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Opened 13 months ago
Closed 13 months ago
#16089 closed defect (limitation)
Movie recording: No space left on device
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/wang/Documents/Zeytuni_lab/fimbriae_movies_chimeraX/movie_Mfa1_views_draft1.cxs
> format session
Opened Mfa1_volmax_EMhancer.mrc as #3, grid size 640,640,640, pixel 0.675,
shown at step 1, values float32
Log from Tue Oct 8 19:48:35 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/wang/Documents/Zeytuni_lab/fimbriae_movies_chimeraX/movie_Mfa1_views_draft1.cxs
Opened Mfa1_volmax_EMhancer.mrc as #3, grid size 640,640,640, pixel 0.675,
shown at level 0.126, step 1, values float32
Log from Tue Oct 8 14:51:28 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/wang/Documents/CIHR_2024/Mfa_blue_theme.cxs
Opened Mfa1_volmax_EMhancer.mrc as #3, grid size 640,640,640, pixel 0.675,
shown at level 0.1, step 1, values float32
Log from Mon Aug 19 12:50:52 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/wang/Documents/Mfa_blue_theme.cxs format session
Opened Mfa1_volmax_EMhancer.mrc as #3, grid size 640,640,640, pixel 0.675,
shown at level 0.1, step 1, values float32
Log from Mon Aug 19 12:29:48 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/wang/Documents/FimA_Mfa_map_colour.cxs format session
Error opening map
"/Users/wang/Documents/Zeytuni_lab/FimA_processing/5nf2.pdb": File 5nf2.pdb,
format mrc
MRC header value nsymbt (1212489798) is invalid
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "VolumeImage" returned None
Opened Mfa1_volmax_EMhancer.mrc as #3, grid size 640,640,640, pixel 0.675,
shown at level 0.1, step 1, values float32
restore_snapshot for "ZoneColor" returned None
Log from Thu Aug 15 06:35:57 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/wang/Documents/FimA_Mfa.cxs
Opened Mfa1_volmax_EMhancer.mrc as #3, grid size 640,640,640, pixel 0.675,
shown at level 0.1, step 1, values float32
Opened EMhancer_J306.mrc as #4, grid size 480,480,480, pixel 0.855, shown at
level 0.15, step 1, values float32
Log from Wed Aug 14 18:37:43 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/wang/Downloads/Fim_Mfa_colour.cxs format session
Opened Mfa1_volmax_EMhancer.mrc as #3, grid size 640,640,640, pixel 0.675,
shown at level 0.15, step 2, values float32
Opened EMhancer_J306.mrc as #4, grid size 480,480,480, pixel 0.855, shown at
level 0.15, step 1, values float32
Log from Wed Aug 14 16:39:39 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/wang/Desktop/nFimA_colored.cxs
Log from Tue Jul 30 15:51:36 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/wang/Documents/Zeytuni_lab/POSTER/FimA_colored.cxs format
> session
Log from Mon Jun 10 21:04:48 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
still retrieving bundle list from toolshed
> file:///Users/wang/Documents/Zeytuni lab/FimA_processing/chimera_aliases.com
Error running startup command 'file:///Users/wang/Documents/Zeytuni
lab/FimA_processing/chimera_aliases.com': Unknown command:
file:///Users/wang/Documents/Zeytuni lab/FimA_processing/chimera_aliases.com
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/wang/Downloads/real_space_refin_FimA-coot-0.pdb
Chain information for real_space_refin_FimA-coot-0.pdb #1
---
Chain | Description
A | No description available
B C | No description available
D | No description available
> show atoms
[Repeated 1 time(s)]
> hide atoms
> show cartoons
[Repeated 1 time(s)]
> color bychain
> 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
Alignment identifier is 1/A
Alignment identifier is 1
Alignment identifier is 1/D
> select /A
