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Opened 13 months ago
Closed 13 months ago
#16142 closed defect (nonchimerax)
Foldseek: permission error writing temp file
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22621
ChimeraX Version: 1.9.dev202410132109 (2024-10-13 21:09:13 UTC)
Description
foldseek #1/A database afdb50
Log:
UCSF ChimeraX version: 1.9.dev202410132109 (2024-10-13)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:\Documents\Projects\Tat\Figs\Figure2\TatC_alignment.cxs format
> session
Log from Sun Oct 13 21:16:30 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.cxs
Log from Sun Oct 13 21:02:02 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.cxs
Log from Sun Oct 13 18:30:54 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.cxs
Log from Tue Sep 24 16:41:58 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.cxs
Log from Mon Sep 23 11:15:31 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.cxs
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2466_008_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.2, shown at level 0.12, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2943_007_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.2, shown at level 0.233, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #9, grid size
256,256,256, pixel 1.2, shown at level 0.2, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc zone as #10, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc zone as #11, grid size
256,256,256, pixel 1.2, shown at level 0.203, step 1, values float32
Log from Mon Sep 23 10:40:28 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:/Documents/Projects/Tat/Figs/Figure6/TatC_alignment.cxs
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2466_008_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.2, shown at level 0.12, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2943_007_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.2, shown at level 0.233, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #9, grid size
256,256,256, pixel 1.2, shown at level 0.2, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc zone as #10, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc zone as #11, grid size
256,256,256, pixel 1.2, shown at level 0.203, step 1, values float32
Log from Mon Sep 2 21:52:32 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:/Documents/Projects/Tat/Figs/Figure6/TatC_alignment.cxs
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2466_008_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.2, shown at level 0.12, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2943_007_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.2, shown at level 0.233, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #9, grid size
256,256,256, pixel 1.2, shown at level 0.2, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc zone as #10, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc zone as #11, grid size
256,256,256, pixel 1.2, shown at level 0.203, step 1, values float32
Log from Mon Sep 2 21:15:37 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:/Documents/Projects/Tat/Figs/Figure6/dockingSite_open.cxs
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2466_008_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.2, shown at level 0.12, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2943_007_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.2, shown at level 0.233, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #9, grid size
256,256,256, pixel 1.2, shown at level 0.2, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc zone as #10, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc zone as #11, grid size
256,256,256, pixel 1.2, shown at level 0.203, step 1, values float32
Log from Mon Sep 2 15:28:58 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TM3_carA.cxs
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2466_008_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.2, shown at level 0.12, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2943_007_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.2, shown at level 0.233, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #9, grid size
256,256,256, pixel 1.2, shown at level 0.731, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc zone as #10, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc zone as #11, grid size
256,256,256, pixel 1.2, shown at level 0.203, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc zone as #17, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #18, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Log from Sun Sep 1 23:27:44 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Sun Sep 1 22:28:23 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TM3_carA.cxs
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2466_008_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.2, shown at level 0.12, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2943_007_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.2, shown at level 0.233, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #9, grid size
256,256,256, pixel 1.2, shown at level 0.731, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc zone as #10, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc zone as #11, grid size
256,256,256, pixel 1.2, shown at level 0.203, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc zone as #17, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #18, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Log from Sun Sep 1 22:18:06 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TM3_carA.cxs
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2466_008_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.2, shown at level 0.12, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2943_007_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.2, shown at level 0.233, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #9, grid size
256,256,256, pixel 1.2, shown at level 0.731, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc zone as #10, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc zone as #11, grid size
256,256,256, pixel 1.2, shown at level 0.203, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc zone as #17, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #18, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Log from Sun Sep 1 19:20:25 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes_TM1_A.cxs
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2466_008_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.2, shown at level 0.12, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2943_007_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.2, shown at level 0.233, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #9, grid size
256,256,256, pixel 1.2, shown at level 0.731, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc zone as #10, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc zone as #11, grid size
256,256,256, pixel 1.2, shown at level 0.203, step 1, values float32
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #16, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Log from Sun Sep 1 15:28:33 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes_overall_BCto2S.cxs
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2466_008_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.2, shown at level 0.12, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2943_007_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.2, shown at level 0.233, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #9, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc zone as #10, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc zone as #11, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Log from Sun Sep 1 10:29:36 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Sat Aug 31 23:34:18 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Wed Aug 21 14:47:47 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:/Documents/Projects/Tat/Figs/Figure1/maps_and_models.cxs
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2466_008_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.2, shown at level 0.12, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2943_007_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.2, shown at level 0.233, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #9, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc zone as #10, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc zone as #11, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Log from Wed Aug 21 14:09:35 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:/Documents/Projects/Tat/Figs/Figure1/maps_and_models.cxs
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2466_008_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.2, shown at level 0.12, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2943_007_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.2, shown at level 0.233, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #9, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc zone as #10, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc zone as #11, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Log from Wed Aug 21 14:06:13 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:/Documents/Projects/Tat/Figs/Figure1/maps_and_models.cxs
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Opened cryosparc_P25_J2466_008_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.2, shown at level 0.12, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.2, shown at level 0.38, step 1, values float32
Opened cryosparc_P25_J2943_007_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.2, shown at level 0.233, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.2, shown at level 0.262, step 1, values float32
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #9, grid size
256,256,256, pixel 1.2, shown at level 0.18, step 1, values float32
Log from Wed Aug 21 13:42:49 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:/Documents/Projects/Tat/Figs/Figure1/maps_and_models.cxs
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.2, shown at level 0.15, step 1, values float32
Opened cryosparc_P25_J2466_008_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.2, shown at level 0.12, step 1, values float32
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.2, shown at level 0.15, step 1, values float32
Opened cryosparc_P25_J2943_007_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.2, shown at level 0.12, step 1, values float32
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.2, shown at level 0.165, step 1, values float32
Log from Wed Aug 21 13:10:43 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> D:/Documents/Projects/Tat/deposition/deposition/cryosparc_P25_J3036_009_volume_map_sharp.mrc
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.2, shown at level 0.139, step 1, values float32
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> lighting soft
> open
> D:/Documents/Projects/Tat/deposition/deposition/RealSpaceRefine_192/output_J3036_coot-20240807_real_space_refined_192.pdb
Chain information for output_J3036_coot-20240807_real_space_refined_192.pdb #2
---
Chain | Description
A B | No description available
C | No description available
D | No description available
E F | No description available
G | No description available
H | No description available
> open
> D:/Documents/Projects/Tat/deposition/deposition/cryosparc_P25_J2466_008_volume_map_sharp.mrc
Opened cryosparc_P25_J2466_008_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.2, shown at level 0.109, step 1, values float32
> open
> D:/Documents/Projects/Tat/deposition/deposition/RealSpaceRefine_197/output_J2629_coot-20240807_real_space_refined_197.pdb
Chain information for output_J2629_coot-20240807_real_space_refined_197.pdb #4
---
Chain | Description
A | No description available
B C | No description available
D | No description available
E F | No description available
G | No description available
H | No description available
> open
> D:/Documents/Projects/Tat/deposition/deposition/cryosparc_P25_J2943_007_volume_map_sharp.mrc
Opened cryosparc_P25_J2943_007_volume_map_sharp.mrc as #5, grid size
256,256,256, pixel 1.2, shown at level 0.106, step 1, values float32
> open
> D:/Documents/Projects/Tat/deposition/deposition/RealSpaceRefine_195/output_J3003_coot-20240807_real_space_refined_195.pdb
Chain information for output_J3003_coot-20240807_real_space_refined_195.pdb #6
---
Chain | Description
A B C | No description available
D E | No description available
F | No description available
> hide #6 models
> close #6#5
> close #4
> open
> D:/Documents/Projects/Tat/deposition/deposition/cryosparc_P25_J2629_005_volume_map_sharp.mrc
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.2, shown at level 0.078, step 1, values float32
> open
> D:/Documents/Projects/Tat/deposition/deposition/RealSpaceRefine_197/output_J2629_coot-20240807_real_space_refined_197.pdb
Chain information for output_J2629_coot-20240807_real_space_refined_197.pdb #5
---
Chain | Description
A | No description available
B C | No description available
D | No description available
E F | No description available
G | No description available
H | No description available
> open
> D:/Documents/Projects/Tat/deposition/deposition/cryosparc_P25_J2943_007_volume_map_sharp.mrc
Opened cryosparc_P25_J2943_007_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.2, shown at level 0.106, step 1, values float32
> open
> D:/Documents/Projects/Tat/deposition/deposition/cryosparc_P25_J3003_004_volume_map_sharp.mrc
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.2, shown at level 0.0602, step 1, values float32
> open
> D:/Documents/Projects/Tat/deposition/deposition/RealSpaceRefine_195/output_J3003_coot-20240807_real_space_refined_195.pdb
Chain information for output_J3003_coot-20240807_real_space_refined_195.pdb #8
---
Chain | Description
A B C | No description available
D E | No description available
F | No description available
> vop level 0.15
> surface dust
Missing or invalid "surfaces" argument: empty atom specifier
> surface dust volume
Missing or invalid "surfaces" argument: invalid surfaces specifier
> surface dust #1-8
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #8 models
> show #!6 models
> hide #!7 models
> surface undust #1-8
> hide #!6 models
> show #!3 models
