #10
8988 atoms, 9324 bonds, 6 pseudobonds, 1014 residues, 2 models selected
> ui tool show "Selection Inspector"
> setattr =sel p display false
Assigning display attribute to 6 items
> size =sel stickRadius 0.3
Changed 9324 bond radii
> select clear
> select #10:203-235
1536 atoms, 1572 bonds, 186 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 1
Assigning ss_type attribute to 186 items
> select clear
> close #10
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231112_N55H_CBX_211.pdb"
Chain information for 231112_N55H_CBX_211.pdb #10
---
Chain | Description
A B C D E F | No description available
> color #10 #aa55ffff
> show #!10 atoms
> hide #!10 atoms
> show #!10 cartoons
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 8250 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> color #10 #aa55ffff
> rename #10:203-230
No name or id option specified for renaming
> select #10:203-230
1362 atoms, 1386 bonds, 168 residues, 1 model selected
> select #10:203-235
1536 atoms, 1572 bonds, 186 residues, 1 model selected
> select #10:203-235, 74-103
3114 atoms, 3204 bonds, 366 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 1
Assigning ss_type attribute to 366 items
> ui tool show "Selection Inspector"
> select clear
> select add #10
8988 atoms, 9324 bonds, 6 pseudobonds, 1014 residues, 2 models selected
> ui tool show "Selection Inspector"
> setattr =sel p display false
Assigning display attribute to 6 items
> size =sel stickRadius 0.3
Changed 9324 bond radii
> ui mousemode right "rotate selected models"
> show #!5 models
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.96209,0.14332,-0.23205,19.307,0.23467,-0.86853,0.43656,202.11,-0.13898,-0.47446,-0.86923,398.43
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.96209,0.14332,-0.23205,-13.646,0.23467,-0.86853,0.43656,179.06,-0.13898,-0.47446,-0.86923,383.18
> fitmap #10 inMap #5
Fit molecule 231112_N55H_CBX_211.pdb (#10) to map
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) using 8988 atoms
average map value = 0.04985, steps = 104
shifted from previous position = 3.53
rotated from previous position = 9.71 degrees
atoms outside contour = 6910, contour level = 0.091964
Position of 231112_N55H_CBX_211.pdb (#10) relative to
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.12411431 -0.92048405 0.37054657 289.51364275
0.98605083 -0.15615162 -0.05762314 39.96927776
0.11090263 0.35822590 0.92702471 -62.21118018
Axis 0.21124551 0.13189550 0.96849311
Axis point 134.63185769 148.68995698 0.00000000
Rotation angle (degrees) 100.17298124
Shift along axis 6.17912602
> view matrix models
> #10,0.98696,0.069915,-0.14497,-16.317,0.11674,-0.93104,0.34575,222.62,-0.1108,-0.35817,-0.92706,364.67
> fitmap #10 inMap #5
Fit molecule 231112_N55H_CBX_211.pdb (#10) to map
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) using 8988 atoms
average map value = 0.04985, steps = 84
shifted from previous position = 4.58
rotated from previous position = 0.00725 degrees
atoms outside contour = 6913, contour level = 0.091964
Position of 231112_N55H_CBX_211.pdb (#10) relative to
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.12411325 -0.92047209 0.37057662 289.50228486
0.98606407 -0.15611017 -0.05750887 39.94403812
0.11078609 0.35827467 0.92701980 -62.20237392
Axis 0.21121151 0.13196951 0.96849045
Axis point 134.63464530 148.67742621 0.00000000
Rotation angle (degrees) 100.17188722
Shift along axis 6.17520629
> fitmap #10 inMap #5
Fit molecule 231112_N55H_CBX_211.pdb (#10) to map
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) using 8988 atoms
average map value = 0.04985, steps = 48
shifted from previous position = 0.00471
rotated from previous position = 0.00764 degrees
atoms outside contour = 6912, contour level = 0.091964
Position of 231112_N55H_CBX_211.pdb (#10) relative to
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.12411660 -0.92043705 0.37066254 289.48790830
0.98607297 -0.15608850 -0.05741506 39.92543657
0.11070310 0.35837414 0.92699126 -62.20014697
Axis 0.21121458 0.13205543 0.96847806
Axis point 134.63563545 148.66534541 0.00000000
Rotation angle (degrees) 100.17218436
Shift along axis 6.17696121
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.8314,-0.5417,-0.12381,107.64,-0.51534,-0.83501,0.19283,338.46,-0.20784,-0.096517,-0.97339,348.41
> fitmap #10 inMap #5
Fit molecule 231112_N55H_CBX_211.pdb (#10) to map
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) using 8988 atoms
average map value = 0.1263, steps = 208
shifted from previous position = 10
rotated from previous position = 21 degrees
atoms outside contour = 3173, contour level = 0.091964
Position of 231112_N55H_CBX_211.pdb (#10) relative to
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.50004942 -0.86599687 0.00002654 392.76076694
0.86599687 -0.50004942 -0.00008829 105.28637156
0.00008973 -0.00002116 1.00000000 -0.01720079
Axis 0.00003876 -0.00003648 1.00000000
Axis point 165.98882916 166.01598164 0.00000000
Rotation angle (degrees) 120.00326979
Shift along axis -0.00581935
> fitmap #10 inMap #5
Fit molecule 231112_N55H_CBX_211.pdb (#10) to map
