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Opened 2 years ago
Closed 2 years ago
#10250 closed defect (can't reproduce)
HtmlView temp file name: Invalid argument
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
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"
[had to delete a bunch of stuff to fit within ticket limits]
> 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
Change History (2)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Input/Output |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → HtmlView temp file name: Invalid argument |
comment:2 by , 2 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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Get Invalid argument in Python open() for the path on Windows. This error code means the syntax of the path is wrong. The path is to a temp file created by Python. The only suspicious thing is the 3 backslashes in the name. Some investigation showed that those are really two backslashes, but the bug reporter incorrectly gets 3 because converting the Log html to plain text is broken (ticket #10252).
The only other thing that stands out is the locale is Korean (Locale: ko_KR.cp949).
I tested what happens if the directory does not exist of file or directory does not have permissions and those give different errors (File not found, Permission denied).
So I don't have a clue how this failed.