> hide #!3 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!5 models
> select add #3
2 models selected
> select add #4
4 models selected
> select add #5
10582 atoms, 10854 bonds, 2 pseudobonds, 1350 residues, 6 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,1,0,0,113.42,0,1,0,-46.9,0,0,1,-17.648,#4,1,0,0,113.42,0,1,0,-46.9,0,0,1,-17.648,#5,1,0,0,113.42,0,1,0,-46.9,0,0,1,-17.648
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.99495,-0.065317,0.076202,429.93,0.10034,-0.66356,0.74136,122.45,0.0021418,0.74526,0.66677,-100.27,#4,-0.99495,-0.065317,0.076202,429.93,0.10034,-0.66356,0.74136,122.45,0.0021418,0.74526,0.66677,-100.27,#5,-0.99495,-0.065317,0.076202,429.93,0.10034,-0.66356,0.74136,122.45,0.0021418,0.74526,0.66677,-100.27
> view matrix models
> #3,-0.91322,-0.4043,-0.050641,491.49,0.31604,-0.78129,0.53824,135.89,-0.25717,0.47553,0.84127,-37.176,#4,-0.91322,-0.4043,-0.050641,491.49,0.31604,-0.78129,0.53824,135.89,-0.25717,0.47553,0.84127,-37.176,#5,-0.91322,-0.4043,-0.050641,491.49,0.31604,-0.78129,0.53824,135.89,-0.25717,0.47553,0.84127,-37.176
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.91322,-0.4043,-0.050641,451.03,0.31604,-0.78129,0.53824,220.27,-0.25717,0.47553,0.84127,-59.786,#4,-0.91322,-0.4043,-0.050641,451.03,0.31604,-0.78129,0.53824,220.27,-0.25717,0.47553,0.84127,-59.786,#5,-0.91322,-0.4043,-0.050641,451.03,0.31604,-0.78129,0.53824,220.27,-0.25717,0.47553,0.84127,-59.786
> view matrix models
> #3,-0.91322,-0.4043,-0.050641,442.37,0.31604,-0.78129,0.53824,233.5,-0.25717,0.47553,0.84127,-66.482,#4,-0.91322,-0.4043,-0.050641,442.37,0.31604,-0.78129,0.53824,233.5,-0.25717,0.47553,0.84127,-66.482,#5,-0.91322,-0.4043,-0.050641,442.37,0.31604,-0.78129,0.53824,233.5,-0.25717,0.47553,0.84127,-66.482
> view matrix models
> #3,-0.91322,-0.4043,-0.050641,399.53,0.31604,-0.78129,0.53824,264.46,-0.25717,0.47553,0.84127,-71.742,#4,-0.91322,-0.4043,-0.050641,399.53,0.31604,-0.78129,0.53824,264.46,-0.25717,0.47553,0.84127,-71.742,#5,-0.91322,-0.4043,-0.050641,399.53,0.31604,-0.78129,0.53824,264.46,-0.25717,0.47553,0.84127,-71.742
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.020418,0.9032,-0.42874,87.566,-0.99144,-0.073592,-0.10782,438.79,-0.12893,0.42287,0.89697,-91.01,#4,-0.020418,0.9032,-0.42874,87.566,-0.99144,-0.073592,-0.10782,438.79,-0.12893,0.42287,0.89697,-91.01,#5,-0.020418,0.9032,-0.42874,87.566,-0.99144,-0.073592,-0.10782,438.79,-0.12893,0.42287,0.89697,-91.01
> view matrix models
> #3,-0.35133,0.93528,0.042749,72.132,-0.93266,-0.34562,-0.1034,475.58,-0.081936,-0.076199,0.99372,-25.722,#4,-0.35133,0.93528,0.042749,72.132,-0.93266,-0.34562,-0.1034,475.58,-0.081936,-0.076199,0.99372,-25.722,#5,-0.35133,0.93528,0.042749,72.132,-0.93266,-0.34562,-0.1034,475.58,-0.081936,-0.076199,0.99372,-25.722
> view matrix models
> #3,-0.36932,0.92891,0.027107,78.094,-0.92527,-0.36485,-0.10371,477.75,-0.086449,-0.063385,0.99424,-27.269,#4,-0.36932,0.92891,0.027107,78.094,-0.92527,-0.36485,-0.10371,477.75,-0.086449,-0.063385,0.99424,-27.269,#5,-0.36932,0.92891,0.027107,78.094,-0.92527,-0.36485,-0.10371,477.75,-0.086449,-0.063385,0.99424,-27.269
> view matrix models
> #3,-0.31281,0.94708,-0.072059,79.336,-0.94355,-0.31855,-0.090773,471.01,-0.10892,0.039596,0.99326,-41.151,#4,-0.31281,0.94708,-0.072059,79.336,-0.94355,-0.31855,-0.090773,471.01,-0.10892,0.039596,0.99326,-41.151,#5,-0.31281,0.94708,-0.072059,79.336,-0.94355,-0.31855,-0.090773,471.01,-0.10892,0.039596,0.99326,-41.151
> view matrix models
> #3,-0.34012,0.93977,-0.033785,79.763,-0.93758,-0.34166,-0.064852,470.58,-0.072489,0.0096181,0.99732,-42.259,#4,-0.34012,0.93977,-0.033785,79.763,-0.93758,-0.34166,-0.064852,470.58,-0.072489,0.0096181,0.99732,-42.259,#5,-0.34012,0.93977,-0.033785,79.763,-0.93758,-0.34166,-0.064852,470.58,-0.072489,0.0096181,0.99732,-42.259
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.34012,0.93977,-0.033785,71.636,-0.93758,-0.34166,-0.064852,375.8,-0.072489,0.0096181,0.99732,21.095,#4,-0.34012,0.93977,-0.033785,71.636,-0.93758,-0.34166,-0.064852,375.8,-0.072489,0.0096181,0.99732,21.095,#5,-0.34012,0.93977,-0.033785,71.636,-0.93758,-0.34166,-0.064852,375.8,-0.072489,0.0096181,0.99732,21.095
> view matrix models
> #3,-0.34012,0.93977,-0.033785,64.644,-0.93758,-0.34166,-0.064852,362.98,-0.072489,0.0096181,0.99732,13.398,#4,-0.34012,0.93977,-0.033785,64.644,-0.93758,-0.34166,-0.064852,362.98,-0.072489,0.0096181,0.99732,13.398,#5,-0.34012,0.93977,-0.033785,64.644,-0.93758,-0.34166,-0.064852,362.98,-0.072489,0.0096181,0.99732,13.398
> view matrix models
> #3,-0.34012,0.93977,-0.033785,66.434,-0.93758,-0.34166,-0.064852,363.46,-0.072489,0.0096181,0.99732,11.596,#4,-0.34012,0.93977,-0.033785,66.434,-0.93758,-0.34166,-0.064852,363.46,-0.072489,0.0096181,0.99732,11.596,#5,-0.34012,0.93977,-0.033785,66.434,-0.93758,-0.34166,-0.064852,363.46,-0.072489,0.0096181,0.99732,11.596
> view matrix models
> #3,-0.34012,0.93977,-0.033785,66.513,-0.93758,-0.34166,-0.064852,363.32,-0.072489,0.0096181,0.99732,11.452,#4,-0.34012,0.93977,-0.033785,66.513,-0.93758,-0.34166,-0.064852,363.32,-0.072489,0.0096181,0.99732,11.452,#5,-0.34012,0.93977,-0.033785,66.513,-0.93758,-0.34166,-0.064852,363.32,-0.072489,0.0096181,0.99732,11.452
> ui tool show "Fit in Map"
Correlation = 0.2279, Correlation about mean = 0.03845, Overlap = 3451
> fitmap #3 inMap #1
Fit map cryosparc_P25_J2466_008_volume_map_sharp.mrc in map
cryosparc_P25_J3036_009_volume_map_sharp.mrc using 92712 points
correlation = 0.3074, correlation about mean = 0.1152, overlap = 4842
steps = 68, shift = 2.46, angle = 1.96 degrees
Position of cryosparc_P25_J2466_008_volume_map_sharp.mrc (#3) relative to
cryosparc_P25_J3036_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.31800830 0.94752153 -0.03276698 63.50912259
-0.94681063 -0.31918355 -0.04088414 359.37163027
-0.04919728 0.01802263 0.99862646 6.66822830
Axis 0.03108013 0.00866888 -0.99947930
Axis point 161.00126586 156.87550088 0.00000000
Rotation angle (degrees) 108.61955078
Shift along axis -1.57553289
Correlation = 0.359, Correlation about mean = 0.0558, Overlap = 3851
> fitmap #4 inMap #3
Fit map cryosparc_P25_J2629_005_volume_map_sharp.mrc in map
cryosparc_P25_J2466_008_volume_map_sharp.mrc using 78763 points
correlation = 0.9836, correlation about mean = 0.9613, overlap = 1.482e+04
steps = 140, shift = 2.35, angle = 1.91 degrees
Position of cryosparc_P25_J2629_005_volume_map_sharp.mrc (#4) relative to
cryosparc_P25_J2466_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99998931 -0.00240317 0.00395024 -0.11607644
0.00240148 0.99999702 0.00043164 -0.41373182
-0.00395127 -0.00042215 0.99999210 0.47187840
Axis -0.09193509 0.85081851 0.51735462
Axis point 132.08883178 -0.00000000 32.00451413
Rotation angle (degrees) 0.26605240
Shift along axis -0.09721072
Average map value = 0.151 for 10582 atoms, 5577 outside contour
> fitmap #5 inMap #4
Fit molecule output_J2629_coot-20240807_real_space_refined_197.pdb (#5) to map
cryosparc_P25_J2629_005_volume_map_sharp.mrc (#4) using 10582 atoms
average map value = 0.4241, steps = 52
shifted from previous position = 2.3
rotated from previous position = 1.93 degrees
atoms outside contour = 1933, contour level = 0.15
Position of output_J2629_coot-20240807_real_space_refined_197.pdb (#5)
relative to cryosparc_P25_J2629_005_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99999994 -0.00000618 -0.00033481 0.06303871
0.00000611 0.99999998 -0.00021693 0.03230441
0.00033481 0.00021693 0.99999992 -0.08913921
Axis 0.54370068 -0.83913774 0.01540877
Axis point 266.54846547 0.00000000 178.83190246
Rotation angle (degrees) 0.02286046
Shift along axis 0.00579282
> select subtract #4
10582 atoms, 10854 bonds, 2 pseudobonds, 1350 residues, 4 models selected
> hide #!4 models
> hide #!1 models
> volume #3 level 0.13
> show #!1 models
> surface undust #1-4
> surface dust #1-4
> volume #3 level 0.12
> volume #3 level 0.1
> volume #3 level 0.11
> volume #3 level 0.12
> hide #!1 models
> hide #!5 models
> select subtract #5
2 models selected
> show #!1 models
> select subtract #3
Nothing selected
> save D:/Documents/Projects/Tat/Figs/Figure1/fig1c_mapsAndModels.cxs
> hide #!3 models
> show #!6 models
> hide #!1 models
> volume #6 level 0.1074
> surface dust #1-8
> select add #6
2 models selected
> select add #7
4 models selected
> select add #8
6887 atoms, 7069 bonds, 874 residues, 5 models selected
> view matrix models
> #6,1,0,0,-0.076,0,1,0,59.149,0,0,1,-39.952,#7,1,0,0,-0.076,0,1,0,59.149,0,0,1,-39.952,#8,1,0,0,-0.076,0,1,0,59.149,0,0,1,-39.952
> view matrix models
> #6,1,0,0,1.5175,0,1,0,103.99,0,0,1,-68.471,#7,1,0,0,1.5175,0,1,0,103.99,0,0,1,-68.471,#8,1,0,0,1.5175,0,1,0,103.99,0,0,1,-68.471
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.483,0.3686,0.79426,59.709,-0.35891,0.74404,-0.56356,285.38,-0.79868,-0.55726,-0.22707,329.2,#7,-0.483,0.3686,0.79426,59.709,-0.35891,0.74404,-0.56356,285.38,-0.79868,-0.55726,-0.22707,329.2,#8,-0.483,0.3686,0.79426,59.709,-0.35891,0.74404,-0.56356,285.38,-0.79868,-0.55726,-0.22707,329.2
> view matrix models
> #6,-0.20761,0.35654,0.91092,0.22672,-0.46737,0.7819,-0.41256,273.88,-0.85934,-0.51139,0.0042998,296.71,#7,-0.20761,0.35654,0.91092,0.22672,-0.46737,0.7819,-0.41256,273.88,-0.85934,-0.51139,0.0042998,296.71,#8,-0.20761,0.35654,0.91092,0.22672,-0.46737,0.7819,-0.41256,273.88,-0.85934,-0.51139,0.0042998,296.71
> view matrix models
> #6,-0.26703,0.3508,0.89757,12.538,-0.50638,0.74137,-0.44039,290.46,-0.81993,-0.57211,-0.020331,303.46,#7,-0.26703,0.3508,0.89757,12.538,-0.50638,0.74137,-0.44039,290.46,-0.81993,-0.57211,-0.020331,303.46,#8,-0.26703,0.3508,0.89757,12.538,-0.50638,0.74137,-0.44039,290.46,-0.81993,-0.57211,-0.020331,303.46
> view matrix models
> #6,0.074979,0.90669,-0.41508,72.742,-0.49777,-0.32665,-0.80344,507.06,-0.86406,0.26686,0.42683,114.66,#7,0.074979,0.90669,-0.41508,72.742,-0.49777,-0.32665,-0.80344,507.06,-0.86406,0.26686,0.42683,114.66,#8,0.074979,0.90669,-0.41508,72.742,-0.49777,-0.32665,-0.80344,507.06,-0.86406,0.26686,0.42683,114.66
> view matrix models
> #6,-0.038439,0.92082,-0.38808,84.456,-0.50549,-0.35293,-0.78735,509.85,-0.86198,0.1659,0.47903,121.81,#7,-0.038439,0.92082,-0.38808,84.456,-0.50549,-0.35293,-0.78735,509.85,-0.86198,0.1659,0.47903,121.81,#8,-0.038439,0.92082,-0.38808,84.456,-0.50549,-0.35293,-0.78735,509.85,-0.86198,0.1659,0.47903,121.81
> view matrix models
> #6,-0.02534,0.92124,-0.38818,82.333,-0.53704,-0.34006,-0.77198,510.55,-0.84318,0.1889,0.50335,111.63,#7,-0.02534,0.92124,-0.38818,82.333,-0.53704,-0.34006,-0.77198,510.55,-0.84318,0.1889,0.50335,111.63,#8,-0.02534,0.92124,-0.38818,82.333,-0.53704,-0.34006,-0.77198,510.55,-0.84318,0.1889,0.50335,111.63
> view matrix models
> #6,-0.038809,0.96975,-0.24101,54.739,-0.54025,-0.22326,-0.81134,499.22,-0.84061,0.098718,0.53258,120.55,#7,-0.038809,0.96975,-0.24101,54.739,-0.54025,-0.22326,-0.81134,499.22,-0.84061,0.098718,0.53258,120.55,#8,-0.038809,0.96975,-0.24101,54.739,-0.54025,-0.22326,-0.81134,499.22,-0.84061,0.098718,0.53258,120.55
> view matrix models
> #6,-0.065045,0.96941,-0.23667,58.288,-0.48635,-0.23789,-0.84075,497.37,-0.87134,0.060418,0.48695,138.18,#7,-0.065045,0.96941,-0.23667,58.288,-0.48635,-0.23789,-0.84075,497.37,-0.87134,0.060418,0.48695,138.18,#8,-0.065045,0.96941,-0.23667,58.288,-0.48635,-0.23789,-0.84075,497.37,-0.87134,0.060418,0.48695,138.18
> view matrix models
> #6,-0.081293,-0.23639,0.96825,61.944,-0.63458,0.76139,0.13261,220.78,-0.76857,-0.60366,-0.21191,329.2,#7,-0.081293,-0.23639,0.96825,61.944,-0.63458,0.76139,0.13261,220.78,-0.76857,-0.60366,-0.21191,329.2,#8,-0.081293,-0.23639,0.96825,61.944,-0.63458,0.76139,0.13261,220.78,-0.76857,-0.60366,-0.21191,329.2
> view matrix models
> #6,0.019003,-0.80041,-0.59916,369.88,-0.62285,-0.47826,0.61914,334.16,-0.78211,0.36142,-0.50762,229.03,#7,0.019003,-0.80041,-0.59916,369.88,-0.62285,-0.47826,0.61914,334.16,-0.78211,0.36142,-0.50762,229.03,#8,0.019003,-0.80041,-0.59916,369.88,-0.62285,-0.47826,0.61914,334.16,-0.78211,0.36142,-0.50762,229.03
> view matrix models
> #6,-0.058928,-0.8177,-0.57263,380.84,-0.51334,-0.46715,0.7199,299.83,-0.85616,0.33638,-0.39223,227.08,#7,-0.058928,-0.8177,-0.57263,380.84,-0.51334,-0.46715,0.7199,299.83,-0.85616,0.33638,-0.39223,227.08,#8,-0.058928,-0.8177,-0.57263,380.84,-0.51334,-0.46715,0.7199,299.83,-0.85616,0.33638,-0.39223,227.08
> select subtract #7
6887 atoms, 7069 bonds, 874 residues, 3 models selected
> hide #!6 models
> select subtract #6
6887 atoms, 7069 bonds, 874 residues, 1 model selected
> show #8 models
> show #!6 models
> hide #!6 models
> show #!2 models
> hide #!1 models
> style sel stick
Changed 6887 atom styles
> select clear
> style #8#!2 stick
Changed 20922 atom styles
> show #8#!2 cartoons
> select add #8
6887 atoms, 7069 bonds, 874 residues, 1 model selected
> select add #7
6887 atoms, 7069 bonds, 874 residues, 3 models selected
> select add #6
6887 atoms, 7069 bonds, 874 residues, 5 models selected
> view matrix models
> #6,-0.14605,-0.80187,-0.57938,393.29,-0.20186,-0.54918,0.81096,249.17,-0.96846,0.2354,-0.08166,213.95,#7,-0.14605,-0.80187,-0.57938,393.29,-0.20186,-0.54918,0.81096,249.17,-0.96846,0.2354,-0.08166,213.95,#8,-0.14605,-0.80187,-0.57938,393.29,-0.20186,-0.54918,0.81096,249.17,-0.96846,0.2354,-0.08166,213.95
> view matrix models
> #6,-0.026345,0.96329,0.26717,-26.196,-0.46093,0.22545,-0.85832,421.42,-0.88704,-0.14576,0.43807,181.86,#7,-0.026345,0.96329,0.26717,-26.196,-0.46093,0.22545,-0.85832,421.42,-0.88704,-0.14576,0.43807,181.86,#8,-0.026345,0.96329,0.26717,-26.196,-0.46093,0.22545,-0.85832,421.42,-0.88704,-0.14576,0.43807,181.86
> view matrix models
> #6,0.12489,0.95406,0.27234,-49.663,-0.52218,0.2966,-0.7996,411.36,-0.84364,-0.042348,0.53524,144.33,#7,0.12489,0.95406,0.27234,-49.663,-0.52218,0.2966,-0.7996,411.36,-0.84364,-0.042348,0.53524,144.33,#8,0.12489,0.95406,0.27234,-49.663,-0.52218,0.2966,-0.7996,411.36,-0.84364,-0.042348,0.53524,144.33
> view matrix models
> #6,0.024368,0.96666,0.2549,-32.961,-0.55852,0.22463,-0.7985,428.13,-0.82913,-0.12291,0.54537,152.96,#7,0.024368,0.96666,0.2549,-32.961,-0.55852,0.22463,-0.7985,428.13,-0.82913,-0.12291,0.54537,152.96,#8,0.024368,0.96666,0.2549,-32.961,-0.55852,0.22463,-0.7985,428.13,-0.82913,-0.12291,0.54537,152.96
> view matrix models
> #6,0.081882,0.98059,-0.17814,20.779,-0.44397,-0.12414,-0.8874,477.2,-0.89229,0.15175,0.42519,138.59,#7,0.081882,0.98059,-0.17814,20.779,-0.44397,-0.12414,-0.8874,477.2,-0.89229,0.15175,0.42519,138.59,#8,0.081882,0.98059,-0.17814,20.779,-0.44397,-0.12414,-0.8874,477.2,-0.89229,0.15175,0.42519,138.59