2403 atoms, 2449 bonds, 316 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium purple
> select chain B
Expected an objects specifier or a keyword
> select /B
2568 atoms, 2619 bonds, 337 residues, 1 model selected
> ui tool show "Color Actions"
> color sel sandy brown
> color sel light salmon
[Repeated 1 time(s)]
> select /C
2568 atoms, 2619 bonds, 337 residues, 1 model selected
> color sel light green
> select /D
165 atoms, 169 bonds, 21 residues, 1 model selected
> color sel light blue
> color sel royal blue
> color sel deep sky blue
> color sel royal blue
> color sel cornflower blue
> select clear
> select /D
165 atoms, 169 bonds, 21 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark salmon
> color sel dodger blue
> color sel medium blue
> color sel midnight blue
> color sel dark slate blue
> select clear
> select /B
2568 atoms, 2619 bonds, 337 residues, 1 model selected
> select /C
2568 atoms, 2619 bonds, 337 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light sky blue
> select /D
165 atoms, 169 bonds, 21 residues, 1 model selected
> color sel gold
> color sel orange
> color sel gold
> color sel light goldenrod yellow
> color sel khaki
> color sel pale goldenrod
> select clear
> select /D
165 atoms, 169 bonds, 21 residues, 1 model selected
> color sel yellow
> ui tool show "Modeller Comparative"
> select clear
> select /B
2568 atoms, 2619 bonds, 337 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark orange
> color sel orange
> color sel steel blue
> color sel sandy brown
> color sel orange
> select clear
> select
7704 atoms, 7856 bonds, 1011 residues, 1 model selected
> transparency #1 80%
Missing or invalid "percent" argument: Expected a number
> transparency #1 80
> transparency #1 80 cartoons
> transparency #1 20 cartoons
> select clear
> save /Users/wang/Desktop/image2.png supersample 3
> save /Users/wang/Desktop/FimA_colored.cxs
——— End of log from Mon Jun 10 21:04:48 2024 ———
opened ChimeraX session
> open
> /Users/wang/Documents/Zeytuni_lab/FimA_processing/Phenix_output/RealSpaceRefine_18/real_space_refin_FimA-
> coot-0_real_space_refined_018.pdb
Chain information for real_space_refin_FimA-coot-0_real_space_refined_018.pdb
#2
---
Chain | Description
A | No description available
B C | No description available
D | No description available
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> select #2/A
2403 atoms, 2449 bonds, 316 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium purple
> select #2/B
2568 atoms, 2619 bonds, 337 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orange
> select #2/C
2568 atoms, 2619 bonds, 337 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light sky blue
> close #1
> select clear
> save /Users/wang/Desktop/nFimA_colored.cxs
——— End of log from Tue Jul 30 15:51:36 2024 ———
opened ChimeraX session
> open /Users/wang/Documents/Zeytuni_lab/Mfa1_Krios/Mfa1_processing/Mfa1_noH-
> coot-15-1.pdb format pdb
Chain information for Mfa1_noH-coot-15-1.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> hide #2 models
> select #1/D
167 atoms, 172 bonds, 20 residues, 1 model selected
> 98D5F1
Unknown command: 98D5F1
> color sel #98d5f1ff
[Repeated 1 time(s)]
> dssp
> select #1/C
3929 atoms, 4025 bonds, 514 residues, 1 model selected
> color sel #235caaff
> select #1/B
3935 atoms, 4030 bonds, 516 residues, 1 model selected
> color sel #95b4deff
[Repeated 1 time(s)]
> select #1/A
3781 atoms, 3872 bonds, 496 residues, 1 model selected
> color sel #98d5f1ff
[Repeated 1 time(s)]
> select clear
> dssp
> 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
> hide #1 models
> show #2 models
> select #2/D