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) using 8988 atoms
average map value = 0.1263, steps = 28
shifted from previous position = 0.0217
rotated from previous position = 0.0229 degrees
atoms outside contour = 3180, contour level = 0.091964
Position of 231112_N55H_CBX_211.pdb (#10) relative to
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.50027893 -0.86586427 0.00022924 392.75456944
0.86586430 -0.50027891 0.00013316 105.33071507
-0.00000061 0.00026510 0.99999997 -0.04872020
Axis 0.00007619 0.00013273 0.99999999
Axis point 165.98223634 166.00167297 0.00000000
Rotation angle (degrees) 120.01845611
Shift along axis -0.00481482
> show #!9 models
> hide #!10 models
> hide #!5 models
> show #!10 models
> select #6-10/b,c,e,f
35360 atoms, 36288 bonds, 20 pseudobonds, 3932 residues, 10 models selected
> hide sel ribobn
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel ribbons
> view 1
> select add #6
39246 atoms, 40244 bonds, 22 pseudobonds, 4350 residues, 10 models selected
> select subtract #6
27588 atoms, 28376 bonds, 16 pseudobonds, 3096 residues, 8 models selected
> select add #7
31092 atoms, 31988 bonds, 18 pseudobonds, 3492 residues, 8 models selected
> select add #8
34998 atoms, 35980 bonds, 20 pseudobonds, 3904 residues, 8 models selected
> select subtract #8
23280 atoms, 24004 bonds, 14 pseudobonds, 2668 residues, 6 models selected
> select subtract #7
12768 atoms, 13168 bonds, 8 pseudobonds, 1480 residues, 4 models selected
> select add #7
23280 atoms, 24004 bonds, 14 pseudobonds, 2668 residues, 6 models selected
> select subtract #7
12768 atoms, 13168 bonds, 8 pseudobonds, 1480 residues, 4 models selected
> select add #9
16156 atoms, 16644 bonds, 10 pseudobonds, 1882 residues, 4 models selected
> select subtract #9
5992 atoms, 6216 bonds, 4 pseudobonds, 676 residues, 2 models selected
> select add #10
8988 atoms, 9324 bonds, 6 pseudobonds, 1014 residues, 2 models selected
> select subtract #10
Nothing selected
> select add #10
8988 atoms, 9324 bonds, 6 pseudobonds, 1014 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.21069,-0.9755,-0.063364,272.5,-0.97374,-0.21514,0.074442,321.24,-0.08625,0.046016,-0.99521,312.13
> fitmap #10 inMap #5
Fit molecule 231112_N55H_CBX_211.pdb (#10) to map
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) using 8988 atoms
average map value = 0.1264, steps = 72
shifted from previous position = 0.181
rotated from previous position = 5.84 degrees
atoms outside contour = 3173, contour level = 0.091964
Position of 231112_N55H_CBX_211.pdb (#10) relative to
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.99999995 0.00029523 -0.00015150 331.94671908
-0.00029522 -0.99999996 -0.00007498 332.06687572
-0.00015152 -0.00007494 0.99999999 0.03266709
Axis 0.00007528 0.00003671 -1.00000000
Axis point 165.99786967 166.00893842 0.00000000
Rotation angle (degrees) 179.98308465
Shift along axis 0.00451343
> select clear
> view 1
> select ::name="CBO"
738 atoms, 810 bonds, 18 residues, 1 model selected
> show sel atoms
> color sel lime
> color sel byhetero
> select #10/b,c,e,f
5992 atoms, 6216 bonds, 4 pseudobonds, 676 residues, 2 models selected
> hide sel atoms
> hide #!9 models
> select clear
> view 1
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/2_MBCD/a_Align.cxs"
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/2_MBCD/a_Align.cxs"
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> view 1
> hide #!9 models
> show #!6 models
> hide #!10 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/2_MBCD/a_Align.cxs"
——— End of log from Mon Nov 13 01:25:53 2023 ———
opened ChimeraX session
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!6 models
> view 1
> select clear
> show #!10 models
> hide #!10 models
> select clear
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231113_N55H_CBX_213.pdb"
Chain information for 231113_N55H_CBX_213.pdb #11
---
Chain | Description
A B C D E F | No description available
> color #11 #aa55ffff
> select add #11
9318 atoms, 9672 bonds, 6 pseudobonds, 1026 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.70657,-0.33221,-0.62481,437.43,-0.11638,0.92548,-0.36046,88.825,0.698,-0.18198,-0.69259,182.66
> view matrix models
> #11,-0.86291,-0.36059,-0.35407,425.17,-0.45163,0.86462,0.22014,62.537,0.22676,0.34987,-0.90894,206.88
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.86291,-0.36059,-0.35407,407.7,-0.45163,0.86462,0.22014,25.065,0.22676,0.34987,-0.90894,190.73
> view matrix models
> #11,-0.86291,-0.36059,-0.35407,396.3,-0.45163,0.86462,0.22014,29.913,0.22676,0.34987,-0.90894,198.15
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.58231,0.39183,-0.71231,281.6,0.66744,0.73066,-0.1437,-75.907,0.46415,-0.55911,-0.687,274.47
> view matrix models
> #11,-0.57582,0.74766,-0.3308,160.98,0.77333,0.62939,0.07639,-111.56,0.26532,-0.21183,-0.9406,290.02
> view matrix models
> #11,0.23685,-0.029551,-0.9711,256.62,0.12859,-0.98979,0.061483,266.62,-0.963,-0.13944,-0.23064,369.32
> view matrix models
> #11,0.98247,-0.18271,-0.037075,10.244,-0.18274,-0.98316,0.0026481,326.52,-0.036935,0.0041736,-0.99931,313.63