> view matrix models
> #6,0.10261,0.97865,-0.17809,17.766,-0.54499,-0.094459,-0.8331,480.55,-0.83214,0.18254,0.52367,109.43,#7,0.10261,0.97865,-0.17809,17.766,-0.54499,-0.094459,-0.8331,480.55,-0.83214,0.18254,0.52367,109.43,#8,0.10261,0.97865,-0.17809,17.766,-0.54499,-0.094459,-0.8331,480.55,-0.83214,0.18254,0.52367,109.43
> view matrix models
> #6,0.067942,0.98261,-0.17283,21.893,-0.54467,-0.10861,-0.83159,482.47,-0.83589,0.15064,0.52782,114.34,#7,0.067942,0.98261,-0.17283,21.893,-0.54467,-0.10861,-0.83159,482.47,-0.83589,0.15064,0.52782,114.34,#8,0.067942,0.98261,-0.17283,21.893,-0.54467,-0.10861,-0.83159,482.47,-0.83589,0.15064,0.52782,114.34
> view matrix models
> #6,0.067533,0.96322,-0.26011,38.074,-0.54761,-0.18214,-0.81667,492.07,-0.83401,0.19759,0.51516,108.68,#7,0.067533,0.96322,-0.26011,38.074,-0.54761,-0.18214,-0.81667,492.07,-0.83401,0.19759,0.51516,108.68,#8,0.067533,0.96322,-0.26011,38.074,-0.54761,-0.18214,-0.81667,492.07,-0.83401,0.19759,0.51516,108.68
> view matrix models
> #6,0.067651,0.96819,-0.24089,34.396,-0.54696,-0.16594,-0.82055,490.04,-0.83442,0.18727,0.51834,109.86,#7,0.067651,0.96819,-0.24089,34.396,-0.54696,-0.16594,-0.82055,490.04,-0.83442,0.18727,0.51834,109.86,#8,0.067651,0.96819,-0.24089,34.396,-0.54696,-0.16594,-0.82055,490.04,-0.83442,0.18727,0.51834,109.86
> show #!1 models
> show #!6 models
> view matrix models
> #6,-0.10057,0.96887,-0.22622,58.715,-0.56748,-0.24262,-0.78683,499.87,-0.81722,0.049245,0.57422,119.71,#7,-0.10057,0.96887,-0.22622,58.715,-0.56748,-0.24262,-0.78683,499.87,-0.81722,0.049245,0.57422,119.71,#8,-0.10057,0.96887,-0.22622,58.715,-0.56748,-0.24262,-0.78683,499.87,-0.81722,0.049245,0.57422,119.71
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.10057,0.96887,-0.22622,58.722,-0.56748,-0.24262,-0.78683,391.38,-0.81722,0.049245,0.57422,162.61,#7,-0.10057,0.96887,-0.22622,58.722,-0.56748,-0.24262,-0.78683,391.38,-0.81722,0.049245,0.57422,162.61,#8,-0.10057,0.96887,-0.22622,58.722,-0.56748,-0.24262,-0.78683,391.38,-0.81722,0.049245,0.57422,162.61
> view matrix models
> #6,-0.10057,0.96887,-0.22622,56.804,-0.56748,-0.24262,-0.78683,405.07,-0.81722,0.049245,0.57422,191.18,#7,-0.10057,0.96887,-0.22622,56.804,-0.56748,-0.24262,-0.78683,405.07,-0.81722,0.049245,0.57422,191.18,#8,-0.10057,0.96887,-0.22622,56.804,-0.56748,-0.24262,-0.78683,405.07,-0.81722,0.049245,0.57422,191.18
Correlation = 0.2953, Correlation about mean = 0.05576, Overlap = 3557
> fitmap #6 inMap #1
Fit map cryosparc_P25_J2943_007_volume_map_sharp.mrc in map
cryosparc_P25_J3036_009_volume_map_sharp.mrc using 162932 points
correlation = 0.6817, correlation about mean = 0.6048, overlap = 9562
steps = 96, shift = 1.9, angle = 6.94 degrees
Position of cryosparc_P25_J2943_007_volume_map_sharp.mrc (#6) relative to
cryosparc_P25_J3036_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.13243629 0.93506517 -0.32880654 82.40709185
-0.59112573 -0.34078937 -0.73104923 415.13959771
-0.79563245 0.09754856 0.59787396 178.63692517
Axis 0.46077607 0.25959786 -0.84870158
Axis point 243.21551521 203.53099677 0.00000000
Rotation angle (degrees) 115.95568493
Shift along axis -5.86887431
Correlation = 0.4724, Correlation about mean = 0.1489, Overlap = 2241
> fitmap #7 inMap #6
Fit map cryosparc_P25_J3003_004_volume_map_sharp.mrc in map
cryosparc_P25_J2943_007_volume_map_sharp.mrc using 48881 points
correlation = 0.9655, correlation about mean = 0.9091, overlap = 6387
steps = 108, shift = 2.08, angle = 6.82 degrees
Position of cryosparc_P25_J3003_004_volume_map_sharp.mrc (#7) relative to
cryosparc_P25_J2943_007_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.99999905 -0.00123089 0.00061629 -0.05391621
0.00122976 0.99999757 0.00183028 -0.44941763
-0.00061854 -0.00182952 0.99999814 0.34409443
Axis -0.79913368 0.26962917 0.53729458
Axis point 0.00000000 156.45023591 261.48545541
Rotation angle (degrees) 0.13119918
Shift along axis 0.10679023
Average map value = 0.1364 for 6887 atoms, 4007 outside contour
> fitmap #8 inMap #7
Fit molecule output_J3003_coot-20240807_real_space_refined_195.pdb (#8) to map
cryosparc_P25_J3003_004_volume_map_sharp.mrc (#7) using 6887 atoms
average map value = 0.3428, steps = 100
shifted from previous position = 2.06
rotated from previous position = 6.83 degrees
atoms outside contour = 1428, contour level = 0.15
Position of output_J3003_coot-20240807_real_space_refined_195.pdb (#8)
relative to cryosparc_P25_J3003_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.99999989 -0.00017022 0.00043172 -0.01831326
0.00017032 0.99999996 -0.00024218 -0.00347003
-0.00043168 0.00024226 0.99999988 0.03180211
Axis 0.46271566 0.82468054 0.32526333
Axis point 74.40588895 0.00000000 41.37514647
Rotation angle (degrees) 0.02999297
Shift along axis -0.00099144
> hide #!2 models
> show #!7 models
> hide #8 models
> hide #!1 models
> select subtract #6
6887 atoms, 7069 bonds, 874 residues, 3 models selected
> select subtract #7
6887 atoms, 7069 bonds, 874 residues, 1 model selected
> select subtract #8
Nothing selected
> show #8 models
> hide #!6 models
> hide #!7 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!5 models
> hide #8 models
> style #!2,5 stick
Changed 24617 atom styles
> show #!2,5 cartoons
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> select add #1
2 models selected
> select subtract #1
Nothing selected
> show #!3 models
> select add #3
2 models selected
> view matrix models
> #3,-0.31801,0.94752,-0.032767,63.199,-0.94681,-0.31918,-0.040884,355.19,-0.049197,0.018023,0.99863,2.9514
Correlation = 0.5535, Correlation about mean = 0.3763, Overlap = 1.066e+04
> fitmap #3 inMap #1
Fit map cryosparc_P25_J2466_008_volume_map_sharp.mrc in map
cryosparc_P25_J3036_009_volume_map_sharp.mrc using 142119 points
correlation = 0.8197, correlation about mean = 0.7439, overlap = 1.668e+04
steps = 88, shift = 1.51, angle = 1.01 degrees
Position of cryosparc_P25_J2466_008_volume_map_sharp.mrc (#3) relative to
cryosparc_P25_J3036_009_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.30451524 0.95221891 -0.02344415 58.68016932
-0.95116400 -0.30530040 -0.04559295 355.56211770
-0.05057198 0.00841549 0.99868496 3.66333765
Axis 0.02836068 0.01424525 -0.99949625
Axis point 159.10022731 156.42989752 0.00000000
Rotation angle (degrees) 107.79217924
Shift along axis 3.06778751
Correlation = 0.3765, Correlation about mean = 0.1091, Overlap = 3869
> fitmap #4 inMap #3
Fit map cryosparc_P25_J2629_005_volume_map_sharp.mrc in map
cryosparc_P25_J2466_008_volume_map_sharp.mrc using 78763 points
correlation = 0.3718, correlation about mean = 0.1161, overlap = 3961
steps = 60, shift = 0.188, angle = 0.292 degrees
Position of cryosparc_P25_J2629_005_volume_map_sharp.mrc (#4) relative to
cryosparc_P25_J2466_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99986893 0.01546957 0.00477579 -6.33648157
-0.01543353 0.99985281 -0.00749402 3.29509390
-0.00489102 0.00741933 0.99996051 4.13145796
Axis 0.41833775 0.27116565 -0.86686949
Axis point 304.74870595 267.81866825 0.00000000
Rotation angle (degrees) 1.02132517
Shift along axis -5.33870803
> hide #!1 models
> show #!4 models
> select subtract #3
Nothing selected
> select add #4
2 models selected
> view matrix models
> #4,-0.31906,0.94719,-0.032033,63.732,-0.9461,-0.32031,-0.047846,356.97,-0.05558,0.015042,0.99834,3.1868
Correlation = 0.8433, Correlation about mean = 0.6724, Overlap = 1.134e+04
> fitmap #4 inMap #3
Fit map cryosparc_P25_J2629_005_volume_map_sharp.mrc in map
cryosparc_P25_J2466_008_volume_map_sharp.mrc using 78763 points
correlation = 0.9836, correlation about mean = 0.9613, overlap = 1.478e+04
steps = 124, shift = 0.799, angle = 1.12 degrees
Position of cryosparc_P25_J2629_005_volume_map_sharp.mrc (#4) relative to
cryosparc_P25_J2466_008_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99998904 -0.00242317 0.00400659 -0.12049359
0.00242152 0.99999698 0.00041625 -0.40538895
-0.00400759 -0.00040655 0.99999189 0.46746148
Axis -0.08752457 0.85249950 0.51534847
Axis point 128.68438135 0.00000000 32.48247903
Rotation angle (degrees) 0.26931414
Shift along axis -0.09414217
> hide #!4 models
> select subtract #4
Nothing selected
> show #!1 models
Correlation = 0.9836, Correlation about mean = 0.9613, Overlap = 1.478e+04
Correlation = 0.8197, Correlation about mean = 0.7439, Overlap = 1.668e+04
> volume #1 level 0.3464
> volume #3 level 0.3237
> volume #3 level 0.2062
> hide #!5 models
> hide #!3 models
> show #!6 models
> volume #7 level 0.1646
> volume #6 level 0.3509
> hide #!6 models
> show #!6 models
> volume #1 level 0.15
> volume #3 level 0.13
> volume #3 level 0.12
> volume #3 level 0.11
> volume #3 level 0.12
> volume #6 level 0.11
> volume #6 level 0.12
> volume #6 level 0.13
> volume #6 level 0.12
> save D:/Documents/Projects/Tat/Figs/Figure1/fig1c_mapsAndModels.cxs
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!3 models
> save D:/Documents/Projects/Tat/Figs/Figure1/maps_and_models.cxs
——— End of log from Wed Aug 21 13:10:43 2024 ———
opened ChimeraX session
> hide #!2 models
> show #!3 models
> hide #!1 models
> show #!4 models
> show #!1 models
> hide #!3 models
> hide #!4 models
> show #!6 models
> hide #!1 models
> show #!7 models
> ui tool show "Fit in Map"
Correlation = 0.9673, Correlation about mean = 0.9092, Overlap = 6276
> fitmap #7 inMap #6
Fit map cryosparc_P25_J3003_004_volume_map_sharp.mrc in map
cryosparc_P25_J2943_007_volume_map_sharp.mrc using 43598 points
correlation = 0.9673, correlation about mean = 0.9093, overlap = 6271
steps = 80, shift = 0.0098, angle = 0.0122 degrees
Position of cryosparc_P25_J3003_004_volume_map_sharp.mrc (#7) relative to
cryosparc_P25_J2943_007_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.99999917 -0.00105611 0.00073719 -0.10732086
0.00105477 0.99999781 0.00180702 -0.41303505
-0.00073910 -0.00180624 0.99999810 0.36287894
Axis -0.81426628 0.33268876 0.47569802
Axis point 0.00000000 168.35078568 251.34809204
Rotation angle (degrees) 0.12712322
Shift along axis 0.12259643
> volume #6 level 0.2332
> volume #7 level 0.2622
> show #8 models
> show #!3 models
> hide #!3 models
> show #!4 models
> volume #4 level 0.3798
> show #!1 models
> volume #1 level 0.3027
> hide #!6 models
> hide #!7 models
> hide #8 models
> open D:/Documents/Projects/Tat/deposition/output_J3003_coot-20240807.pdb
Summary of feedback from opening
D:/Documents/Projects/Tat/deposition/output_J3003_coot-20240807.pdb
---
warning | End residue of secondary structure not found: HELIX 55 55 ARG F 24 SER F 62 1 39
Chain information for output_J3003_coot-20240807.pdb #9
---
Chain | Description
A B C | No description available
D | No description available
E F | No description available
> mmaker #9 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker output_J3003_coot-20240807_real_space_refined_195.pdb, chain C (#8)
with output_J3003_coot-20240807.pdb, chain A (#9), sequence alignment score =
1214.3
RMSD between 231 pruned atom pairs is 0.000 angstroms; (across all 231 pairs:
0.000)
> hide #!1 models
> hide #!4 models
> style #9 stick
Changed 6887 atom styles
> show #9 cartoons
> show #8 models
> hide #8 models
> show #8 models
> hide #9 models
> close #8
> open D:/Documents/Projects/Tat/deposition/output_J3003_coot-20240807.pdb
Summary of feedback from opening
D:/Documents/Projects/Tat/deposition/output_J3003_coot-20240807.pdb
---
warning | End residue of secondary structure not found: HELIX 55 55 ARG F 24 SER F 62 1 39
Chain information for output_J3003_coot-20240807.pdb #8
---
Chain | Description
A B C | No description available
D | No description available
E F | No description available
> mmaker #8 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker output_J3003_coot-20240807.pdb, chain A (#9) with
output_J3003_coot-20240807.pdb, chain A (#8), sequence alignment score =
1214.3
RMSD between 231 pruned atom pairs is 0.000 angstroms; (across all 231 pairs:
0.000)
> close #9
> style #8 stick
Changed 6887 atom styles
> show #8 cartoons
> show #!5 models
> show #!2 models
> hide atoms
> hide #!2 models
> hide #!5 models
> color /A rgb(252,140,192)
> color /B rgb(141,231,188)
> color /C mediumpurple
> color /D rgb(255,255,150)
> color /E rgb(242,201,182)
> color /F lightsalmon
> color /G cyan
> color /H silver
> volume #1 level 0.18
> show #!1 models
> hide #8 models
> volume zone #1 nearAtoms #2 range 2
> hide #!1 models
> show #!1 models
> volume unzone #1
> hide #8 models
> save D:/Documents/Projects/Tat/Figs/Figure1/fig1c_mapsAndModels.cxs
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> volume zone #1 nearAtoms #2 range 2 newMap true
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #9, grid size
256,256,256, pixel 1.2, shown at step 1, values float32
> color zone #3 near #2 distance 6
> surface dust #3 size 4.08
> surface dust #9 size 4.08
> surface dust #9 size 3
> surface dust #9 size 2
> color zone #3 near #2 distance 6
> show #!3 models
> hide #!3 models
> color zone #9 near #2 distance 6
> turn x 90
[Repeated 3 time(s)]
> save D:/Documents/Projects/Tat/Figs/Figure1/maps_and_models.cxs
——— End of log from Wed Aug 21 13:42:49 2024 ———
opened ChimeraX session
> volume #4 level 0.18
> hide #!9 models
> hide #!2 models
> volume zone #4 nearAtoms #5 range 2 newMap true
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc zone as #10, grid size
256,256,256, pixel 1.2, shown at step 1, values float32
> color zone #10 near #5 distance 6
> surface dust #3 size 2
> surface dust #10 size 2
> show #!5 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> hide #!5 models
> show #8 models
> hide #!10 models
> close #10
> show #!7 models
> show #8 atoms
> ui tool show "Fit in Map"
Average map value = 0.3428 for 6887 atoms, 2938 outside contour
> fitmap #8 inMap #7
Fit molecule output_J3003_coot-20240807.pdb (#8) to map
cryosparc_P25_J3003_004_volume_map_sharp.mrc (#7) using 6887 atoms
average map value = 0.3428, steps = 64
shifted from previous position = 0.0218
rotated from previous position = 0.0287 degrees
atoms outside contour = 2939, contour level = 0.26219
Position of output_J3003_coot-20240807.pdb (#8) relative to
cryosparc_P25_J3003_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.99999993 0.00015424 0.00035202 -0.06859111
-0.00015417 0.99999997 -0.00019643 0.03109752
-0.00035205 0.00019637 0.99999992 0.02025598
Axis 0.45505088 0.81564522 -0.35728361
Axis point 44.21711406 0.00000000 177.94666218
Rotation angle (degrees) 0.02472875
Shift along axis -0.01308503
Average map value = 0.1319 for 10582 atoms, 7064 outside contour