165 atoms, 169 bonds, 21 residues, 1 model selected
> color sel #8aa081ff
> select #2/C
2568 atoms, 2619 bonds, 337 residues, 1 model selected
> color sel #8aa081ff
> select #2/D
165 atoms, 169 bonds, 21 residues, 1 model selected
> color sel #cdc875ff
[Repeated 1 time(s)]
> select #2/B
2568 atoms, 2619 bonds, 337 residues, 1 model selected
> color sel #aaba96ff
[Repeated 1 time(s)]
> color sel #c8d2aaff
> select #2/A
2403 atoms, 2449 bonds, 316 residues, 1 model selected
> color sel #cdc875ff
[Repeated 4 time(s)]
> color sel #cdc874ff
[Repeated 3 time(s)]
> color sel #cdc873ff
[Repeated 3 time(s)]
> color sel #cdc872ff
[Repeated 2 time(s)]
> color sel #cdc871ff
[Repeated 2 time(s)]
> color sel #cdc870ff
[Repeated 3 time(s)]
> color sel #cdc86fff
> color sel #cdc86eff
> color sel #cdc86dff
> color sel #cdc86cff
[Repeated 2 time(s)]
> color sel #cdc86bff
[Repeated 1 time(s)]
> color sel #cdc86aff
[Repeated 2 time(s)]
> color sel #cdc869ff
[Repeated 3 time(s)]
> color sel #cdc868ff
[Repeated 2 time(s)]
> color sel #cdc867ff
> color sel #cdc865ff
> color sel #cdc864ff
> color sel #cdc863ff
> color sel #cdc862ff
> color sel #cdc861ff
> color sel #cdc860ff
> color sel #cdc85eff
> color sel #cdc85bff
> color sel #cdc859ff
[Repeated 2 time(s)]
> color sel #cdc864ff
> color sel #cdc86bff
> color sel #cdc86cff
[Repeated 1 time(s)]
> color sel #cdc86dff
> color sel #cdc871ff
> color sel #cdc875ff
> color sel #cdc876ff
> color sel #cdc877ff
> color sel #cdc87aff
> color sel #cdc880ff
> color sel #cdc882ff
> color sel #cdc883ff
[Repeated 1 time(s)]
> color sel #cdc884ff
[Repeated 1 time(s)]
> color sel #cdc887ff
> color sel #cdc88bff
> color sel #cdc88dff
> color sel #cdc88fff
[Repeated 1 time(s)]
> color sel #cdc890ff
[Repeated 2 time(s)]
> color sel #cdc891ff
[Repeated 1 time(s)]
> color sel #cdc892ff
[Repeated 1 time(s)]
> color sel #cdc893ff
> color sel #cdc895ff
> color sel #cdc897ff
> color sel #cdc898ff
> color sel #cdc899ff
[Repeated 1 time(s)]
> color sel #cdc89aff
[Repeated 1 time(s)]
> color sel #cdc89bff
[Repeated 1 time(s)]
> color sel #cdc89cff
[Repeated 2 time(s)]
> color sel #cdc89dff
[Repeated 1 time(s)]
> color sel #cdc89eff
[Repeated 1 time(s)]
> color sel #cdc89fff
[Repeated 2 time(s)]
> color sel #cdc8a0ff
[Repeated 3 time(s)]
> color sel #cdc89eff
> color sel #cdc89cff
> color sel #cdc89bff
> color sel #cdc897ff
> color sel #cdc891ff
> color sel #cdc88cff
> color sel #cdc889ff
> color sel #cdc887ff
[Repeated 2 time(s)]
> color sel #cdc886ff
[Repeated 1 time(s)]
> color sel #cdc885ff
[Repeated 1 time(s)]
> color sel #cdc884ff
[Repeated 1 time(s)]
> color sel #cdc883ff
[Repeated 2 time(s)]
> color sel #cdc882ff
> color sel #cdc881ff
[Repeated 1 time(s)]
> color sel #cdc880ff
[Repeated 2 time(s)]
> color sel #cdc882ff
> color sel #cdc883ff
> color sel #cdc882ff
[Repeated 1 time(s)]
> color sel #cdc881ff
[Repeated 1 time(s)]
> color sel #cdc880ff
[Repeated 1 time(s)]
> color sel #cdc87bff
> color sel #cdc87aff
> color sel #cdc879ff
[Repeated 1 time(s)]
> color sel #cdc878ff
[Repeated 2 time(s)]
> color sel #cdc877ff
[Repeated 1 time(s)]
> color sel #cdc876ff
[Repeated 2 time(s)]
> color sel #cdc875ff
[Repeated 1 time(s)]
> color sel #cdc874ff
> color sel #cdc875ff
[Repeated 3 time(s)]
> color sel #cdc876ff
[Repeated 4 time(s)]
> color sel #cdc875ff
[Repeated 4 time(s)]
> color sel #cbc875ff
> color sel #cac875ff
[Repeated 1 time(s)]
> color sel #c9c875ff
[Repeated 2 time(s)]
> color sel #c8c875ff
> color sel #c7c875ff
[Repeated 1 time(s)]
> color sel #c6c875ff
[Repeated 1 time(s)]
> color sel #c5c875ff
[Repeated 1 time(s)]
> color sel #c4c875ff
[Repeated 1 time(s)]