> view matrix models
> #11,0.92302,-0.35443,-0.14972,66.474,-0.37887,-0.90506,-0.1932,377.15,-0.067033,0.23505,-0.96967,275.6
> view matrix models
> #11,0.7256,-0.68209,-0.090821,144.3,-0.66509,-0.72905,0.16167,339.18,-0.17649,-0.056907,-0.98266,344.29
> view matrix models
> #11,0.62408,-0.7507,-0.21674,192.5,-0.68106,-0.65859,0.32004,305.03,-0.383,-0.052119,-0.92228,368.2
> view matrix models
> #11,0.44855,-0.85567,-0.25814,245.62,-0.85182,-0.49672,0.16633,330.86,-0.27055,0.14528,-0.95168,321.43
> view matrix models
> #11,0.57191,-0.8146,-0.096701,192.74,-0.8197,-0.57206,-0.028982,369,-0.03171,0.095841,-0.99489,296.85
> ui tool show "Fit in Map"
> fitmap #11 inMap #5
Fit molecule 231113_N55H_CBX_213.pdb (#11) to map
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) using 9318 atoms
average map value = 0.05144, steps = 76
shifted from previous position = 2.88
rotated from previous position = 5.77 degrees
atoms outside contour = 6890, contour level = 0.091964
Position of 231113_N55H_CBX_213.pdb (#11) relative to
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-0.93537555 -0.35365548 0.00064556 379.86409516
0.35365496 -0.93537563 -0.00079635 262.71709740
0.00088547 -0.00051658 0.99999949 -3.20401361
Axis 0.00039554 -0.00033919 0.99999986
Axis point 165.92935339 166.06480338 0.00000000
Rotation angle (degrees) 159.28894860
Shift along axis -3.14287395
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.52401,-0.83409,-0.17235,214.5,-0.82676,-0.54676,0.13237,342.7,-0.20464,0.073131,-0.9761,327.39
> view matrix models
> #11,0.50324,-0.83746,-0.21312,224.97,-0.84654,-0.52729,0.073074,352.15,-0.17357,0.14364,-0.97429,310.25
> view matrix models
> #11,0.37796,-0.91979,-0.10551,242.37,-0.92083,-0.38529,0.060229,342.94,-0.096049,0.074389,-0.99259,311.78
> fitmap #11 inMap #5
Fit molecule 231113_N55H_CBX_213.pdb (#11) to map
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) using 9318 atoms
average map value = 0.124, steps = 100
shifted from previous position = 3.14
rotated from previous position = 11.1 degrees
atoms outside contour = 3470, contour level = 0.091964
Position of 231113_N55H_CBX_213.pdb (#11) relative to
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-1.00000000 -0.00000292 -0.00016522 332.00962518
0.00000287 -0.99999997 0.00029735 331.97404550
-0.00016522 0.00029735 0.99999996 -0.02843516
Axis -0.00030940 0.00015150 0.99999994
Axis point 166.00456809 165.98726503 0.00000000
Rotation angle (degrees) 179.99983424
Shift along axis -0.08086456
> select clear
> hide #!11 models
> show #!11 models
> hide #!11 models
> select add #11
9318 atoms, 9672 bonds, 6 pseudobonds, 1026 residues, 2 models selected
> hide #!8 models
> show #!11 models
> ui tool show "Selection Inspector"
> setattr =sel p display false
Assigning display attribute to 6 items
> size =sel stickRadius 0.3
Changed 9672 bond radii
> select #11:74-103
1578 atoms, 1632 bonds, 180 residues, 1 model selected
> select #11:74-103,203-240
3114 atoms, 3204 bonds, 366 residues, 1 model selected
> select #11:74-103,203-232
3048 atoms, 3132 bonds, 360 residues, 1 model selected
> show #!8 models
> ui tool show "Selection Inspector"
> select #11:74-103,203-232
3048 atoms, 3132 bonds, 360 residues, 1 model selected
> setattr sel r ss_type 1
Assigning ss_type attribute to 360 items
> select clear
> select ::name="CBO"
1722 atoms, 1890 bonds, 42 residues, 2 models selected
> color sel lime
> color sel byhetero
> select clear
> hide #!8 models
> show #!8 models
> select ::name="CBO"
1722 atoms, 1890 bonds, 42 residues, 2 models selected
> show sel atoms
> select clear
> select #11/F:304@O32
1 atom, 1 residue, 1 model selected
> select add #11/F:303@O33
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #11/F:304@O32 #11/F:303@O33
Distance between 231113_N55H_CBX_213.pdb #11/F CBO 304 O32 and CBO 303 O33:
4.6Å
> ~distance #11/F:304@O32 #11/F:303@O33
> select clear
[Repeated 1 time(s)]
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 8250 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> view 1
> select #6-11/b,c,e,f
41572 atoms, 42736 bonds, 24 pseudobonds, 4616 residues, 12 models selected
> hide sel ribbons
> select clear
> select #11/b,c,e,f
6212 atoms, 6448 bonds, 4 pseudobonds, 684 residues, 2 models selected
> hide sel atoms
> select clear
> show #!10 models
> select #10/b,c,e,f
5992 atoms, 6216 bonds, 4 pseudobonds, 676 residues, 2 models selected
> hide sel atoms
> hide #!10 models
> show #!10 models
> hide #!8 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> select clear
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/4_CBX/a_Align.cxs"
> show #!8 models
> hide #!11 models
> open
> C:/Users/OJS/Desktop/Phenix/230901_MBCD_Chol_N55H/RealSpaceRefine_67/231114_From60_real_space_refined_067.pdb
Chain information for 231114_From60_real_space_refined_067.pdb #12
---
Chain | Description
A B C D E F | No description available
> close #12
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231114_N55H_MBCD10_67.pdb"
Chain information for 231114_N55H_MBCD10_67.pdb #12