> hide #8 models
> hide #!7 models
> show #!4 models
> show #!5 models
> fitmap #5 inMap #4
Fit molecule output_J2629_coot-20240807_real_space_refined_197.pdb (#5) to map
cryosparc_P25_J2629_005_volume_map_sharp.mrc (#4) using 10582 atoms
average map value = 0.1329, steps = 48
shifted from previous position = 0.318
rotated from previous position = 0.592 degrees
atoms outside contour = 7072, contour level = 0.18
Position of output_J2629_coot-20240807_real_space_refined_197.pdb (#5)
relative to cryosparc_P25_J2629_005_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99995578 0.00879474 -0.00333147 -4.45771076
-0.00880084 0.99995961 -0.00182135 1.39255376
0.00331531 0.00185059 0.99999279 3.54118904
Axis 0.19160373 -0.34683262 -0.91814767
Axis point -24.46268622 406.77350485 0.00000000
Rotation angle (degrees) 0.54902297
Shift along axis -4.58843155
> select add #5
10582 atoms, 10854 bonds, 2 pseudobonds, 1350 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.31057,0.95022,-0.024997,59.905,-0.94917,-0.31143,-0.045808,355.02,-0.051312,0.0094997,0.99864,3.8985
Average map value = 0.3217 for 10582 atoms, 3826 outside contour
> fitmap #5 inMap #4
Fit molecule output_J2629_coot-20240807_real_space_refined_197.pdb (#5) to map
cryosparc_P25_J2629_005_volume_map_sharp.mrc (#4) using 10582 atoms
average map value = 0.4241, steps = 68
shifted from previous position = 1.25
rotated from previous position = 0.541 degrees
atoms outside contour = 2546, contour level = 0.18
Position of output_J2629_coot-20240807_real_space_refined_197.pdb (#5)
relative to cryosparc_P25_J2629_005_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99999990 -0.00005146 -0.00044672 0.08353882
0.00005137 0.99999998 -0.00020710 0.02646441
0.00044673 0.00020708 0.99999988 -0.09560008
Axis 0.41830996 -0.90234716 0.10385753
Axis point 214.31608682 0.00000000 185.89421676
Rotation angle (degrees) 0.02836517
Shift along axis 0.00113625
> show sel atoms
Average map value = 0.4241 for 10582 atoms, 2546 outside contour
> fitmap #5 inMap #4
Fit molecule output_J2629_coot-20240807_real_space_refined_197.pdb (#5) to map
cryosparc_P25_J2629_005_volume_map_sharp.mrc (#4) using 10582 atoms
average map value = 0.4241, steps = 64
shifted from previous position = 0.0145
rotated from previous position = 0.00357 degrees
atoms outside contour = 2547, contour level = 0.18
Position of output_J2629_coot-20240807_real_space_refined_197.pdb (#5)
relative to cryosparc_P25_J2629_005_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99999988 -0.00001864 -0.00049236 0.09794655
0.00001855 0.99999998 -0.00018043 0.02227151
0.00049237 0.00018042 0.99999986 -0.10201872
Axis 0.34385682 -0.93835323 0.03543599
Axis point 207.91436023 0.00000000 192.47912523
Rotation angle (degrees) 0.03006374
Shift along axis 0.00916591
> volume zone #4 nearAtoms #5 range 2 newMap true
Opened cryosparc_P25_J2629_005_volume_map_sharp.mrc zone as #10, grid size
256,256,256, pixel 1.2, shown at step 1, values float32
> color zone #10 near #5 distance 6
> select subtract #5
Nothing selected
> surface dust #10 size 2
> hide #!5 models
> hide #!10 models
> volume #7 level 0.18
> volume zone #7 nearAtoms #8 range 2 newMap true
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc zone as #11, grid size
256,256,256, pixel 1.2, shown at step 1, values float32
> color zone #11 near #8 distance 6
> surface dust #3 size 2
> surface dust #3 size 7
> surface dust #11 size 2
> surface dust #11 size 7
> surface dust #11 size 3
> show #8 models
> surface dust #11 size 2
> turn x 90
[Repeated 7 time(s)]
> show #!1 models
> hide #!1 models
> hide #8 models
> show #!9 models
> show #!10 models
> hide #!10 models
> hide #!9 models
> turn x 90
[Repeated 2 time(s)]
> show #!10 models
> turn x 90
[Repeated 4 time(s)]
> hide #!10 models
> turn x 90
[Repeated 2 time(s)]
> show #!9 models
> show #!10 models
> turn x 90
[Repeated 11 time(s)]
> hide #!9 models
> hide #!10 models
> turn x 90
[Repeated 4 time(s)]
> show #!9 models
> show #!10 models
> turn x 90
[Repeated 3 time(s)]
> hide #!10 models
> hide #!9 models
> turn x 90
[Repeated 3 time(s)]
> show #!9 models
> turn x 90
[Repeated 7 time(s)]
> hide #!9 models
> turn x 90
[Repeated 2 time(s)]
> show #!9 models
> show #!10 models
> turn x 90
[Repeated 4 time(s)]
> hide #!9 models
> hide #!10 models
> hide #!11 models
> show #!9 models
> show #!10 models
> hide #!10 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!11 models
> hide #!10 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!10 models
> hide #!10 models
> hide #!9 models
> turn x 90
[Repeated 2 time(s)]
> show #!10 models
> show #!9 models
> turn x 90
[Repeated 12 time(s)]
> save D:/Documents/Projects/Tat/Figs/Figure1/maps_and_models.cxs
> hide #!11 models
> hide #!10 models
> show #!10 models
> show #!11 models
> turn x 90
[Repeated 2 time(s)]
> hide #!10 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!10 models
> hide #!9 models
> ui tool show "Side View"
> turn x 90
[Repeated 14 time(s)]
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> turn x 90
[Repeated 21 time(s)]
> turn x -90
> turn x 90
[Repeated 8 time(s)]
> turn x -90
> turn x 90
> save D:/Documents/Projects/Tat/Figs/Figure1/maps_and_models.cxs
——— End of log from Wed Aug 21 14:06:13 2024 ———
opened ChimeraX session
> turn x 90
[Repeated 3 time(s)]
> save D:/Documents/Projects/Tat/Figs/Figure1/maps_and_models.cxs
——— End of log from Wed Aug 21 14:09:35 2024 ———
opened ChimeraX session
> turn x 90
> save D:\Documents\Projects\Tat\Figs\Figure1\BC_top.png width 3000 height
> 3000 supersample 6 transparentBackground true
> turn x 90
[Repeated 1 time(s)]
> save D:\Documents\Projects\Tat\Figs\Figure1\BC_bottom.png width 3000 height
> 3000 supersample 6 transparentBackground true
> save D:\Documents\Projects\Tat\Figs\Figure1\BC1S_bottom.png width 3000
> height 3000 supersample 6 transparentBackground true
> turn x 90
> show #!2 models
> lighting soft
> lighting depthCue true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> set silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> set silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> hide #!2 models
> lighting gentle
> lighting soft
> save D:/Documents/Projects/Tat/Figs/Figure1/maps_and_models.cxs
> save D:\Documents\Projects\Tat\Figs\Figure1\BC2S_side.png width 3000 height
> 3000 supersample 6 transparentBackground true
> show #!10 models
> hide #!9 models
> save D:\Documents\Projects\Tat\Figs\Figure1\BC1S_side.png width 3000 height
> 3000 supersample 6 transparentBackground true
> show #!11 models
> hide #!10 models
> save D:\Documents\Projects\Tat\Figs\Figure1\BC_side.png width 3000 height
> 3000 supersample 6 transparentBackground true
> show #!10 models
> show #!9 models
> turn x 90
> hide #!9 models
> hide #!10 models
> save D:\Documents\Projects\Tat\Figs\Figure1\BC_top.png width 3000 height
> 3000 supersample 6 transparentBackground true
> surface dust #11 size 3
> show #!10 models
> show #!9 models
> turn x 90
[Repeated 2 time(s)]
> save D:/Documents/Projects/Tat/Figs/Figure1/maps_and_models.cxs
> turn x 90
[Repeated 3 time(s)]
> hide #!9 models
> hide #!10 models
> save D:\Documents\Projects\Tat\Figs\Figure1\BC_side.png width 3000 height
> 3000 supersample 6 transparentBackground true
> show #!10 models
> show #!9 models
> turn x 90
> hide #!9 models
> hide #!10 models
> save D:\Documents\Projects\Tat\Figs\Figure1\BC_top.png width 3000 height
> 3000 supersample 6 transparentBackground true
> show #!10 models
> show #!9 models
> turn x 90
[Repeated 1 time(s)]
> hide #!10 models
> hide #!9 models
> save D:\Documents\Projects\Tat\Figs\Figure1\BC_bottom.png width 3000 height
> 3000 supersample 6 transparentBackground true
> show #!10 models
> hide #!11 models
> save D:\Documents\Projects\Tat\Figs\Figure1\BC1S_bottom.png width 3000
> height 3000 supersample 6 transparentBackground true
> show #!11 models
> show #!9 models
> turn x 90
> hide #!11 models
> hide #!10 models
> hide #!9 models
> show #!2 models
> save D:\Documents\Projects\Tat\Figs\Figure1\BC2S_side_model.png width 3000
> height 3000 supersample 6 transparentBackground true
> hide #!2 models
> show #!11 models
> show #!10 models
> show #!9 models
> turn x 90
> hide #!10 models
> hide #!9 models
> show #!10 models
> show #!9 models
> turn x 90
[Repeated 1 time(s)]
> hide #!9 models
> hide #!10 models
> show #!10 models
> show #!9 models
> hide #!9 models
> show #!9 models
> turn x 90
[Repeated 1 time(s)]
> hide #!9 models
> hide #!10 models
> show #!10 models
> show #!9 models
> turn x 90
[Repeated 2 time(s)]
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> turn x 90
> hide #!10 models
> hide #!9 models
> show #!9 models
> show #!10 models
> turn x 90
[Repeated 1 time(s)]
> hide #!10 models
> show #!10 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!10 models
> show #!10 models
> show #!9 models
> turn x 90
> save D:/Documents/Projects/Tat/Figs/Figure1/maps_and_models.cxs
> hide #!11 models
> hide #!10 models
> save D:\Documents\Projects\Tat\Figs\Figure1\BC2S_side.png width 3000 height
> 3000 supersample 6 transparentBackground true
> show #!10 models
> hide #!9 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!9 models
> hide #!11 models
> hide #!10 models
> show #!10 models
> hide #!9 models
> show #!9 models
> show #!11 models
> hide #!9 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!9 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!9 models
> show #!9 models
> hide #!10 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!9 models
> hide #!10 models
> show #!10 models
> turn x 90
> hide #!10 models
> hide #!9 models
> show #!10 models
> show #!9 models
> turn x 90
[Repeated 1 time(s)]
> hide #!10 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!10 models
> show #!9 models
> turn x 90
[Repeated 9 time(s)]
> hide #!10 models
> hide #!9 models
> show #!9 models
> show #!10 models
> turn x 90
[Repeated 1 time(s)]
> hide #!10 models
> hide #!9 models
> show #!9 models
> show #!10 models
> turn x 90
> save D:/Documents/Projects/Tat/Figs/Figure1/maps_and_models.cxs
——— End of log from Wed Aug 21 14:47:47 2024 ———
opened ChimeraX session
> hide #!9 models
> hide #!10 models
> hide #!11 models
> show #!2 models
> open D:/Documents/Projects/Tat/deposition/J3036_20240807.pdb
Chain information for J3036_20240807.pdb #12
---
Chain | Description
A B | No description available
C | No description available
D | No description available
E F | No description available
G | No description available
H | No description available
> hide #!2,12 atoms
> show #!2,12 cartoons
> close #12
> close #2
> open D:/Documents/Projects/Tat/deposition/J3036_20240807.pdb
Chain information for J3036_20240807.pdb #2
---
Chain | Description
A B | No description available
C | No description available
D | No description available
E F | No description available
G | No description available
H | No description available
> hide #!2 atoms
> show #!2 atoms
> style #!2 stick
Changed 14035 atom styles
> show #!2 cartoons
> show #!5 models
> open D:/Documents/Projects/Tat/deposition/J2629_20240827.pdb
Chain information for J2629_20240827.pdb #12
---
Chain | Description
A | No description available
B C | No description available
D | No description available
E F | No description available
G | No description available
H | No description available
> style #!2,5,12 stick
Changed 35199 atom styles
> show #!2,5,12 cartoons
> mmaker #12 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240807.pdb, chain G (#2) with J2629_20240827.pdb, chain G
(#12), sequence alignment score = 2241.7
RMSD between 432 pruned atom pairs is 0.474 angstroms; (across all 455 pairs:
1.856)
> hide #!12 models
> show #!12 models
> mmaker #12 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker output_J2629_coot-20240807_real_space_refined_197.pdb, chain G (#5)
with J2629_20240827.pdb, chain G (#12), sequence alignment score = 2352.9
RMSD between 455 pruned atom pairs is 0.000 angstroms; (across all 455 pairs:
0.000)
> close #5
> open D:/Documents/Projects/Tat/deposition/J2629_20240827.pdb
Chain information for J2629_20240827.pdb #5
---
Chain | Description
A | No description available
B C | No description available
D | No description available
E F | No description available
G | No description available
H | No description available
> style #!2,5,12 stick
Changed 35199 atom styles
> show #!2,5,12 cartoons
> mmaker #5 to #12
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J2629_20240827.pdb, chain G (#12) with J2629_20240827.pdb, chain G
(#5), sequence alignment score = 2352.9
RMSD between 455 pruned atom pairs is 0.000 angstroms; (across all 455 pairs:
0.000)
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!5 models
> show #!5 models
> close #12
> open D:/Documents/Projects/Tat/deposition/J3003_20240831.pdb
Chain information for J3003_20240831.pdb #12
---
Chain | Description
A B C | No description available
D | No description available
E F | No description available
> style #12#!2,5 stick
Changed 31486 atom styles
> show #12#!2,5 cartoons
> mmaker #12 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker output_J3003_coot-20240807.pdb, chain A (#8) with
J3003_20240831.pdb, chain A (#12), sequence alignment score = 1214.3
RMSD between 231 pruned atom pairs is 0.000 angstroms; (across all 231 pairs:
0.000)
> show #8 models
> hide #!5 models
> close #8
> open D:/Documents/Projects/Tat/deposition/J3003_20240831.pdb
Chain information for J3003_20240831.pdb #8
---
Chain | Description
A B C | No description available
D | No description available
E F | No description available
> style #8,12#!2 stick
Changed 27773 atom styles
> show #8,12#!2 cartoons
> mmaker #8 to #12
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3003_20240831.pdb, chain A (#12) with J3003_20240831.pdb, chain A
(#8), sequence alignment score = 1214.3
RMSD between 231 pruned atom pairs is 0.000 angstroms; (across all 231 pairs:
0.000)
> close #12
> color #8#!2 byhetero
> save D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes.cxs
> hide pbonds
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> color #2 red
> color #5 gray
> color #8 green
> color #2 orange
> color byhetero
> color /A rgb(141,231,188)
> color /B lightsalmon
> color /C mediumpurple
> color /D rgb(252,140,192)
> color /E rgb(242,201,182)
> color /F rgb(255,255,150)
> color /G cyan
> color /H gray
> color /A-C rgb(141,231,188)
> color /D-F rgb(252,140,192)
> color #8 orange
> color byhetero
> hide #!5 models
> show #!5 models
> color #5 yellow