> color sel #c3c875ff
[Repeated 1 time(s)]
> color sel #c2c875ff
[Repeated 1 time(s)]
> color sel #c1c875ff
> color sel #c0c875ff
> color sel #bfc875ff
[Repeated 1 time(s)]
> color sel #bec875ff
[Repeated 1 time(s)]
> color sel #bdc875ff
> color sel #bcc875ff
[Repeated 1 time(s)]
> color sel #bbc875ff
[Repeated 1 time(s)]
> color sel #bac875ff
[Repeated 1 time(s)]
> color sel #b9c875ff
> color sel #b8c875ff
> color sel #b7c875ff
[Repeated 2 time(s)]
> color sel #b6c875ff
[Repeated 1 time(s)]
> color sel #b5c875ff
> color sel #b4c875ff
[Repeated 1 time(s)]
> color sel #b3c875ff
[Repeated 2 time(s)]
> color sel #b2c875ff
> color sel #b1c875ff
[Repeated 4 time(s)]
> color sel #b2c875ff
[Repeated 3 time(s)]
> color sel #b3c875ff
[Repeated 4 time(s)]
> color sel #b2c875ff
[Repeated 1 time(s)]
> color sel #b1c875ff
[Repeated 1 time(s)]
> color sel #b0c875ff
[Repeated 1 time(s)]
> color sel #aec875ff
> color sel #adc875ff
[Repeated 2 time(s)]
> color sel #acc875ff
[Repeated 1 time(s)]
> color sel #abc875ff
[Repeated 1 time(s)]
> color sel #aac875ff
> color sel #a9c875ff
> color sel #a8c875ff
[Repeated 1 time(s)]
> color sel #a7c875ff
[Repeated 2 time(s)]
> color sel #a6c875ff
[Repeated 1 time(s)]
> color sel #a5c875ff
> color sel #a4c875ff
> color sel #a3c875ff
[Repeated 1 time(s)]
> color sel #a2c875ff
[Repeated 1 time(s)]
> color sel #a1c875ff
[Repeated 1 time(s)]
> color sel #a0c875ff
[Repeated 1 time(s)]
> color sel #9fc875ff
> color sel #9ec875ff
> color sel #9cc875ff
[Repeated 2 time(s)]
> color sel #9ac875ff
[Repeated 1 time(s)]
> color sel #99c875ff
> color sel #98c875ff
[Repeated 3 time(s)]
> color sel #97c875ff
[Repeated 1 time(s)]
> color sel #96c875ff
[Repeated 1 time(s)]
> color sel #95c875ff
[Repeated 1 time(s)]
> color sel #94c875ff
[Repeated 1 time(s)]
> color sel #93c875ff
> color sel #92c875ff
[Repeated 1 time(s)]
> color sel #91c875ff
[Repeated 2 time(s)]
> color sel #90c875ff
[Repeated 2 time(s)]
> color sel #8fc875ff
[Repeated 1 time(s)]
> color sel #8ec875ff
[Repeated 2 time(s)]
> color sel #8dc875ff
[Repeated 2 time(s)]
> color sel #8cc875ff
[Repeated 2 time(s)]
> color sel #8bc875ff
> color sel #8ac875ff
[Repeated 2 time(s)]
> color sel #89c875ff
[Repeated 3 time(s)]
> color sel #88c875ff
> color sel #87c875ff
[Repeated 1 time(s)]
> color sel #86c875ff
> color sel #85c875ff
[Repeated 1 time(s)]
> color sel #84c875ff
> color sel #83c875ff
[Repeated 1 time(s)]
> color sel #81c875ff
[Repeated 1 time(s)]
> color sel #80c875ff
[Repeated 2 time(s)]
> color sel #7bc875ff
> color sel #7ac875ff
> color sel #79c875ff
> color sel #77c875ff
[Repeated 3 time(s)]
> color sel #76c875ff
[Repeated 2 time(s)]
> color sel #75c875ff
[Repeated 3 time(s)]
> color sel #78c875ff
> color sel #7ec875ff
> color sel #82c875ff
> color sel #84c875ff
> color sel #87c875ff
> color sel #89c875ff
> color sel #8ac875ff
> color sel #8bc875ff
> color sel #8cc875ff
> color sel #8ec875ff
> color sel #91c875ff
> color sel #93c875ff
> color sel #95c875ff
[Repeated 1 time(s)]
> color sel #98c875ff
> color sel #99c875ff
> color sel #9bc875ff
[Repeated 1 time(s)]
> color sel #9dc875ff
[Repeated 1 time(s)]
> color sel #9ec875ff
[Repeated 1 time(s)]
> color sel #9fc875ff
> color sel #a0c875ff
> color sel #a1c875ff
[Repeated 1 time(s)]
> color sel #a2c875ff
[Repeated 3 time(s)]
> color sel #a3c875ff
> color sel #a4c875ff
[Repeated 1 time(s)]
> color sel #a5c875ff
[Repeated 1 time(s)]
> color sel #a6c875ff
[Repeated 1 time(s)]
> color sel #a7c875ff
[Repeated 1 time(s)]
> color sel #a8c875ff
> color sel #a9c875ff
[Repeated 1 time(s)]
> color sel #abc875ff
[Repeated 1 time(s)]
> color sel #acc875ff