---
Chain | Description
A B C D E F | No description available
> hide #!8 models
> hide #!12 models
> color #12 cyan
> show #!12 models
> select add #12
11922 atoms, 12168 bonds, 6 pseudobonds, 1248 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> ui tool show "Selection Inspector"
> setattr =sel p display false
Assigning display attribute to 6 items
> size =sel stickRadius 0.3
Changed 12168 bond radii
> select clear
> select
> ::name="6OU"::name="CBO"::name="CLR"::name="HOH"::name="MC3"::name="PIO"::name="PTY"::name="Y01"
14238 atoms, 14256 bonds, 366 residues, 8 models selected
> show sel atoms
> select ::name="6OU"
4410 atoms, 4320 bonds, 90 residues, 4 models selected
> color sel orange
> select ::name="CLR"
840 atoms, 930 bonds, 30 residues, 3 models selected
> color sel yellow
> select ::name="HOH"
6 atoms, 6 residues, 1 model selected
> color sel red
> select ::name="PTY"
2622 atoms, 2556 bonds, 66 residues, 5 models selected
> color sel orange
> select
98418 atoms, 100644 bonds, 48 pseudobonds, 9456 residues, 26 models selected
> color sel byhetero
> select clear
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 9684 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> show #!12 cartoons
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select clear
> select #6-12
74280 atoms, 76272 bonds, 42 pseudobonds, 8172 residues, 14 models selected
> select #6-12/b,c,e,f
49520 atoms, 50848 bonds, 28 pseudobonds, 5448 residues, 14 models selected
> hide sel ribbons
> hide sel atoms
> select clear
> view 1
[Repeated 1 time(s)]
> show #!11 models
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!6 models
> hide #!12 models
> hide #!6 models
> show #!7 models
> select #7:30
66 atoms, 66 bonds, 6 residues, 1 model selected
> color sel blue
> color sel #00aaffff
> select clear
> show #!8 models
> hide #!7 models
> hide #!8 models
> show #!9 models
> select #9:30
66 atoms, 66 bonds, 6 residues, 1 model selected
> color sel byelement
> color sel #aaffffff
> select clear
> view 1
> select clear
> show #!5 models
> hide #!5 models
> select clear
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/2_MBCD/a_Align.cxs"
——— End of log from Tue Nov 14 06:22:00 2023 ———
opened ChimeraX session
> close #10-11
> close #8
> rename #12 id #8
> select clear
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> select clear
> open "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231116_N55H_CBX_217.pdb"
Chain information for 231116_N55H_CBX_217.pdb #10
---
Chain | Description
A B C D E F | No description available
> color #10 #aa00ffff
> select add #10
8988 atoms, 9324 bonds, 6 pseudobonds, 1014 residues, 2 models selected
> hide sel atoms
> show sel cartoons
[Repeated 1 time(s)]
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 8250 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.64294,-0.76571,-0.017668,189.19,-0.76571,-0.64207,-0.037889,405.72,0.017668,0.037889,-0.99913,307.66
> ui mousemode right "rotate selected models"
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.64294,-0.76571,-0.017668,176.27,-0.76571,-0.64207,-0.037889,378.02,0.017668,0.037889,-0.99913,296.96
> view matrix models
> #10,0.64294,-0.76571,-0.017668,160.14,-0.76571,-0.64207,-0.037889,377.13,0.017668,0.037889,-0.99913,303.89
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.38542,-0.92216,-0.03266,231.23,-0.91774,-0.37941,-0.11752,371.37,0.095984,0.075269,-0.99253,283.64
> ui tool show "Fit in Map"
> fitmap #10 inMap #5
Fit molecule 231116_N55H_CBX_217.pdb (#10) to map
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) using 8988 atoms
average map value = 0.1258, steps = 104
shifted from previous position = 7.36
rotated from previous position = 11.1 degrees
atoms outside contour = 3195, contour level = 0.091964
Position of 231116_N55H_CBX_217.pdb (#10) relative to
N55H_CBX_P52_J662_003_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
-1.00000002 -0.00001213 -0.00013602 332.01208025
0.00001211 -1.00000002 0.00014970 331.98319667
-0.00013603 0.00014970 1.00000001 -0.00031559
Axis -0.00010328 0.00014043 0.99999998
Axis point 166.00503393 165.99260462 0.00000000
Rotation angle (degrees) 179.99930539
Shift along axis 0.01201700
> color #10 #aa55ffff
> color #10 #aa00ffff
> color #10 #aa55ffff
> color #10 #aa00ffff
> select clear
> select #10:74-103
1578 atoms, 1632 bonds, 180 residues, 1 model selected
> hide #!9 models
> select #10:74-103, 203
1620 atoms, 1674 bonds, 186 residues, 1 model selected
> select #10:74-103, 203-234
3114 atoms, 3204 bonds, 366 residues, 1 model selected
> select #10:74-103, 203-230
2940 atoms, 3018 bonds, 348 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 1
Assigning ss_type attribute to 348 items
> select clear
> select add #10
8988 atoms, 9324 bonds, 6 pseudobonds, 1014 residues, 2 models selected
> ui tool show "Selection Inspector"
> setattr =sel p display false
Assigning display attribute to 6 items
> size =sel stickRadius 0.4
Changed 9324 bond radii
> size =sel stickRadius 0.5
Changed 9324 bond radii
> select clear
> show #!9 models