> color bynucleotide
> color byhetero
> hide #8 models
> show #8 models
> hide #!2 models
> color #2/A-C rgb(141,231,188)
> color #2/D-F rgb(252,140,192)
> color /G,H cyan
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> color #8 slateblue
> color #8 gray
> color #8 gold
> color #8#!2 byhetero
> color #8 mediumslateblue
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> color #8#!2 byhetero
> hide #8 models
> show #!5 models
> color #!2,5 byhetero
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> color #5 gold
> color #!2,5 byhetero
> color #5 orange
> color #5 salmon
> color #5 coral
> color #5 lightsalmon
> color #5 orchid
> color #5 goldenrod
> color #5 gold
> color #5 silver
> color #5 gray
> color #!2,5 byhetero
> hide #!2,5 atoms
> show #8 models
> hide atoms
> hide #!5 models
> show #!5 models
> hide #8 models
> color #5 gold
> show #8 models
> color #5 slateblue
> hide #8 models
> show #8 models
> hide #!5 models
> show #!5 models
> hide #8 models
> show #8 models
> hide #!5 models
> color #5 mediumslateblue
> color /G,H cyan
> color #5 mediumslateblue
> color #8 gold
> color #8 hotpink
> color #8 red
> color #8 blue
> color #8 purple
> color #8 mediumpurple
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> color #8 mediumseagreen
> color #8 wheat
> color #8 burn
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #8 burlywood
> show #!5 models
> hide #!5 models
> color #8 gold
> show #!5 models
> hide #8 models
> show #!2,5 atoms
> color #!2,5 byhetero
> show #8 models
> hide #!5 models
> color #8 darkorange
> show #!5 models
> hide #!5 models
> color #8 gold
> color #8#!2 byhetero
> show #8#!2 atoms
> show #!5 models
> hide atoms
> save D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes.cxs
——— End of log from Sat Aug 31 23:34:18 2024 ———
opened ChimeraX session
> show atoms
> hide #!5 models
> hide #8#!2 atoms
> show #!5 models
> hide #8 models
> hide #!2,5 atoms
> show #!2,5 atoms
> show #8 models
> show atoms
> color byhetero
> hide #8 models
> hide #!2 models
> show #8 models
> hide #!5 models
> show #!2 models
> show #!4 models
> hide #8 models
> hide #!4 models
> show #!5 models
> show #8 models
> hide #!5 models
> hide #8 models
> show #!5 models
> show #8 models
> hide #!5 models
> show #!5 models
> hide #8 models
> show #8 models
> hide #!5 models
> show #!5 models
> hide #8 models
> show #8 models
> hide #!5 models
> hide #8 models
> show #!5 models
> hide #!2,5 atoms
> morph #2 #5
Computed 51 frame morph #12
> coordset #12 1,51
> close #12
> morph #5 #2
Computed 51 frame morph #12
> coordset #12 1,51
> show #!12 atoms
> morph #8 #2
models have different number of chains, 6 (Morph - J3003_20240831.pdb
#/A,Morph - J3003_20240831.pdb #/B,Morph - J3003_20240831.pdb #/C,Morph -
J3003_20240831.pdb #/D,Morph - J3003_20240831.pdb #/E,Morph -
J3003_20240831.pdb #/F) and 8 (J3036_20240807.pdb #2/A,J3036_20240807.pdb
#2/B,J3036_20240807.pdb #2/C,J3036_20240807.pdb #2/D,J3036_20240807.pdb
#2/E,J3036_20240807.pdb #2/F,J3036_20240807.pdb #2/G,J3036_20240807.pdb #2/H)
> morph #8 #2 same true
Computed 51 frame morph #13
> coordset #13 1,51
> hide #!12 models
> morph #8 #5 #2 same true
Computed 101 frame morph #14
> coordset #14 1,101
> hide #13 models
> movie record
> close #14
> morph #8 #5 same true
Computed 51 frame morph #14
> coordset #14 1,51
> show #13 models
> hide #14 models
> hide #13 models
> show #!12 models
> hide #!12 models
> show #13 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #8 models
> hide #13 models
> hide /G:30-470
> hide /G:30-470 cartoons
> hide /H:30-470 cartoons
> show #13 models
> hide #!2 models
> hide #8 models
> show #8 models
> show #!2 models
> hide #13 models
> hide #8#!2 atoms
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> graphics silhouettes true
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> show #!5 models
> hide #8 models
> show #8 models
> hide #!5 models
> color #8 slateblue
> color #8 gray
> color #8 mediumslateblue
> save
> D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes_overall_BCto2S.cxs
——— End of log from Sun Sep 1 10:29:36 2024 ———
opened ChimeraX session
> show #!5 models
> hide #!5 models
> show /B:110 atoms
> show #!5 models
> show /B:112 atoms
> show /A:108 atoms
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!9 models
> hide #!9 models
> show #8#!2,5 atoms
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!9 models
> show #!10 models
> hide #!10 models
> hide #!9 models
> hide #8 models
> hide #!2 models
> show #!9 models
> show #!10 models
> color zone #9 near #2 distance 5
> color #2/A-C rgb(141,231,188)
> color #2/D-F rgb(252,140,192)
> color /G,H cyan
> color #5 mediumslateblue
> color #8 gold
> color zone #9 near #2 distance 5
> color zone #10 near #8 distance 5
> hide #!10 models
> show #!11 models
> color zone #10 near #5 distance 5
> color zone #11 near #8 distance 5
> show #!10 models
> hide #!10 models
> volume #11 level 0.3074
> volume #9 level 0.7309
> volume #11 level 0.2032
> hide #!11 models
> hide #!9 models
> show #!2 models
> show #8 models
> color #8#!2 byhetero
> show #!5 models
> hide #8 models
> show #8 models
> hide #8#!2,5 atoms
> cartoon style modeHelix default arrows false xsection round width 1
> thickness 1
> cartoon style modeHelix default arrows false xsection round width 0.5
> thickness 0.5
> hide #!2 models
> show /B:7,8,10 atoms
> hide #8#!5 atoms
> show /B:7,8,11 atoms
> hide #8#!5 atoms
> show /B:7,8,10 atoms
> color #8#!5 byhetero
> open D:/Documents/Projects/Tat/deposition/J3036_20240807.pdb
Chain information for J3036_20240807.pdb #15
---
Chain | Description
A B | No description available
C | No description available
D | No description available
E F | No description available
G | No description available
H | No description available
> style #8#!5,15 stick
Changed 31486 atom styles
> hide #8#!5,15 atoms
> show #8#!5,15 cartoons
> mmaker #15/C to #2/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240807.pdb, chain A (#2) with J3036_20240807.pdb, chain C
(#15), sequence alignment score = 1162.4
RMSD between 185 pruned atom pairs is 0.885 angstroms; (across all 231 pairs:
1.599)
> mmaker #15/C:10-20 to #2/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240807.pdb, chain A (#2) with J3036_20240807.pdb, chain C
(#15), sequence alignment score = 56.9
RMSD between 11 pruned atom pairs is 0.228 angstroms; (across all 11 pairs:
0.228)
> mmaker #15/C:10-20 to #2/A:10-20
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240807.pdb, chain A (#2) with J3036_20240807.pdb, chain C
(#15), sequence alignment score = 56.9
RMSD between 11 pruned atom pairs is 0.228 angstroms; (across all 11 pairs:
0.228)
> hide #!5 models
> show #!2 models
> hide #8 models
> mmaker #15/C:10-20 to #2/B:10-20
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240807.pdb, chain B (#2) with J3036_20240807.pdb, chain C
(#15), sequence alignment score = 56.9
RMSD between 11 pruned atom pairs is 0.222 angstroms; (across all 11 pairs:
0.222)
> mmaker #15/C:10-20 to #2/A:10-20
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240807.pdb, chain A (#2) with J3036_20240807.pdb, chain C
(#15), sequence alignment score = 56.9
RMSD between 11 pruned atom pairs is 0.228 angstroms; (across all 11 pairs:
0.228)
> color #15 gray
> color #!2,15 byhetero
> show #2,15/7,8 atoms
> show #/2,15:7,8 atoms
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #2/A:7,8 #15/C:7,8 atoms
> save D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes_TM1.cxs
> cartoon style modeHelix default arrows false xsection round width 0.5
> thickness 0.5
> select #2/G:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #15 cartoons
> show #15/C cartoons
> save D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes_TM1.cxs
[Repeated 1 time(s)]
> save D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes_TM1.png
> width 3000 height 3000 supersample 6 transparentBackground true
> style #!2,15 ball
Changed 28070 atom styles
> select clear
> save D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes_TM1.cxs
> save D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes_TM1.png
> width 3000 height 3000 supersample 6 transparentBackground true
> save D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes_TM1.cxs
> save D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes_TM1.png
> width 3000 height 3000 supersample 6 transparentBackground true
> select #2/A:5-11 #2/G:2-3
68 atoms, 67 bonds, 9 residues, 1 model selected
> volume zone #1 nearAtoms sel range 2 newMap true
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #16, grid size
256,256,256, pixel 1.2, shown at step 1, values float32
> volume #16 style mesh
> volume #16 level 0.4266
> volume #16 level 0.2136
> hide #!15 models
> show sel atoms
> style sel stick
Changed 68 atom styles
> volume #16 color #00007f
> volume #16 color black
> volume #16 color #550000
> volume #16 color #0055ff
> volume #16 color blue
> lighting simple
> select clear
> lighting full
> lighting shadows false
> close #16
> select #2/A:5-10 #2/G:2-3
61 atoms, 60 bonds, 8 residues, 1 model selected
> volume zone #1 nearAtoms sel range 2 newMap true
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #16, grid size
256,256,256, pixel 1.2, shown at step 1, values float32
> volume #11 style mesh
> volume #16 style mesh
> volume #16 color #00007f
> volume #16 color blue
[Repeated 1 time(s)]
> select clear
> select #2/A:11@CB
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> undo
> select clear
> hide #2/A:11 atoms
> save D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes_TM1_A.cxs
> save D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes_TM1_A.png
> width 3000 height 3000 supersample 6 transparentBackground true
> hide cartoons
> save D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes_TM1_A.cxs
> save D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes_TM1_A.png
> width 3000 height 3000 supersample 6 transparentBackground true
> graphics silhouettes false
> graphics silhouettes true
> volume #11 style surface
> volume #16 style surface
> transparency #16 50
> volume #16 color #00aaff80
> save D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes_TM1_A.cxs
——— End of log from Sun Sep 1 15:28:33 2024 ———
opened ChimeraX session
> close #16
> select #2/A:7-9 #2/G:2-3
38 atoms, 37 bonds, 5 residues, 1 model selected
> volume zone #1 nearAtoms sel range 2 newMap true
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #16, grid size
256,256,256, pixel 1.2, shown at step 1, values float32
> volume #16 style surface
> transparency #16 50
> volume #16 color #00aaff80
> volume #16 color #55ffff80
> volume #16 color #ffaa7f80
> volume #16 color #ffff7f80
> volume #16 color #00ffff80
> volume #16 color #aaffff80
> hide ~sel atoms
> transparency #16 50
> volume #16 color #aaffff
> transparency #16 50
> select clear
> save D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes_TM1_A.cxs
> save D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes_TM1_A.png
> width 3000 height 3000 supersample 6 transparentBackground true
> select #2/C:7-9
24 atoms, 24 bonds, 3 residues, 1 model selected
> hide ~sel atoms
> volume zone #1 nearAtoms sel range 2 newMap true
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #17, grid size
256,256,256, pixel 1.2, shown at step 1, values float32
> volume #17 style surface
> volume #17 color #aaffff
> transparency #17 50
> ~select
Nothing selected
> close #16
> hide #!17 models
> show #!17 models
> dust
Unknown command: dust
> hide dust
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ui tool show "Hide Dust"
> surface dust #17 size 7.2
> show sel atoms
> style sel stick
Changed 0 atom styles
> select #2/C:7-9
24 atoms, 24 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 24 atom styles
> select clear
> select #2/C:7-9
24 atoms, 24 bonds, 3 residues, 1 model selected
> color gray
> color sel gray
> color sel byhetero
> select clear
> save D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes_TM1_C.cxs
> save D:/Documents/Projects/Tat/Figs/Figure5/conformation_changes_TM1_C.png
> width 3000 height 3000 supersample 6 transparentBackground true
> select clear
> hide #!17 models
> select clear
> show #!2 atoms
> show #!2 cartoons
> hide #!2 atoms
> show #8 models
> show #8#!2 cartoons
> hide /G,H cartoons
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> hide ~/A cartoons
> show /G:1-29 cartoons
> select #2,8/A:10,94,100,108@Ca
8 atoms, 8 residues, 2 models selected
> show sel atoms
> hide sel cartoons
> style sel sphere
Changed 8 atom styles
> style sel ball
Changed 8 atom styles
> style sel sphere
Changed 8 atom styles
> hide sel cartoons
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> style sel stick
Changed 8 atom styles
> show sel cartoons
> show sel atoms
> select clear
> select #2,8/A:10,94,100,108
76 atoms, 72 bonds, 8 residues, 2 models selected
> show sel atoms
> style sel ball
Changed 76 atom styles
> color sel byhetero
> select clear
[Repeated 1 time(s)]
> hide #8#!2,15 atoms
> select #2,8/A:10,94,100,108@Ca,C
16 atoms, 8 bonds, 8 residues, 2 models selected
> show sel atoms
> style sel sphere
Changed 16 atom styles
> style sel ball
Changed 16 atom styles
> hide sel cartoons
> show sel cartoons
> select #2,8/A:10,94,100,108@O
8 atoms, 8 residues, 2 models selected
> show sel atoms
> style sel sphere
Changed 8 atom styles
> cartoon
> close #17
> undo
> open D:/Documents/Projects/Tat/deposition/J3003_20240831.pdb
Chain information for J3003_20240831.pdb #16
---
Chain | Description
A B C | No description available
D | No description available
E F | No description available
> style sel stick
Changed 8 atom styles
> select clear
> style #8,16#!2,15 stick
Changed 41808 atom styles
> show #8,16#!2,15 cartoons
> hide #8,16#!2,15 atoms
> mmaker #16 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3003_20240831.pdb, chain A (#8) with J3003_20240831.pdb, chain A
(#16), sequence alignment score = 1214.3
RMSD between 231 pruned atom pairs is 0.000 angstroms; (across all 231 pairs:
0.000)
> cartoon style #1 modeHelix default arrows false xsection round width 0.5
> thickness 0.5
> cartoon style #16 modeHelix default arrows false xsection round width 0.5
> thickness 0.5
> hide ~/A cartoons
> color #16 gold
> color #15/A-C rgb(141,231,188)
> color #15/D-F rgb(252,140,192)
> volume #11 style mesh
> vop #11 subdivide f
> vop #11 subdivide 2
> volume #11 subdivideSurface 2
Invalid "subdivideSurface" argument: Expected true or false (or 1 or 0)