> color sel #aec875ff
> color sel #afc875ff
> color sel #b1c875ff
> color sel #b2c875ff
> color sel #b3c875ff
> color sel #b4c875ff
> color sel #b6c875ff
[Repeated 1 time(s)]
> color sel #b7c875ff
> color sel #b8c875ff
[Repeated 1 time(s)]
> color sel #b9c875ff
> color sel #bac875ff
[Repeated 1 time(s)]
> color sel #bbc875ff
[Repeated 1 time(s)]
> color sel #bcc875ff
[Repeated 1 time(s)]
> color sel #bdc875ff
> color sel #bec875ff
[Repeated 2 time(s)]
> color sel #bfc875ff
> color sel #c0c875ff
[Repeated 1 time(s)]
> color sel #c1c875ff
[Repeated 1 time(s)]
> color sel #c2c875ff
[Repeated 1 time(s)]
> color sel #c3c875ff
[Repeated 1 time(s)]
> color sel #c4c875ff
> color sel #c5c875ff
[Repeated 1 time(s)]
> color sel #c6c875ff
[Repeated 3 time(s)]
> color sel #c7c875ff
[Repeated 2 time(s)]
> color sel #c8c875ff
[Repeated 2 time(s)]
> color sel #c9c875ff
[Repeated 2 time(s)]
> color sel #cac875ff
[Repeated 1 time(s)]
> color sel #cbc875ff
[Repeated 4 time(s)]
> color sel #ccc875ff
[Repeated 3 time(s)]
> color sel #cdc875ff
> color sel #cec875ff
[Repeated 1 time(s)]
> color sel #cfc875ff
[Repeated 2 time(s)]
> color sel #d0c875ff
[Repeated 2 time(s)]
> color sel #cdc875ff
> color sel #c8c875ff
> color sel #c6c875ff
> color sel #c5c875ff
[Repeated 1 time(s)]
> color sel #c4c875ff
[Repeated 1 time(s)]
> color sel #c3c875ff
[Repeated 1 time(s)]
> color sel #c2c875ff
> color sel #c1c875ff
[Repeated 3 time(s)]
> color sel #c0c875ff
> color sel #bfc875ff
[Repeated 2 time(s)]
> color sel #bec875ff
[Repeated 6 time(s)]
> color sel #bec876ff
[Repeated 1 time(s)]
> color sel #bec877ff
> color sel #bec878ff
> color sel #bec879ff
[Repeated 2 time(s)]
> color sel #bec87aff
[Repeated 1 time(s)]
> color sel #bec87bff
[Repeated 3 time(s)]
> color sel #bec87cff
[Repeated 2 time(s)]
> color sel #bec87aff
[Repeated 1 time(s)]
> color sel #bec879ff
> color sel #bec878ff
> color sel #bec876ff
> color sel #bec875ff
[Repeated 1 time(s)]
> color sel #bec874ff
[Repeated 1 time(s)]
> color sel #bec873ff
[Repeated 1 time(s)]
> color sel #bec872ff
[Repeated 2 time(s)]
> color sel #bec871ff
[Repeated 1 time(s)]
> color sel #bec870ff
[Repeated 1 time(s)]
> color sel #bec86fff
[Repeated 1 time(s)]
> color sel #bec86dff
> color sel #bec86cff
[Repeated 2 time(s)]
> color sel #bec86bff
> color sel #bec86aff
[Repeated 1 time(s)]
> color sel #bec869ff
[Repeated 1 time(s)]
> color sel #bec86aff
[Repeated 1 time(s)]
> color sel #bec86bff
[Repeated 1 time(s)]
> color sel #bec86cff
[Repeated 2 time(s)]
> color sel #bec86dff
[Repeated 2 time(s)]
> color sel #bec86eff
[Repeated 2 time(s)]
> color sel #bec86fff
[Repeated 1 time(s)]
> color sel #bec870ff
[Repeated 1 time(s)]
> color sel #bec871ff
[Repeated 3 time(s)]
> color sel #bec872ff
[Repeated 3 time(s)]
> color sel #bec873ff
[Repeated 2 time(s)]
> color sel #bec874ff
[Repeated 1 time(s)]
> color sel #bec875ff
[Repeated 1 time(s)]
> color sel #bec877ff
> color sel #bec878ff
[Repeated 1 time(s)]
> color sel #bec879ff
> color sel #bec87aff
[Repeated 1 time(s)]
> color sel #cdc875ff
> save /Users/wang/Downloads/Fim_Mfa_colour.cxs
> hide #2 models
> show #1 models
> show #2 models
> ui tool show Matchmaker
> matchmaker #2/B to #1/B pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Mfa1_noH-coot-15-1.pdb, chain B (#1) with real_space_refin_FimA-
coot-0_real_space_refined_018.pdb, chain B (#2), sequence alignment score =
111.9
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: Mfa1_noH-coot-15-1.pdb #1/B,
real_space_refin_FimA-coot-0_real_space_refined_018.pdb #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 17 pruned atom pairs is 1.324 angstroms; (across all 283 pairs:
25.765)
> select clear
> view
> hide #2 models
> show #2 models
> hide #2 models
> hide #1 models
> show #1 models
> show #2 models
> hide #2 models
> show #2 models
> select #1/D
167 atoms, 172 bonds, 20 residues, 1 model selected
> select #1/D
167 atoms, 172 bonds, 20 residues, 1 model selected
> select #2/D
165 atoms, 169 bonds, 21 residues, 1 model selected
> select clear
> select add #1
11812 atoms, 12099 bonds, 1546 residues, 1 model selected
> make copy #1
Unknown command: make copy #1
> mcopy #1
Missing required "to_atoms" argument
> copy #1
Unknown command: copy #1
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-37.673,0,1,0,-64.939,0,0,1,-1.0564
> select clear
> open
> /Users/wang/Documents/Zeytuni_lab/Mfa1_Krios/Mfa1_processing/Mfa1_volmax_EMhancer.mrc
Opened Mfa1_volmax_EMhancer.mrc as #3, grid size 640,640,640, pixel 0.675,
shown at level 2.89e-05, step 4, values float32
> volume #3 step 1
> volume #3 level 0.08305
> volume #3 level 0.1913
> ui tool show "Fit in Map"
> fitmap #1 inMap #3
Fit molecule Mfa1_noH-coot-15-1.pdb (#1) to map Mfa1_volmax_EMhancer.mrc (#3)
using 11812 atoms
average map value = -6.796e-06, steps = 324
shifted from previous position = 1.13
rotated from previous position = 2.34 degrees
atoms outside contour = 11812, contour level = 0.19133
Position of Mfa1_noH-coot-15-1.pdb (#1) relative to Mfa1_volmax_EMhancer.mrc
(#3) coordinates:
Matrix rotation and translation
0.99921748 0.03942425 0.00318820 -47.08351628
-0.03945530 0.99916777 0.01034620 -59.56540550
-0.00277765 -0.01046389 0.99994139 1.75841146
Axis -0.25441364 0.07293543 -0.96434129
Axis point -1544.40703012 1125.30058937 0.00000000
Rotation angle (degrees) 2.34394517
Shift along axis 5.93855131
> select add #2
7704 atoms, 7856 bonds, 1011 residues, 1 model selected
> view matrix models
> #2,-0.96572,0.2272,0.12555,381.39,0.18637,0.94353,-0.27389,100.23,-0.18069,-0.24111,-0.95353,472.29
> select add #1
19516 atoms, 19955 bonds, 2557 residues, 2 models selected
> select subtract #2
11812 atoms, 12099 bonds, 1546 residues, 1 model selected
> view matrix models
> #1,0.99922,0.039424,0.0031882,-9.0592,-0.039455,0.99917,0.010346,4.8733,-0.0027777,-0.010464,0.99994,1.5537
> fitmap #1 inMap #3
Fit molecule Mfa1_noH-coot-15-1.pdb (#1) to map Mfa1_volmax_EMhancer.mrc (#3)
using 11812 atoms
average map value = 0.4213, steps = 72
shifted from previous position = 2.05
rotated from previous position = 2.33 degrees
atoms outside contour = 3651, contour level = 0.19133
Position of Mfa1_noH-coot-15-1.pdb (#1) relative to Mfa1_volmax_EMhancer.mrc
(#3) coordinates:
Matrix rotation and translation
0.99999994 0.00033116 0.00009147 -0.05006297
-0.00033116 0.99999995 0.00000203 0.10126606
-0.00009147 -0.00000206 1.00000000 0.04589193
Axis -0.00595181 0.26622812 -0.96389168
Axis point 319.41890957 151.53849377 0.00000000
Rotation angle (degrees) 0.01968462
Shift along axis -0.01697702
> select clear
> volume #3 level 0.1372
> open /Users/wang/Documents/Zeytuni_lab/FimA_processing/EMhancer_J306.mrc
Opened EMhancer_J306.mrc as #4, grid size 480,480,480, pixel 0.855, shown at
level 0.000113, step 2, values float32
> volume #4 step 1
> volume #4 level 0.2141
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = -2.436e-05, steps = 116
shifted from previous position = 5.83
rotated from previous position = 3.81 degrees
atoms outside contour = 7704, contour level = 0.21412
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
-0.97678573 0.16553013 0.13597576 391.92803034
0.12160914 0.95103375 -0.28415845 111.40700349
-0.17635432 -0.26102603 -0.94908617 479.24159933
Axis 0.07314594 0.98760412 -0.13888046