> hide #!9 models
> select #6-10/a,d
17748 atoms, 18208 bonds, 10 pseudobonds, 1970 residues, 10 models selected
> select #6-10/b,c,e,f
35496 atoms, 36416 bonds, 20 pseudobonds, 3940 residues, 10 models selected
> hide sel ribbons
> view 1
> select clear
> select
> ::name="6OU"::name="CBO"::name="CLR"::name="HOH"::name="MC3"::name="PIO"::name="PTY"::name="Y01"
11136 atoms, 11088 bonds, 288 residues, 6 models selected
> show sel atoms
> select #5-10/b,c,e,f
35496 atoms, 36416 bonds, 20 pseudobonds, 3940 residues, 10 models selected
> hide sel atoms
> select
77382 atoms, 78996 bonds, 36 pseudobonds, 7194 residues, 22 models selected
> select clear
> select :CBO
738 atoms, 810 bonds, 18 residues, 1 model selected
> color sel dark green
> select clear
> show #!9 models
> hide #!10 models
> select #6-9
44256 atoms, 45300 bonds, 24 pseudobonds, 4896 residues, 8 models selected
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.5
Changed 45300 bond radii
> size =sel stickRadius 0.7
Changed 45300 bond radii
> size =sel stickRadius 1
Changed 45300 bond radii
> select clear
> show #!10 models
> hide #!9 models
> show #!9 models
> hide #!10 models
> view 1
> show #!8 models
> hide #!9 models
> select #67:401
Nothing selected
> select #8:401
6 atoms, 6 residues, 1 model selected
> hide sel atoms
> select clear
> select #6-10
53244 atoms, 54624 bonds, 30 pseudobonds, 5910 residues, 10 models selected
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.7
Changed 54624 bond radii
> size =sel stickRadius 0.6
Changed 54624 bond radii
> size =sel stickRadius 0.5
Changed 54624 bond radii
> select clear
> show #!6 models
> hide #!8 models
> hide #!6 models
> show #!10 models
> hide #!10 models
> show #!8 models
> select
77382 atoms, 78996 bonds, 36 pseudobonds, 7194 residues, 22 models selected
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.6
Changed 78996 bond radii
> size =sel stickRadius 0.7
Changed 78996 bond radii
> size =sel stickRadius 0.8
Changed 78996 bond radii
> size =sel stickRadius 1
Changed 78996 bond radii
> select clear
> hide #!8 models
> show #!6 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!6 models
> show #!7 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!6 models
> show #!9 models
> hide #!2 models
> show #!4 models
> view 1
> hide #!4 models
> select clear
> ribbon style thickness 0.6
> ribbon style thickness 1
> ribbon style thickness 0.6
> ribbon style thickness 1
> ribbon style thickness 2
> ribbon style thickness 1
> select clear
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!8 models
> show #!8 models
> select #8:30
66 atoms, 66 bonds, 6 residues, 1 model selected
> show sel atoms
> undo
> view w1
Expected an objects specifier or a view name or a keyword
> view 1
> select clear
> show #!5 models
> hide #!5 models
> show #!10 models
> hide #!8 models
> hide #!10 models
> show #!9 models
> select #9
10164 atoms, 10428 bonds, 6 pseudobonds, 1206 residues, 2 models selected
> color sel sienna
> hide #!9 models
> show #!8 models
> select #8
11922 atoms, 12168 bonds, 6 pseudobonds, 1248 residues, 2 models selected
> color sel olive
> select clear
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> hide #!9 models
> show #!7 models
> select #7
10512 atoms, 10836 bonds, 6 pseudobonds, 1188 residues, 2 models selected
> color sel cyan
> select clear
> hide #!7 models
> show #!6 models
> select ::name="PIO"
258 atoms, 258 bonds, 6 residues, 1 model selected
> color sel gray
> color sel byhetero
> select clear
> select ::name="CLR"
672 atoms, 744 bonds, 24 residues, 2 models selected
> color sel hotpink
> hide #!6 models
> show #!7 models
> select ::name="6OU"
2940 atoms, 2880 bonds, 60 residues, 3 models selected
> color sel orange
> show #!8 models
> hide #!7 models
> select clear
> select ::name="PTY"
2226 atoms, 2172 bonds, 54 residues, 4 models selected
> color sel orange
> show #!9 models
> hide #!8 models
> select clear
> show #!10 models
> select
77382 atoms, 78996 bonds, 36 pseudobonds, 7194 residues, 22 models selected
> color sel byhetero
> select clear
> hide #!9 models
> ui tool show "Selection Inspector"
> select clear
> show #!7 models
> hide #!10 models
> hide #!7 models
> show #!8 models
> select #6-10
53244 atoms, 54624 bonds, 30 pseudobonds, 5910 residues, 10 models selected
> ui tool show "Selection Inspector"
> select clear
> view 1
> show #!7 models
> show #!6 models
> show #!10 models
> show #!9 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!10 models
> show #!7 models
> show #!8 models
> hide #!8 models
> hide #!10 models
> show #!9 models
> hide #!7 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/2_MBCD/a_Align.cxs"
——— End of log from Thu Nov 16 05:45:38 2023 ———
opened ChimeraX session
> show #!8 models
> show #!7 models
> hide #!8 models
> hide #!9 models
> show #!8 models
> hide #!7 models
> show #!9 models
> hide #!8 models
> select ::name="MC3"
3288 atoms, 3180 bonds, 108 residues, 3 models selected
> color sel gray
> select clear
> select ::name="MC3"
3288 atoms, 3180 bonds, 108 residues, 3 models selected