> vop #11 subdivide t
> vop #11 subdivide f
> mmaker #15 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240807.pdb, chain G (#2) with J3036_20240807.pdb, chain G
(#15), sequence alignment score = 2388.4
RMSD between 461 pruned atom pairs is 0.000 angstroms; (across all 461 pairs:
0.000)
> hide #16 models
> show #16 models
> hide #8 models
> show #8 models
> hide #8 models
> hide #16 models
> show #16 models
> select #8/A:1-120
912 atoms, 936 bonds, 114 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 912 atom styles
> hide ~sel atoms
> volume zone #7 nearAtoms sel range 2 newMap true
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc zone as #17, grid size
256,256,256, pixel 1.2, shown at step 1, values float32
> volume #17 style surface
> volume #17 color #aaffff
> transparency #17 50
> ~select
Nothing selected
> surface dust #17 size 7.2
> show #16#!2,15 atoms
> hide #16#!2,15 atoms
> select #8/A:1-120
912 atoms, 936 bonds, 114 residues, 1 model selected
> show sel atoms
> show #8 models
> hide #!2 models
> hide #!15 models
> hide ~sel cartoons
> select clear
> color #8,16 byhetero
> select clear
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TM3_3003.cxs
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TM3_3003.png width
> 3000 height 3000 supersample 6 transparentBackground true
> hide #8,16 atoms
> hide #8,16 cartoons
> select #2/A:1-120
947 atoms, 971 bonds, 119 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 947 atom styles
> hide ~sel atoms
> volume zone #1 nearAtoms sel range 2 newMap true
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #18, grid size
256,256,256, pixel 1.2, shown at step 1, values float32
> volume #18 style surface
> volume #18 color #aaffff
> transparency #18 50
> surface dust #18 size 7.2
> show #!2 models
> select clear
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TM3_3036.cxs
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TM3_3036.png width
> 3000 height 3000 supersample 6 transparentBackground true
> hide #8,16#!2 atoms
> show #2,8/A cartoons
> hide #8,16#!2 cartoons
> show #2,8/A:1-120 cartoons
> show #2,8/A:1-120,/G:1-29car
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #2,8/A:1-120 #2/G:1-29 cartoons
> select #15,16:10,97,108@Ca
30 atoms, 30 residues, 2 models selected
> hide ~sel atoms,cartoons
> show sel atoms
> style sel sphere
Changed 30 atom styles
> size atomRadius 2
Changed 76631 atom radii
> show #2,8/A cartoons
> select clear
> hide #8,16#!2 atoms
> hide #8,16#!2 cartoons
> select #15,16/A:10,97,108@Ca
6 atoms, 6 residues, 2 models selected
> hide ~sel atoms,cartoons
> show sel atoms
> style sel sphere
Changed 6 atom styles
> size atomRadius 2
Changed 76631 atom radii
> show #2,8/A cartoons
> show #!15 models
> size atomRadius 1
Changed 76631 atom radii
> hide #2,8/A:1-6 cartoons
> select clear
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TM3_car.cxs
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TM3_car.png width
> 3000 height 3000 supersample 6 transparentBackground true
> select #15,16/A:10,97,108
44 atoms, 40 bonds, 6 residues, 2 models selected
> show sel atoms
> hide sel atoms
> undo
[Repeated 1 time(s)]
> select clear
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TM3_car.cxs
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TM3_car.png width
> 3000 height 3000 supersample 6 transparentBackground true
> hide #8,16#!2,15 atoms
> select clear
> hide #8,16#!2,15 atoms
> show #8,16#!2,15 cartoons
> hide #8,16#!2,15 cartoons
> show #2,8/B:1-120 #2/G:1-29 cartoons
> select #15,16/B:10,97,108@Ca
6 atoms, 6 residues, 2 models selected
> hide ~sel atoms,cartoons
> show sel atoms
> style sel sphere
Changed 6 atom styles
> size atomRadius 1
Changed 76631 atom radii
> show #2,8/B cartoons
> hide #2,8/B:1-6 cartoons
> hide sel cartoons
> select clear
> hide #8,16#!2,15 cartoons
> show #2,8/B:120 cartoons
> hide #2,8/B:1-6 cartoons
> show #2,8/B:1-120 cartoons
> hide #2,8/B:1-6 cartoons
> hide #8,16#!2,15 atoms
> select clear
> hide #8,16#!2,15 atoms
> hide #8,16#!2,15 cartoons
> select #15,16/B:10,94,100,108@Ca
8 atoms, 8 residues, 2 models selected
> hide ~sel atoms,cartoons
> show sel atoms
> style sel sphere
Changed 8 atom styles
> size atomRadius 1
Changed 76631 atom radii
> show #2,8/B:1-120 cartoons
> hide #2,8/B:1-6 cartoons
> select clear
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TM3_carB.cxs
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TM3_carB.png width
> 3000 height 3000 supersample 6 transparentBackground true
> hide #8,16#!2,15 atoms
> hide #8,16#!2,15 cartoons
> show #2,8/A:1-120 #2/G:1-29 cartoons
> select #15,16/A:10,94,100,108@Ca
8 atoms, 8 residues, 2 models selected
> hide ~sel atoms,cartoons
> show sel atoms
> style sel sphere
Changed 8 atom styles
> size atomRadius 1
Changed 76631 atom radii
> show #2,8/A:1-120 cartoons
> hide #2,8/A:1-6 cartoons
> select clear
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TM3_carA.cxs
——— End of log from Sun Sep 1 19:20:25 2024 ———
opened ChimeraX session
> show #2/G:1-29 cartoons
> show #2/G:5-6 atoms
> select clear
> show #2/G:5-9 atoms
> show #2/G:5-8 atoms
> hide #8,16#!2,15 atoms
> undo
[Repeated 1 time(s)]
> show #2/G:5,6,8,9 atoms
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TM3_carA.cxs
——— End of log from Sun Sep 1 22:18:06 2024 ———
opened ChimeraX session
> hide /G:11-29 cartoons
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TM3_carA.cxs
——— End of log from Sun Sep 1 22:28:23 2024 ———
opened ChimeraX session
> select #2/G:10
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TM3_carA.cxs
——— End of log from Sun Sep 1 23:27:44 2024 ———
opened ChimeraX session
> select clear
> hide #8,16#!2,15 atoms
> hide #8,16#!2,15 cartoons
> show #2,8/A-F cartoons
> show #2/G,H:1-29 cartoons
> ui tool show "Side View"
> morph #8 #2
models have different number of chains, 6 (Morph - J3003_20240831.pdb
#/A,Morph - J3003_20240831.pdb #/B,Morph - J3003_20240831.pdb #/C,Morph -
J3003_20240831.pdb #/D,Morph - J3003_20240831.pdb #/E,Morph -
J3003_20240831.pdb #/F) and 8 (J3036_20240807.pdb #2/A,J3036_20240807.pdb
#2/B,J3036_20240807.pdb #2/C,J3036_20240807.pdb #2/D,J3036_20240807.pdb
#2/E,J3036_20240807.pdb #2/F,J3036_20240807.pdb #2/G,J3036_20240807.pdb #2/H)
> morph #8 #2 same true
Computed 51 frame morph #19
> coordset #19 1,51
> show #16,19#!15 atoms
> undo
> show #19 atoms
> hide #19 models
> hide #16 models
> hide #!15 models
> show #!2 models
> show #8 models
> show #19 models
> hide #19 models
> show #19 models
> hide #19 models
> hide #2,8/A-C cartoons
> show #19 models
> hide /A-C cartoons
> hide /A-C atoms
> hide /F atoms,cartoons
> cartoon style modeHelix tube radius 2 sides 24 thickness 0.6
> undo
> hide /G cartoons
> hide /D,E:1-21 cartoons,atoms
> hide #19 models
> show #19 models
> hide /H cartoons
> show /G:1-29 cartoons
> cartoon style #2/G:1-29 modeHelix tube radius 2 sides 24 thickness 0.6
> cartoon style (#2/G:1-29) modeHelix tube radius 2 sides 24 thickness 0.6
> cartoon style (#2/G) modeHelix tube radius 2 sides 24 thickness 0.6
> hide /G cartoons
> show #15/G:1-29 cartoons
> show #!15 models
> color #15/G cyan
> color #8,19#!2,15 byhetero
> cartoon style #15 modeHelix tube radius 2 sides 24 thickness 0.6
> hide #19 models
> show #19 models
> hide #19 models
> show #19 models
> show #16 models
> hide #16 models
> show #16 models
> show #8,16,19#!2,15 cartoons
> undo
> show #16 cartoons
> hide #16 models
> morph #5 #2
Computed 51 frame morph #20
> coordset #20 1,51
> hide #19 models
> show #20/D,E:22-63 cartoons,atoms
> show #20/G:1-29 cartoons,atoms
> hide #!20 models
> show #!2 models
> show #2,8/D:35,36 atoms
> show #19 models
> hide #19 models
> show #19 models
> hide #19 models
> show #19 models
> select clear
> hide #2,8/D:35,36 atoms
> show #15/D:26,35@Ca atoms
> select #15/D:26,35@Ca atoms
Expected a keyword
> select #15/D:26,35@Ca
2 atoms, 2 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> style sel sphere
Changed 2 atom styles
> style sel ball
Changed 2 atom styles
> style sel sphere
Changed 2 atom styles
> size atomRadius 2
Changed 94048 atom radii
> size atomRadius 1
Changed 94048 atom radii
> size atomRadius 0.5
Changed 94048 atom radii
> size atomRadius 0.8
Changed 94048 atom radii
> select #16/D:26,35@Ca
2 atoms, 2 residues, 1 model selected
> show #8,19#!2,15 atoms
> undo
> show #16 models
> hide ~sel atoms,cartoons
> hide #16~sel atoms,car
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #16 & ~sel atoms,cartoons
> select #16/D:26,35@Ca
2 atoms, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 2 atom styles
> hide #19 models
> style sel stick
Changed 2 atom styles
> style sel sphere
Changed 2 atom styles
> select clear
> select #15,16/E:43,46@Ca
4 atoms, 4 residues, 2 models selected
> show sel atoms
> style sel sphere
Changed 4 atom styles
> select clear
> undo
[Repeated 2 time(s)]
> select #15,16/E:43,36@Ca
4 atoms, 4 residues, 2 models selected
> size atomRadius 0.6
Changed 94048 atom radii
> select #15,16/E:43,36@Ca
4 atoms, 4 residues, 2 models selected
> show sel atoms
> style sel sphere
Changed 4 atom styles
> select clear
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TatB_sliding.cxs
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TatB_sliding.png
> width 3000 height 3000 supersample 6 transparentBackground true
> select #2/D:35-37
33 atoms, 34 bonds, 3 residues, 1 model selected
> show sel atoms
> hide ~sel atoms,cartoons
> style sel stick
Changed 33 atom styles
> volume zone #1 nearAtoms sel range 2 newMap true
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #21, grid size
256,256,256, pixel 1.2, shown at step 1, values float32
> volume #21 style surface
> volume #21 color #aaffff
> transparency #21 50
> volume #21 level 0.2
> surface dust #21 size 7.2
> volume #21 level 0.126
> volume #21 level 0.08893
> select clear
> hide #8,16#!2,15 cartoons
> undo
> save
> D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TatB_chainD_BC2S.cxs
> save
> D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TatB_chainD_BC2S.png
> width 3000 height 3000 supersample 6 transparentBackground true
> select #8/D:35-37
33 atoms, 34 bonds, 3 residues, 1 model selected
> show sel atoms
> hide ~sel atoms,cartoons
> style sel stick
Changed 33 atom styles
> volume zone #7 nearAtoms sel range 2 newMap true
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc zone as #22, grid size
256,256,256, pixel 1.2, shown at step 1, values float32
> volume #22 style surface
> volume #22 color #aaffff
> transparency #22 50
> volume #22 level 0.2
> surface dust #22 size 7.2
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TatB_chainD_BC.cxs
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TatB_chainD_BC.png
> width 3000 height 3000 supersample 6 transparentBackground true
> hide #!22 models
> show #!22 models
> volume #22 level 0.1358
> volume #22 level 0.1716
> show sel cartoons
> volume #22 level 0.1447
> surface dust #22 size 7.2
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TatB_chainD_BC.cxs
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_TatB_chainD_BC.png
> width 3000 height 3000 supersample 6 transparentBackground true
> select clear
> close #22
> close #21
> hide #8,16#!2,15 atoms
> hide #8,16#!2,15 cartoons
> close #18
> close #17
> hide #16 models
> hide #!15 models
> show #!15 models
> show #16 models
> show #2,8/A-F cartoons
> hide #8,16#!2,15 cartoons
> show #2,8/A-C:185-235 #2,8/D-F:1-22car
> show #2,8/A-C:185-235 #2,8/D-F:1-22 cartoons
> show #19 models
> show #19 cartoons,atoms
> ui tool show "Side View"
> select #15,16/D-F:2,6 #15,16/A-C:210
174 atoms, 174 bonds, 18 residues, 2 models selected
> show sel atoms
> style sel sphere
Changed 174 atom styles
> size atomRadius 0.8
Changed 94048 atom radii
> style sel ball
Changed 174 atom styles
> style sel stick
Changed 174 atom styles
> style sel ball
Changed 174 atom styles
> hide #19 models
> select clear
> undo
> show sel cartoons
> undo
[Repeated 8 time(s)]
> select #2,8/D-F:2,6 #15,16/A-C:210
174 atoms, 174 bonds, 18 residues, 4 models selected
> show sel atoms
> style sel stick
Changed 174 atom styles
> hide #19 models
> select clear
> color #8,16#!2,15 byhetero
> select clear
> undo
[Repeated 4 time(s)]
> show sel cartoons
> select clear
[Repeated 1 time(s)]
> cartoon style width 2.0 thickness 0.4 modeHelix default arrows false
> cartoon style xsection rectangle width 2 arrows true
> cartoon style xsection oval width 2 arrows true
> cartoon style modeHelix tube radius 2 sides 24 thickness 0.6
> cartoon style modeHelix tube radius 1.5 sides 24 thickness 0.6
> hide :210 atoms
> cartoon style modeHelix tube radius 1.2 sides 24 thickness 0.6
> cartoon style modeHelix tube radius 1 sides 24 thickness 0.6
> cartoon style modeHelix tube radius 1 sides 24 thickness 0.4
> hide #!15 models
> hide #16 models
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_filter.cxs
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_filter.png width
> 3000 height 3000 supersample 6 transparentBackground true
> select #8/F:1-6
42 atoms, 43 bonds, 5 residues, 1 model selected
> show sel atoms
> hide ~sel atoms,cartoons
> style sel stick
Changed 42 atom styles
> volume zone #7 nearAtoms sel range 2 newMap true
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc zone as #17, grid size
256,256,256, pixel 1.2, shown at step 1, values float32
> volume #17 style surface
> volume #17 color #aaffff
> transparency #17 50
> volume #17 level 0.2
> surface dust #17 size 7.2
> volume #17 level 0.1203
> hide sel cartoons
> volume #17 level 0.01985
> volume #17 level 0.1192
> select clear
> volume #17 level 0.1
> select clear
> save
> D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_Filter_chainF_BC.cxs
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_Filter_chainF
> _BC.png w 3000 h 3000 s 6 t t
Cannot determine format for
'D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_Filter_chainF'
> save
> D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_Filter_chainF_BC.png
> width 3000 height 3000 supersample 6 transparentBackground true
> select #2/F:2-6
42 atoms, 43 bonds, 5 residues, 1 model selected
> show sel atoms
> hide ~sel atoms,cartoons
> style sel stick
Changed 42 atom styles
> volume zone #1 nearAtoms sel range 2 newMap true
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #18, grid size
256,256,256, pixel 1.2, shown at step 1, values float32
> volume #18 style surface
> volume #18 color #aaffff
> transparency #18 50