Axis point 211.54619509 0.00000000 231.87937660
Rotation angle (degrees) 170.90191047
Shift along axis 72.13666704
> select add #2
7704 atoms, 7856 bonds, 1011 residues, 1 model selected
> view matrix models
> #2,-0.97679,0.16553,0.13598,363.92,0.12161,0.95103,-0.28416,36.002,-0.17635,-0.26103,-0.94909,471.55
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = 0.09095, steps = 216
shifted from previous position = 6.44
rotated from previous position = 6.64 degrees
atoms outside contour = 6546, contour level = 0.21412
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
-0.99249120 0.10632332 0.06046962 386.57164536
0.09067611 0.97135466 -0.21965420 28.47903216
-0.08209182 -0.21252171 -0.97370194 448.06680135
Axis 0.04967095 0.99280352 -0.10896776
Axis point 200.68201650 0.00000000 218.59704583
Rotation angle (degrees) 175.88276902
Shift along axis -1.34937192
> view matrix models
> #2,-0.99249,0.10632,0.06047,391.72,0.090676,0.97135,-0.21965,28.524,-0.082092,-0.21252,-0.9737,443.98
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = 0.08615, steps = 164
shifted from previous position = 3.51
rotated from previous position = 2.46 degrees
atoms outside contour = 6621, contour level = 0.21412
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
-0.99547454 0.07313409 0.06067827 395.54235164
0.06032332 0.97970316 -0.19116177 28.86089497
-0.07342714 -0.18663636 -0.97968124 438.44664067
Axis 0.03357331 0.99490704 -0.09504107
Axis point 204.71838750 0.00000000 213.89578246
Rotation angle (degrees) 176.13556728
Shift along axis 0.32313637
> select add #4
7704 atoms, 7856 bonds, 1011 residues, 3 models selected
> view matrix models
> #2,-0.99547,0.073134,0.060678,338.16,0.060323,0.9797,-0.19116,28.063,-0.073427,-0.18664,-0.97968,443.1,#4,1,0,0,-57.385,0,1,0,-0.79797,0,0,1,4.653
> view matrix models
> #2,-0.99547,0.073134,0.060678,468.34,0.060323,0.9797,-0.19116,105.3,-0.073427,-0.18664,-0.97968,450.99,#4,1,0,0,72.802,0,1,0,76.439,0,0,1,12.548
> view matrix models
> #2,-0.99547,0.073134,0.060678,469.16,0.060323,0.9797,-0.19116,104.93,-0.073427,-0.18664,-0.97968,460.99,#4,1,0,0,73.619,0,1,0,76.068,0,0,1,22.54
> volume #4 level 0.15
> volume #3 level 0.1492
> volume #3 level 0.15
> select clear
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = 0.08622, steps = 80
shifted from previous position = 0.021
rotated from previous position = 0.566 degrees
atoms outside contour = 6341, contour level = 0.14997
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
-0.99613541 0.06329058 0.06089783 397.60688293
0.05066250 0.98042943 -0.19024051 30.56218482
-0.07174645 -0.18642007 -0.97984693 438.10314311
Axis 0.02866071 0.99508986 -0.09473511
Axis point 205.70780894 0.00000000 213.84135144
Rotation angle (degrees) 176.17843791
Shift along axis 0.30406304
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = 0.08622, steps = 64
shifted from previous position = 0.0287
rotated from previous position = 0.507 degrees
atoms outside contour = 6347, contour level = 0.14997
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
-0.99665693 0.05446001 0.06090219 399.46955487
0.04203072 0.98099952 -0.18940264 32.09223771
-0.07005989 -0.18620969 -0.98000896 437.76458790
Axis 0.02426450 0.99523337 -0.09445516
Axis point 206.58698102 0.00000000 213.79593381
Rotation angle (degrees) 176.22751864
Shift along axis 0.28307198
> select add #2
7704 atoms, 7856 bonds, 1011 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.96232,0.25277,-0.10023,454.89,0.26983,0.9333,-0.23694,79.075,0.033655,-0.25505,-0.96634,450.23
> view matrix models
> #2,-0.97804,-0.13697,0.15707,490.57,-0.17801,0.94098,-0.28786,179.51,-0.10837,-0.3095,-0.9447,486.77