> color sel dark gray
> select clear
> color sel darkgray
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> select ::name="PIO"
258 atoms, 258 bonds, 6 residues, 1 model selected
> color sel gray
> color sel byhetero
> select clear
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!8 models
> show #!9 models
> select ::name="CLR"
672 atoms, 744 bonds, 24 residues, 2 models selected
> select ::name="MC3"
3288 atoms, 3180 bonds, 108 residues, 3 models selected
> color sel gray
> color sel dark gray
> select clear
> hide #!7 models
> hide #!8 models
> hide #!9 models
> show #!5 models
> hide #!5 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> select
77382 atoms, 78996 bonds, 36 pseudobonds, 7194 residues, 22 models selected
> color sel byhetero
> select clear
> view 1
> show #!7 models
> hide #!6 models
> select
> ::name="6OU"::name="CBO"::name="CLR"::name="HOH"::name="MC3"::name="PIO"::name="PTY"::name="Y01"
11136 atoms, 11088 bonds, 288 residues, 6 models selected
> show sel atoms
> select #6-10/b,c,e,f
35496 atoms, 36416 bonds, 20 pseudobonds, 3940 residues, 10 models selected
> hide sel atoms
> select clear
> hide #!7 models
> show #!8 models
> select ::name="HOH"
6 atoms, 6 residues, 1 model selected
> hide sel atoms
> select clear
> hide #!8 models
> show #!9 models
> select ::name="MC3"
3288 atoms, 3180 bonds, 108 residues, 3 models selected
> color (#!9 & sel) #ffff7fff
> select clear
> hide #!9 models
> show #!6 models
> select ::name="MC3"
3288 atoms, 3180 bonds, 108 residues, 3 models selected
> color (#!6 & sel) #ffff00ff
> color (#!6 & sel) #ffff7fff
> select clear
> graphics silhouettes true width 2.5 depthJump 0.01
> select clear
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/2_MBCD/a_Align.cxs"
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!7 models
> show #!5 models
> hide #!5 models
> hide #!7 models
> show #!8 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!10 models
> hide #!8 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/2_MBCD/a_Align.cxs"
> hide #!10 models
> show #!7 models
> show #!8 models
> show #!9 models
> select #7,8,9/30
Nothing selected
> color sel black
> show sel atoms
> hide #!9 models
> hide #!8 models
> select #7,8,9/30
Nothing selected
> select #7,8,9/a,d:30
66 atoms, 66 bonds, 6 residues, 3 models selected
> color sel black
> show sel atoms
> select clear
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> show #!8 models
> hide #!8 models
> show #!7 models
> show #!6 models
> hide #!7 models
> hide #!9 models
> show #!7 models
> hide #!6 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!8 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/2_MBCD/a_Align.cxs"
——— End of log from Thu Nov 16 19:13:21 2023 ———
opened ChimeraX session
> show #!7 models
> hide #!8 models
> color #7 #aaaaffff
> select ::name="CBO"
738 atoms, 810 bonds, 18 residues, 1 model selected
> select ::name="CLR"
672 atoms, 744 bonds, 24 residues, 2 models selected
> color sel hotpink
> select #7
10512 atoms, 10836 bonds, 6 pseudobonds, 1188 residues, 2 models selected
> color sel cyan
> color #7 #00aaffff
> color #7 #55ffffff
> color #7 cyan
> color #7 #55ffffff
> color #7 cyan
> color #7 #55ffffff
> color #7 cyan
> color #7 #55ffffff
> color #7 #aaffffff
> color #7 cyan
> color #7 springgreen
> color #7 #aaff7fff
> color #7 #00aaffff
> color #7 #55ffffff
> color #7 cyan
> color #7 #55ffffff
> color #7 cyan
> color #7 #55ffffff
> select clear
[Repeated 1 time(s)]
> color #3 #aaffff40 models
> select clear
> color #7 #00aeefff
> select clear
> color #7 cyan
> color #7 #55ff00ff
> color #7 cyan
> color #7 #aaffffff
> color #7 cyan
> color #7 #aaffffff
> color #7 #55ff00ff
> color #7 yellow
> color #7 #ffaa00ff
> color #7 #aaaaffff
> color #7 #00aaffff
> color #7 #aaaaffff
> color #7 #00aaffff
> color #7 cyan
> color #7 #00aaffff
> select clear
> select ::name="6OU"
2940 atoms, 2880 bonds, 60 residues, 3 models selected
> color sel orange
> select ::name="CLR"
672 atoms, 744 bonds, 24 residues, 2 models selected
> color sel hotpink
> select ::name="PTY"
2226 atoms, 2172 bonds, 54 residues, 4 models selected
> view 1
> select
77382 atoms, 78996 bonds, 36 pseudobonds, 7194 residues, 22 models selected
> color sel byhetero
> select clear
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!10 models
> show #!8 models
> show #!6 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!10 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!10 models
> show #!7 models
> hide #!10 models
> show #!8 models
> hide #!7 models
> hide #!8 models
> show #!9 models
> show #!8 models
> hide #!9 models
> hide #!8 models
> show #!7 models
> select #6-10:30
330 atoms, 330 bonds, 30 residues, 5 models selected
> hide sel atoms
> select clear
> show #!8 models
> hide #!7 models
> select #8:30
66 atoms, 66 bonds, 6 residues, 1 model selected
> color sel olive
> select clear
> hide #!8 models
> show #!9 models
> select #9:30
66 atoms, 66 bonds, 6 residues, 1 model selected
> color sel sienna
> select clear
> show #!10 models
> hide #!9 models
> show #!6 models