> volume #18 level 0.18
> surface dust #18 size 7.2
> volume #18 level 0.15
> volume #18 level 0.12
> surface dust #18 size 7.2
> select clear
> volume #18 level 0.1
> volume #18 level 0.12
> save
> D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_Filter_chainF_BC2S.cxs
> save
> D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_Filter_chainF_BC2S.png
> width 3000 height 3000 supersample 6 transparentBackground true
> close #17
> close #18
> hide #8#!2 atoms
> show #2,8/A-C:185-235 #2,8/D-F:1-22 cartoons
> show #19 models
> hide #19 models
> show #19 models
> hide /A,D,B,E cartoons
> show #2/F cartoons
> undo
> show #2,8/C:213 atoms
> show #19/C:185-235 #19/F:1-22 cartoons,atoms
> show #2,8/B,C cartoons
> ui tool show "Side View"
> show #19/B,C cartoons,atoms
> hide #19 models
> hide #!2 models
> show #!2 models
> show #2,8/B,C cartoons,atoms
> hide #2,8/B,C cartoons,atoms
> hide #2,8/B cartoons,atoms
> hide #2,8/B:1-184 cartoons,atoms
> hide #2,8/C:1-184 cartoons,atoms
> show #15,16/C:151-180 #15,16/B:65-100 cartoons
> show #15,16/C:157,161 #15,16/B:69,76 atoms
> show #!15 models
> show #16 models
> cartoon style #15 width 2.0 thickness 0.4 modeHelix default arrows false
> cartoon style #16 width 2.0 thickness 0.4 modeHelix default arrows false
> show #19 models
> hide #19 models
> hide #2,8 atoms
> show #2,8/C:213,217 atoms
> style #2,8/C:213,217 ball
Changed 38 atom styles
> style #2,8/C:213,217 ball
Changed 38 atom styles
> size #2,8/C:213,217 atomRadius 2
Changed 38 atom radii
> color #8,16#!2,15 byhetero
> color #2,8/C:213,217 byhetero
> size #2,8/C:213,217 atomRadius 1.5
Changed 38 atom radii
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_switch.cxs
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_switch.png width
> 3000 height 3000 supersample 6 transparentBackground true
> show #15,16/C:151-185 #15,16/B:65-100 cartoons
> show #15,16/C:151-182 #15,16/B:65-100 cartoons
> show #15,16/C:151-181 #15,16/B:65-100 cartoons
[Repeated 1 time(s)]
> show #15,16/C:151-180 #15,16/B:65-100 cartoons
> show #2,8/C:181-186 cartoons
> show #2,8/C:182-186 cartoons
> show #15,16/C:151-181 #15,16/B:65-100 cartoons
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_switch.cxs
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_switch.png width
> 3000 height 3000 supersample 6 transparentBackground true
> select clear
> hide #8,16#!2,15 atoms
> hide #8,16#!2,15 cartoons
> show #2/A surfaces
> size atomRadius 2
Changed 94048 atom radii
> show #2/A surfaces
> hide #8,16#!2,15 surfaces
> show #2/A surfaces
> size #2 atomRadius 2
Changed 14035 atom radii
> select clear
> hide #8,16#!2,15 surfaces
> show #2/A surfaces
> close #2.2
> show #2/A surfaces
> show #2/D:1-22 surfaces
> color #2/D:1-22 #8de7bc
> lighting soft
> color #2/D:1-22 #2/C:185-235 seagreen
> color #2/D:1-22 color #2/C:185-235 sea
Invalid "color" argument: Expected a color or one of 'byatom', 'bychain',
'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer',
'fromatoms', 'fromcartoons', 'fromribbons', or 'random'
> color #2/D:1-22 seagreen color #2/C:185-235 sea
Invalid "color" argument: Expected a color or one of 'byatom', 'bychain',
'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer',
'fromatoms', 'fromcartoons', 'fromribbons', or 'random'
> color #2/C:185-235 seagreen
> color #2/C fromatoms
> color #2/C fromatoms surfaces
> color #2/D:1-22 #2/A:185-235 seagreen
> color #2/D:1-22 #2/A:185-235 mediumseagreen
> color #2/D:1-22 #2/A:185-235 dodgerblue
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_switch_icon.cxs
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_switch_icon.png
> width 3000 height 3000 supersample 6 transparentBackground true
> color #2/D:1-22 #2/A:185-235 rgb(225,92,92)
> color #2/D:1-22 #2/A:185-235 rgb(232,135,213)
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_switch_icon.cxs
> save D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_switch_icon.png
> width 3000 height 3000 supersample 6 transparentBackground true
> hide #8,16#!2,15 cartoons
> hide #8,16#!2,15 surfaces
> select #8/C:212-217 #8/B:69-76
116 atoms, 118 bonds, 14 residues, 1 model selected
> show sel atoms
> hide ~sel atoms,cartoons
> style sel stick
Changed 116 atom styles
> volume zone #7 nearAtoms sel range 2 newMap true
Opened cryosparc_P25_J3003_004_volume_map_sharp.mrc zone as #17, grid size
256,256,256, pixel 1.2, shown at step 1, values float32
> volume #17 style surface
> volume #17 color #aaffff
> transparency #17 50
> volume #17 level 0.1
> surface dust #17 size 7.2
> show sel cartoons
> hide sel cartoons
> volume #17 level 0.1683
> surface dust #17 size 7.2
> select clear
> save
> D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_switch_chainBC_BC.cxs
> save
> D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_switch_chainBC_BC.png
> width 3000 height 3000 supersample 6 transparentBackground true
> select #2/C:212-217 #2/B:69-76
116 atoms, 118 bonds, 14 residues, 1 model selected
> show sel atoms
> hide ~sel atoms,cartoons
> style sel stick
Changed 116 atom styles
> volume zone #1 nearAtoms sel range 2 newMap true
Opened cryosparc_P25_J3036_009_volume_map_sharp.mrc zone as #18, grid size
256,256,256, pixel 1.2, shown at step 1, values float32
> volume #18 style surface
> volume #18 color #aaffff
> transparency #18 50
> volume #18 level 0.1
> surface dust #17 size 7.2
> volume #18 level 0.15
> volume #18 level 0.2
> volume #18 level 0.15
> select clear
> color #2/A-C rgb(141,231,188)
> color #8,16#!2,15 byhetero
> select clear
> volume #18 level 0.1
> save
> D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_switch_chainBC_BC2S.cxs
> save
> D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_switch_chainBC_BC2S.png
> width 3000 height 3000 supersample 6 transparentBackground true
> save
> D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_switch_chainBC_BC2S.cxs
> save
> D:/Documents/Projects/Tat/Figs/Figure5/conf_changes_switch_chainBC_BC2S.png
> width 3000 height 3000 supersample 6 transparentBackground true
> close #17
> close #18
> hide #8,16#!2,15 atoms
> volume #11 style surface
> volume #9 level 0.3243
> volume #9 level 0.2
> close #2.2-3
> show #8,16#!2,15 surfaces
> hide #!8 models
> hide #!15 models
> hide #!16 models
> hide #2/G,H surfaces
> color #2/D-F:1-22 #2/A-C:185-235 rgb(225,92,92)
> color #2/D-F:23-63 orange
> color #2/D-F:1-22 #2/A-C:185-236 rgb(225,92,92)
> color #2/D-F:1-22 #2/A-C:185-237 rgb(225,92,92)
> color #2/D-F:23-63 gold
> color #2/D-F:23-64 gold
> turn x 90
[Repeated 3 time(s)]
> save D:/Documents/Projects/Tat/Figs/Figure6/dockingSite_closed.cxs
> save D:/Documents/Projects/Tat/Figs/Figure6/dockingSite_closed.png width
> 3000 height 3000 supersample 6 transparentBackground true
> turn y 120
[Repeated 1 time(s)]
> save D:/Documents/Projects/Tat/Figs/Figure6/dockingSite_open.cxs
——— End of log from Mon Sep 2 15:28:58 2024 ———
opened ChimeraX session
> close #19#20
> open D:/Documents/Projects/Tat/deposition/J3036_andTatA_20240902.pdb
Chain information for J3036_andTatA_20240902.pdb #17
---
Chain | Description
A B | No description available
C | No description available
D | No description available
E F | No description available
G | No description available
H | No description available
I | No description available
> hide #!2,17 atoms
> show #17/I:6-22 cartoons
> show #17 cartoons
> show #17/I cartoons
> transparency #17 50 cartoons
> open
> D:/Documents/Projects/Tat/deposition/TatA_ECOBD_AF-A0A140NHF3-F1-model_v4.pdb
Summary of feedback from opening
D:/Documents/Projects/Tat/deposition/TatA_ECOBD_AF-A0A140NHF3-F1-model_v4.pdb
---
warning | Ignored bad PDB record found on line 38
DBREF XXXX A 1 89 UNP A0A140NHF3 A0A140NHF3_ECOBD 1 89
TatA_ECOBD_AF-A0A140NHF3-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for sec-independent protein translocase
protein tata (A0A140NHF3) [more info...]
Chain information for TatA_ECOBD_AF-A0A140NHF3-F1-model_v4.pdb #18
---
Chain | Description
A | sec-independent protein translocase protein tata
> mmaker #18 to #17
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_andTatA_20240902.pdb, chain I (#17) with
TatA_ECOBD_AF-A0A140NHF3-F1-model_v4.pdb, chain A (#18), sequence alignment
score = 283
RMSD between 33 pruned atom pairs is 1.114 angstroms; (across all 60 pairs:
11.024)
> mmaker #18:6-22 to #17:6-22
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_andTatA_20240902.pdb, chain I (#17) with
TatA_ECOBD_AF-A0A140NHF3-F1-model_v4.pdb, chain A (#18), sequence alignment
score = 76.5
RMSD between 17 pruned atom pairs is 0.629 angstroms; (across all 17 pairs:
0.629)
> hide #!17 models
> lighting flat
> lighting full
> lighting shadows false
> show #!17 models
> hide #!17 models
> close #12
> close #13
> close #14
> hide #!2 models
> show #!2 models
> hide #18#!2 surfaces
> show #18#!2 cartoons
> open D:/Documents/Projects/Tat/deposition/TatC_AF-P69423-F1-model_v4.pdb
TatC_AF-P69423-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for sec-independent protein translocase
protein tatc (P69423) [more info...]
Chain information for TatC_AF-P69423-F1-model_v4.pdb #12
---
Chain | Description | UniProt
A | sec-independent protein translocase protein tatc | TATC_ECOLI 1-258
> hide #12 models
> cartoon style width 2.0 thickness 0.4 modeHelix default arrows false
> mmaker #18 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240807.pdb, chain D (#2) with
TatA_ECOBD_AF-A0A140NHF3-F1-model_v4.pdb, chain A (#18), sequence alignment
score = 72.2
RMSD between 21 pruned atom pairs is 1.390 angstroms; (across all 49 pairs:
9.980)
> mmaker #18 to #2/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240807.pdb, chain A (#2) with
TatA_ECOBD_AF-A0A140NHF3-F1-model_v4.pdb, chain A (#18), sequence alignment
score = 36.2
RMSD between 18 pruned atom pairs is 0.887 angstroms; (across all 31 pairs:
10.140)
> mmaker #12 to #2/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240807.pdb, chain A (#2) with
TatC_AF-P69423-F1-model_v4.pdb, chain A (#12), sequence alignment score =
1163.6
RMSD between 69 pruned atom pairs is 1.225 angstroms; (across all 236 pairs:
5.573)
> show #12 models
> hide #18 models
> mmaker #12:40-140 to #2/C:40-140
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240807.pdb, chain C (#2) with
TatC_AF-P69423-F1-model_v4.pdb, chain A (#12), sequence alignment score =
497.4
RMSD between 51 pruned atom pairs is 1.167 angstroms; (across all 101 pairs:
3.932)
> mmaker #12:40-100 to #2/C:40-100
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240807.pdb, chain C (#2) with
TatC_AF-P69423-F1-model_v4.pdb, chain A (#12), sequence alignment score =
299.8
RMSD between 45 pruned atom pairs is 0.702 angstroms; (across all 61 pairs:
3.344)
> mmaker #12 to #2/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240807.pdb, chain C (#2) with
TatC_AF-P69423-F1-model_v4.pdb, chain A (#12), sequence alignment score = 1136
RMSD between 63 pruned atom pairs is 1.109 angstroms; (across all 231 pairs:
4.575)
> mmaker #12:153-176 to #2/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240807.pdb, chain C (#2) with
TatC_AF-P69423-F1-model_v4.pdb, chain A (#12), sequence alignment score =
123.7
RMSD between 24 pruned atom pairs is 0.747 angstroms; (across all 24 pairs:
0.747)
> save D:/Documents/Projects/Tat/Figs/Figure6/TatC_alignment.cxs
> mmaker #12:120-170 to #2/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240807.pdb, chain C (#2) with
TatC_AF-P69423-F1-model_v4.pdb, chain A (#12), sequence alignment score = 242
RMSD between 43 pruned atom pairs is 0.683 angstroms; (across all 51 pairs:
1.944)
> save D:/Documents/Projects/Tat/Figs/Figure6/TatC_alignment.cxs
> show #!8 models
> hide #12#!2,8 surfaces
> hide #12#!2,8 cartoons
> show #2,8 cartoons
> hide #!8 models
> hide #!2 models
> show #!2 models
> show #12 cartoons
> hide #2 cartoons
> show #2/C cartoons
> color #12 mediumslateblue
> hide #12:238-300 cartoons
> hide #12:1-6 cartoons
> show #2/F cartoons
> color #2/F rgb(252,140,192)
> select #18:212-235
Nothing selected
> select #12:212-235
199 atoms, 205 bonds, 24 residues, 1 model selected
> cartoon style sel modeHelix tube radius 2 sides 24 thickness 0.6
> undo
> select clear
> show #12:213 #2/C:213 atoms
> style #12:213 #2/C:213 ball
Changed 22 atom styles
> save D:/Documents/Projects/Tat/Figs/Figure6/TatC_alignment.cxs
——— End of log from Mon Sep 2 21:15:37 2024 ———
opened ChimeraX session
> mmaker #12 to #2/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240807.pdb, chain C (#2) with
TatC_AF-P69423-F1-model_v4.pdb, chain A (#12), sequence alignment score = 1136
RMSD between 63 pruned atom pairs is 1.109 angstroms; (across all 231 pairs:
4.575)
> show #!8 models
> hide #!8 models
> show #!8 models
> show #12#!2,8 atoms
> undo
> hide #!8 models
> hide :156-184 cartoons
> hide :100-122 cartoons
> undo
[Repeated 1 time(s)]
> hide :100-122 cartoons
> hide :156-184 cartoons
> select #12/A:207
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/C:207
16 atoms, 14 bonds, 2 residues, 2 models selected
> show sel atoms
> undo
> select clear
> color #12 gold
> show #2,12:207 atoms
> show #2/C:207 #12:207 atoms
> show #2/C:208 #12:208 atoms
> show #2/C:206 #12:206 atoms
> undo
> show #2/C:207 #12:207 atoms
> show #2/C:210 #12:210 atoms
> show #2/C:209 #12:209 atoms
> undo
> save D:/Documents/Projects/Tat/Figs/Figure6/TatC_alignment.cxs
> save D:/Documents/Projects/Tat/Figs/Figure6/TatC_alignment.png width 3000
> height 3000 supersample 6 transparentBackground true
> color #2/A-C rgb(141,231,188)
> color #12 darkorange
> color #12 orange
> color #12 salmon
> color #12 coral
> color #12 tomato
> color #12 cyan
> color #12 dodgerblue
> color #12 yellow
> color #12 deepskyblue
> color #12 lightcyan
> color #12 mediumpurple
> color #12 rgb(252,140,192)
> color #12 rgb(242,201,182)
> color #12 rgb(255,255,150)
> show #12 cartoons
> show #12:1-237 cartoons
> show #12:7-237 cartoons
> show #2/C cartoons
> transparency #2,12/151-185 50 cartoons
> transparency #2,12:151-185 50 cartoons
> undo
[Repeated 1 time(s)]
> save D:/Documents/Projects/Tat/Figs/Figure6/TatC_alignment.cxs
——— End of log from Mon Sep 2 21:52:32 2024 ———
opened ChimeraX session
> open D:/Documents/Projects/Tat/deposition/TatC_4b4a.pdb
Summary of feedback from opening
D:/Documents/Projects/Tat/deposition/TatC_4b4a.pdb
---
warnings | Ignored bad PDB record found on line 2277
CONECT record for nonexistent atom: 1806
TatC_4b4a.pdb title:
Structure of the tatc core of the twin arginine protein translocation system
[more info...]