> show #!7 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> hide #!10 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> show #!6 models
> hide #!9 models
> hide #!6 models
> show #!7 models
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/2_MBCD/a_Align.cxs"
——— End of log from Fri Nov 17 14:41:52 2023 ———
opened ChimeraX session
> show #!1 models
> hide #!7 models
> transparency 0
> volume sdLevel 5
[Repeated 1 time(s)]
> volume sdLevel 6
[Repeated 1 time(s)]
> turn x 90
[Repeated 2 time(s)]
> show #!2 models
> hide #!1 models
> zone clear
> clear zone
Unknown command: clear zone
> ~zone
Unknown command: ~zone
> select clear
> volume unzone #2-5
> select clear
> volume sdLevel 5
> volume sdLevel 6
> show #!7 models
> transparency 30
> transparency 50
> view 1
> turn x 90
[Repeated 6 time(s)]
> show #!1 models
> hide #!2 models
> hide #!7 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> view orient
[Repeated 2 time(s)]
> turn x 180
> transpraency 0
Unknown command: transpraency 0
> transparency 0
> volume sdLevel 5
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> volume sdLevel 6
[Repeated 1 time(s)]
> surface dust #5 size 8.3
[Repeated 3 time(s)]
> show sdust
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show dust
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select #5
2 models selected
> show dust
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show sel dust
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select clear
> view 1
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!3 models
> hide #!5 models
> show #!4 models
> hide #!3 models
> show #!3 models
> volume sdLevel 5
[Repeated 1 time(s)]
> volume sdLevel 6
[Repeated 1 time(s)]
> hide #!4 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!2 models
> show #!5 models
> hide #!3 models
> hide #!2 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> surface dust #1 size 8.48
> surface dust #2 size 8.3
> surface dust #3 size 8.48
> surface dust #4 size 8.48
> surface dust #5 size 8.3
> select clear
> hide #!5 models
> volume #4 level 0.07448
> hide #!3 models
> hide #!2 models
> hide #!1 models
> volume #4 level 0.08964
> show #!3 models
> hide #!4 models
> volume #3 level 0.1723
> hide #!3 models
> show #!4 models
> show #!5 models
> hide #!4 models
> show #!2 models
> hide #!5 models
> show #!1 models
> hide #!2 models
> volume #1 level 0.1427
> show #!2 models
> hide #!1 models
> volume #2 level 0.09186
> volume #2 level 0.09499
> view 1
> turn x 90
[Repeated 2 time(s)]
> show #!3 models
> hide #!2 models
> volume #4 level 0.08888
> hide #!4 models
> select #3
2 models selected
> color sel olive
> select clear
> show #!4 models
> hide #!3 models
> select #4
2 models selected
> color sel sienna
> select clear
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> volume #4 level 0.09343
> show #!5 models
> hide #!4 models
> volume #5 level 0.08178
> select clear
> volume #5 level 0.087
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!4 models
> volume #3 level 0.1379
> view name 2
> volume #3 level 0.1104
> volume #3 level 0.1311
> view 2
[Repeated 1 time(s)]
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!1 models
> hide #!3 models
> view 2
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> volume #3 level 0.1517
> show #!4 models
> hide #!3 models
> show #!5 models
> hide #!4 models
> view 2
> turn x 90
[Repeated 7 time(s)]
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!1 models
> show #!5 models
> hide #!1 models
> volume #5 level 0.08831
> view 2
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/2_MBCD/a_Align.cxs"
——— End of log from Mon Nov 20 10:41:15 2023 ———
opened ChimeraX session
> view 1
> show #!3 models
> hide #!5 models
> show #!8 models
> hide #!3 models
> select #8/a:308
28 atoms, 31 bonds, 1 residue, 1 model selected
> select #8/308
Nothing selected
> select #8:308
168 atoms, 186 bonds, 6 residues, 1 model selected
> hide sel atoms
> show #!10 models
> hide #!8 models
> show #!8 models
> select ::name="HOH"
6 atoms, 6 residues, 1 model selected
> show sel atoms
> select clear
> select ::name="HOH"
6 atoms, 6 residues, 1 model selected
> delete sel
> select #8:308
168 atoms, 186 bonds, 6 residues, 1 model selected
> delete sel
> select clear
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/Map&Models/231129_N55H_MBCD10_delCholH2O_.pdb"
> models #8
> rename #8 231114_N55H_MBCD10_69.pdb
> save "C:/Users/OJS/OneDrive - korea.ac.kr/MCSB/논문/230801_Re/1c_models.cxs"
> show #!7 models
> show #!6 models
> hide #!10 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> show #!10 models
> hide #!10 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!8 models
> hide #!8 models
> show #!6 models
> show #!7 models
> hide #!6 models
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\log\tool.py",
line 437, in _actually_show
lw.setHtml(html)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 244, in setHtml
tf = open(self._tf_name, "wb")
^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: [Errno 22] Invalid argument:
'C:\\\Users\\\OJS\\\AppData\\\Local\\\Temp\\\chbphlbl7aq7.html'
OSError: [Errno 22] Invalid argument:
'C:\\\Users\\\OJS\\\AppData\\\Local\\\Temp\\\chbphlbl7aq7.html'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 244, in setHtml
tf = open(self._tf_name, "wb")
^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> show #!2 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> ui tool show "Color Zone"
> color zone #2 near #7 distance 3
> select clear
> save "C:/Users/OJS/OneDrive - korea.ac.kr/MCSB/논문/230801_Re/1c_models.cxs"
> hide #!2 models
> show #!7 models
> show #!8 models
> hide #!7 models
> save "C:/Users/OJS/OneDrive - korea.ac.kr/MCSB/논문/230801_Re/1c_models.cxs"
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/2b_surfacecolor_heteroX.cxs"
> select #6-10:1-300
46656 atoms, 48042 bonds, 30 pseudobonds, 5712 residues, 10 models selected
> show #!6 models
> hide #!8 models
> select #6:1-300
9618 atoms, 9894 bonds, 6 pseudobonds, 1182 residues, 2 models selected
> color #6 #55aa7fff
> color #6 #ff557fff
> undo
[Repeated 1 time(s)]
> select #6:1-300
9618 atoms, 9894 bonds, 6 pseudobonds, 1182 residues, 2 models selected
> color (#!6 & sel) #55aa7fff
> color (#!6 & sel) #ff557fff
> select #7:1-300
9420 atoms, 9702 bonds, 6 pseudobonds, 1158 residues, 2 models selected
> hide #!6 models
> show #!7 models
> color (#!7 & sel) #00aaffff
> select ~sel & ##selected
1092 atoms, 1134 bonds, 30 residues, 1 model selected
> select ~sel & ##selected
9420 atoms, 9702 bonds, 6 pseudobonds, 1158 residues, 2 models selected
> select ~sel & ##selected
1092 atoms, 1134 bonds, 30 residues, 1 model selected
> select ~sel & ##selected
9420 atoms, 9702 bonds, 6 pseudobonds, 1158 residues, 2 models selected
> show #!8 models
> hide #!7 models
> select ~sel & ##selected
1092 atoms, 1134 bonds, 30 residues, 1 model selected
> select ~sel & ##selected
9420 atoms, 9702 bonds, 6 pseudobonds, 1158 residues, 2 models selected
> select ~sel & ##selected
1092 atoms, 1134 bonds, 30 residues, 1 model selected
> select ~sel & ##selected
9420 atoms, 9702 bonds, 6 pseudobonds, 1158 residues, 2 models selected
> select ~sel & ##selected
1092 atoms, 1134 bonds, 30 residues, 1 model selected
> select #8:1-300
9684 atoms, 9966 bonds, 6 pseudobonds, 1188 residues, 2 models selected
> color sel olive
> select clear
> hide #!8 models
> show #!10 models
> select #10:1-300
8250 atoms, 8514 bonds, 6 pseudobonds, 996 residues, 2 models selected
> color (#!10 & sel) #aa00ffff
> select clear
> color zone #2 near #7 distance 3
> show #!2 models
> hide #!10 models
> show #!3 models
> show #!5 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> hide #!3 models
> color zone #5 near #10 distance 4.98
> color zone #5 near #10 distance 3
[Repeated 4 time(s)]
> color #5 #aa00ffff models
> color zone #5 near #10 distance 3
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/2b_surfacecolor_heteroX.cxs"
> hide #!5 models
> show #!2 models
> color zone #2 near #7 distance 3
> hide #!2 models
> show #!3 models
> color zone #3 near #8 distance 3
> show #!6 models
> hide #!3 models
> show #!1 models
> hide #!6 models
> color zone #1 near #6 distance 3
> save "C:/Users/OJS/OneDrive -
> korea.ac.kr/MCSB/논문/230801_Re/2b_surfacecolor_heteroX.cxs"
> view name 3
> turn x 90
[Repeated 2 time(s)]Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\log\tool.py",
line 437, in _actually_show
lw.setHtml(html)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 244, in setHtml
tf = open(self._tf_name, "wb")
^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: [Errno 22] Invalid argument:
'C:\\\Users\\\OJS\\\AppData\\\Local\\\Temp\\\chbphlbl7aq7.html'
OSError: [Errno 22] Invalid argument:
'C:\\\Users\\\OJS\\\AppData\\\Local\\\Temp\\\chbphlbl7aq7.html'
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 244, in setHtml
tf = open(self._tf_name, "wb")
^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 536.23
OpenGL renderer: NVIDIA GeForce RTX 3070 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: ko_KR.cp949
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Microsoft Windows 10 Education (Build 19045)
Memory: 17,102,655,488
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-10700 CPU @ 2.90GHz
OSLanguage: ko-KR
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.13.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.12
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7rc202311230013
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
comtypes: 1.1.14
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.45.1
funcparserlib: 2.0.0a0
glfw: 2.6.3
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.0
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.7
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.0.0
prompt-toolkit: 3.0.41
psutil: 5.9.5
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pywin32: 305
pyzmq: 25.1.1
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.3
traitlets: 5.9.0
typing-extensions: 4.8.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
WMI: 1.5.1
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