Chain information for TatC_4b4a.pdb #13
---
Chain | Description | UniProt
A | TATC | TATC_AQUAE 1-240
> mmaker #13 to #2/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240807.pdb, chain C (#2) with TatC_4b4a.pdb, chain A (#13),
sequence alignment score = 608.5
RMSD between 66 pruned atom pairs is 1.275 angstroms; (across all 222 pairs:
4.947)
> hide #12 models
> color #13 #aa55ffff
> color #13 yellow
> color #13 #aa00ffff
> color #13 magenta
> color #13 #5555ffff
> color #13 #ffaa00ff
> color #13 #ff5500ff
> color #13 #ffaa7fff
> color #13 #ffaa00ff
> color #13 red
> color #13 #ff5500ff
> color #13 #ffaa00ff
> color #13 #ffaa7fff
> color #13 #ffaa00ff
> transparency 0 cartoons
> show #2/C cartoons
> color #13 slateblue
> color #13 orange
> color #13 tomato
> color #13 rgb(252,140,192)
> color #13 rgb(225,92,92)
> color #15 rainbow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> rainbow #13#!2
> color #2/A-C rgb(141,231,188)
> color #2/D-F rgb(252,140,192)
> close #17
> open D:/Documents/Projects/Tat/deposition/J3036_20240807.pdb
Chain information for J3036_20240807.pdb #14
---
Chain | Description
A B | No description available
C | No description available
D | No description available
E F | No description available
G | No description available
H | No description available
> style #13#!2,14 stick
Changed 29874 atom styles
> hide #13#!2,14 atoms
> mmaker #16/A to #2/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240807.pdb, chain C (#2) with J3003_20240831.pdb, chain A
(#16), sequence alignment score = 1159.4
RMSD between 201 pruned atom pairs is 0.780 angstroms; (across all 231 pairs:
1.315)
> hide #!14 models
> show #!14 models
> mmaker #14/A to #2/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240807.pdb, chain C (#2) with J3036_20240807.pdb, chain A
(#14), sequence alignment score = 1162.4
RMSD between 185 pruned atom pairs is 0.885 angstroms; (across all 231 pairs:
1.599)
> show #14/A cartoons
> hide #!14 models
> color #13 #d9eaf8ff
> color #13 #050708ff
> undo
[Repeated 3 time(s)]
> rainbow #13#!2
> undo
> rainbow #13
> volume #3 color #c86000
> volume #3 color #ff6600
> color #13 #ff6600ff
> cartoon style modeHelix tube radius 2 sides 24 thickness 0.6
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> graphics silhouettes true
> show #!14 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> show #14/D cartoons
> hide #!2 models
> show #!2 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> save D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.cxs
——— End of log from Mon Sep 23 10:40:28 2024 ———
opened ChimeraX session
> color #13 silver
> color #13 gray
> color #13 #c0b5adff
> color #13 #c0a28eff
> color #13 #b8c08eff
> color #13 #8fc096ff
> color #13 #91a1c0ff
> color #13 #a5abc0ff
> color #13 #c0a5bfff
> color #13 #c0b3b8ff
> color #13 #b6b8c0ff
> color #13 #bec0beff
> color #13 silver
> show #!14 models
> hide #13 models
> show #13 models
> hide #!2 models
> hide #!14 models
> show #!14 models
> close #12-13,18#2-11,14-16
> close #1
> open D:/Documents/Projects/Tat/deposition/J3036_20240923.pdb
Chain information for J3036_20240923.pdb #1
---
Chain | Description
A B | No description available
C | No description available
D | No description available
E F | No description available
G | No description available
H | No description available
> open D:/Documents/Projects/Tat/deposition/TatC_4b4a.pdb
Summary of feedback from opening
D:/Documents/Projects/Tat/deposition/TatC_4b4a.pdb
---
warnings | Ignored bad PDB record found on line 2277
CONECT record for nonexistent atom: 1806
TatC_4b4a.pdb title:
Structure of the tatc core of the twin arginine protein translocation system
[more info...]
Chain information for TatC_4b4a.pdb #2
---
Chain | Description | UniProt
A | TATC | TATC_AQUAE 1-240
> mmaker #2 to #1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240923.pdb, chain A (#1) with TatC_4b4a.pdb, chain A (#2),
sequence alignment score = 603.3
RMSD between 70 pruned atom pairs is 1.206 angstroms; (across all 223 pairs:
5.682)
> style stick
Changed 15839 atom styles
> hide atoms
> show #1/A cartoons
> show #1/D cartoons
> lighting shadows false
> lighting soft
> color #1/A-C rgb(141,231,188)
> color #1/D-F rgb(252,140,192)
> color #2 lightsalmon
> color #2 salmon
> color #2 coral
> color #2 lightcoral
> save D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.cxs
> save D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.png width 3000
> height 3000 supersample 6 transparentBackground true
> close #1
> open D:/Documents/Projects/Tat/deposition/J3036_20240923.pdb
Chain information for J3036_20240923.pdb #1
---
Chain | Description
A B | No description available
C | No description available
D | No description available
E F | No description available
G | No description available
H | No description available
> style stick
Changed 15839 atom styles
> hide atoms
> color #1/A-C rgb(141,231,188)
> color #1/D-F rgb(252,140,192)
> show #1/A,D cartoons
> color #2 lightsalmon
> mmaker #2 to #1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J3036_20240923.pdb, chain A (#1) with TatC_4b4a.pdb, chain A (#2),
sequence alignment score = 603.3
RMSD between 70 pruned atom pairs is 1.206 angstroms; (across all 223 pairs:
5.682)
> save D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.cxs
> save D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.png width 3000
> height 3000 supersample 6 transparentBackground true
> save D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.cxs
——— End of log from Mon Sep 23 11:15:31 2024 ———
opened ChimeraX session
> select #1/A:170
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 9 atom styles
> color sel byhetero
> select #2:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 9 atom styles
> color sel byhetero
> select clear
> select #2:165 #1:170
48 atoms, 42 bonds, 6 residues, 2 models selected
> color sel gold
> color sel byhetero
> select clear
> save D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.cxs
> save D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.png width 3000
> height 3000 supersample 6 transparentBackground true
> lighting shadows true intensity 0.5
> lighting shadows false
> save D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.cxs
> save D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.png width 3000
> height 3000 supersample 6 transparentBackground true
> color #1:170 rgb(141,231,188)
> color byhetero
> undo
> color #2:165 light salmon
> color byhetero
> save D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.cxs
——— End of log from Tue Sep 24 16:41:58 2024 ———
opened ChimeraX session
> hide color #1/A-C #5eee6a
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> color #1/D-F rgb(255,123,172)
[Repeated 1 time(s)]
> color #1/A-C #5eee6a
> color byhetero
> color #2 coral
> color byhetero
> save D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.cxs
——— End of log from Sun Oct 13 18:30:54 2024 ———
opened ChimeraX session
> color #2:165 red
> color #1:170 cyan
> color byhetero
> color #2:165 magenta
> color byhetero
> size atomRadius 1
Changed 15839 atom radii
> size atomRadius 1.5
Changed 15839 atom radii
> color #2:165 coral
> color #1:170 rgb(141,231,188)
> color byhetero
> color #2:165 coral
> color #1:170 #5eee6a
> color byhetero
> save D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.cxs
> save D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.png width 3000
> height 3000 supersample 6 transparentBackground true
> cartoon style thickness 0.8
> save D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.cxs
> save D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.png width 3000
> height 3000 supersample 6 transparentBackground true
> color #1/A mediumseagreen
> color byhetero
> save D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.cxs
——— End of log from Sun Oct 13 21:02:02 2024 ———
opened ChimeraX session
> color #2 deepskyblue
> color #1/A-C #5eee6a
> color #2 #00aaffff
> color #2 #55aaffff
> color #2 #00aaffff
> color #2 #55aaffff
> color #2 #00aaffff
> color #2 mediumslateblue
> color byhetero
> save D:/Documents/Projects/Tat/Figs/Figure2/TatC_alignment.cxs
——— End of log from Sun Oct 13 21:16:30 2024 ———
opened ChimeraX session
> ui tool show Foldseek
> foldseek #1/A
Traceback (most recent call last):
File "D:\Program Files\ChimeraX 1.9.dev202410132109\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 238, in _search
run(self.session, cmd)
File "D:\Program Files\ChimeraX 1.9.dev202410132109\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Program Files\ChimeraX 1.9.dev202410132109\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Program Files\ChimeraX 1.9.dev202410132109\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 37, in
foldseek_search
FoldseekWebQuery(session, chain, database=database,
File "D:\Program Files\ChimeraX 1.9.dev202410132109\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 74, in __init__
mmcif_string = _mmcif_as_string(chain)
^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Program Files\ChimeraX 1.9.dev202410132109\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 284, in
_mmcif_as_string
write_mmcif(chain.structure.session, f.name, models = [structure])
File "src\\\mmcif_write.pyx", line 168, in
chimerax.mmcif.mmcif_write.write_mmcif
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\ALBERT~1.ASU\\\AppData\\\Local\\\Temp\\\foldseek_mmcif_rizk13an.cif'
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\ALBERT~1.ASU\\\AppData\\\Local\\\Temp\\\foldseek_mmcif_rizk13an.cif'
File "src\\\mmcif_write.pyx", line 168, in
chimerax.mmcif.mmcif_write.write_mmcif
See log for complete Python traceback.
> sequence search #1/A
Found 4 similar structures to J3036_20240923.pdb #1/A in pdb database using
mmseqs2, name mm1
> sequence search #1/A database afdb
Found 65 similar structures to J3036_20240923.pdb #1/A in afdb database using
mmseqs2, name mm2
> similarstructures sequences
> similarstructures traces
> similarstructures cluster #1/A:172,97,85,209,118 clusterDistance 1.5
> foldseek #1/A database afdb50
Traceback (most recent call last):
File "D:\Program Files\ChimeraX 1.9.dev202410132109\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 238, in _search
run(self.session, cmd)
File "D:\Program Files\ChimeraX 1.9.dev202410132109\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Program Files\ChimeraX 1.9.dev202410132109\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Program Files\ChimeraX 1.9.dev202410132109\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 37, in
foldseek_search
FoldseekWebQuery(session, chain, database=database,
File "D:\Program Files\ChimeraX 1.9.dev202410132109\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 74, in __init__
mmcif_string = _mmcif_as_string(chain)
^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Program Files\ChimeraX 1.9.dev202410132109\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 284, in
_mmcif_as_string
write_mmcif(chain.structure.session, f.name, models = [structure])
File "src\\\mmcif_write.pyx", line 168, in
chimerax.mmcif.mmcif_write.write_mmcif
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\ALBERT~1.ASU\\\AppData\\\Local\\\Temp\\\foldseek_mmcif_x_atawau.cif'
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\ALBERT~1.ASU\\\AppData\\\Local\\\Temp\\\foldseek_mmcif_x_atawau.cif'
File "src\\\mmcif_write.pyx", line 168, in
chimerax.mmcif.mmcif_write.write_mmcif
See log for complete Python traceback.
> foldseek #1/A database afdb50
Traceback (most recent call last):
File "D:\Program Files\ChimeraX 1.9.dev202410132109\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 238, in _search
run(self.session, cmd)
File "D:\Program Files\ChimeraX 1.9.dev202410132109\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Program Files\ChimeraX 1.9.dev202410132109\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Program Files\ChimeraX 1.9.dev202410132109\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 37, in
foldseek_search
FoldseekWebQuery(session, chain, database=database,
File "D:\Program Files\ChimeraX 1.9.dev202410132109\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 74, in __init__
mmcif_string = _mmcif_as_string(chain)
^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Program Files\ChimeraX 1.9.dev202410132109\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 284, in
_mmcif_as_string
write_mmcif(chain.structure.session, f.name, models = [structure])
File "src\\\mmcif_write.pyx", line 168, in
chimerax.mmcif.mmcif_write.write_mmcif
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\ALBERT~1.ASU\\\AppData\\\Local\\\Temp\\\foldseek_mmcif_cvfnag52.cif'
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\ALBERT~1.ASU\\\AppData\\\Local\\\Temp\\\foldseek_mmcif_cvfnag52.cif'
File "src\\\mmcif_write.pyx", line 168, in
chimerax.mmcif.mmcif_write.write_mmcif
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 516.91
OpenGL renderer: NVIDIA GeForce RTX 3060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: ASUSTeK COMPUTER INC.
Model: ASUS TUF Gaming F15 FX507ZM_FX507ZM
OS: Microsoft Windows 11 Pro (Build 22621)
Memory: 16,782,422,016
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700H
OSLanguage: zh-CN
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 2.4.1
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.7.1
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.14
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.7
ChimeraX-AtomicLibrary: 14.1.8
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.7
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.3.4
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9.dev202410132109
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-DeepMutationalScan: 1.0
ChimeraX-Dicom: 1.2.5
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.11
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.2.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.13
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.7
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.54.1
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.12.1
html2text: 2024.2.26
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.1
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.1
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.1
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
Change History (2)
comment:1 by , 13 months ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Foldseek: permission error writing temp file |
comment:2 by , 13 months ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
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I guess some defective virus scan software has locked the temporary file to scan it. We've seen this kind of report several times, always on Windows.