> view matrix models
> #2,-0.43269,-0.9009,0.03405,553.59,-0.89965,0.43392,0.048414,371.03,-0.058391,-0.0096847,-0.99825,425.57
> view matrix models
> #2,-0.94389,-0.3286,0.033023,544.38,-0.32831,0.94447,0.014024,155.81,-0.035798,0.0023953,-0.99936,418.65
> hide #2 models
> show #2 models
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.94389,-0.3286,0.033023,543.67,-0.32831,0.94447,0.014024,149.02,-0.035798,0.0023953,-0.99936,444.95
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.069234,-0.99685,0.038729,496.03,-0.96554,0.076721,0.24868,413.99,-0.25087,-0.020178,-0.96781,488.44
> view matrix models
> #2,0.89557,-0.43875,-0.073887,203.68,-0.42217,-0.89039,0.17023,510.39,-0.14048,-0.12126,-0.98263,488.59
> view matrix models
> #2,0.95263,-0.28303,-0.11133,167.17,-0.28399,-0.9588,0.0075076,524.72,-0.10887,0.024463,-0.99376,454.65
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = 0.07198, steps = 288
shifted from previous position = 0.384
rotated from previous position = 7.03 degrees
atoms outside contour = 6590, contour level = 0.14997
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
0.91805725 -0.39098871 -0.06556458 114.17086512
-0.39010848 -0.92039430 0.02626218 459.54438350
-0.07061348 0.00146711 -0.99750267 429.70901665
Axis -0.97929923 0.19941006 0.03476555
Axis point 0.00000000 242.78560505 215.39247991
Rotation angle (degrees) 179.27463901
Shift along axis -5.23059531
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.91806,-0.39099,-0.065565,186.67,-0.39011,-0.92039,0.026262,541.31,-0.070613,0.0014671,-0.9975,458.64
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = 0.08872, steps = 184
shifted from previous position = 4.34
rotated from previous position = 4.56 degrees
atoms outside contour = 6326, contour level = 0.14997
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
0.89022754 -0.45190116 -0.05727365 126.34115734
-0.45321489 -0.89132355 -0.01177218 478.47530762
-0.04572949 0.03643719 -0.99828911 426.83106388
Axis 0.97216528 -0.23279355 -0.02649214
Axis point 0.00000000 251.64240895 218.18848485
Rotation angle (degrees) 178.57921443
Shift along axis 0.13085344
> view matrix models
> #2,0.89023,-0.4519,-0.057274,199.96,-0.45321,-0.89132,-0.011772,554.53,-0.045729,0.036437,-0.99829,449.54
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.2937,0.95581,0.012688,149.06,-0.93778,-0.29068,0.18994,497.71,0.18524,0.043887,0.98171,44.945
> view matrix models
> #2,0.24668,0.95421,-0.16924,69.984,-0.95885,0.26565,0.10021,406.01,0.14058,0.13755,0.98047,35.543
> view matrix models
> #2,0.88275,0.42206,-0.20642,52.066,-0.43329,0.90119,-0.010325,188.74,0.18167,0.098555,0.97841,35.256
> view matrix models
> #2,0.83605,-0.53639,-0.11533,238.64,0.52427,0.84302,-0.12023,21.654,0.16172,0.040053,0.98602,49.821
> view matrix models
> #2,0.31117,-0.94952,-0.039755,417.2,0.93434,0.3133,-0.16984,52.334,0.17372,0.015705,0.98467,52.484
> view matrix models
> #2,0.11603,-0.99324,-0.0028932,459.86,0.98096,0.11505,-0.15645,80.235,0.15572,0.015314,0.98768,55.755
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = 0.4447, steps = 212
shifted from previous position = 3.71
rotated from previous position = 13.8 degrees
atoms outside contour = 1530, contour level = 0.14997
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
0.29609840 -0.95515743 0.00010845 340.53178332
0.95515720 0.29609824 -0.00074203 -51.39391127
0.00067664 0.00032330 0.99999972 68.17785029
Axis 0.00055767 -0.00029743 0.99999980
Axis point 205.10249682 205.32915760 0.00000000
Rotation angle (degrees) 72.77659935
Shift along axis 68.38302887
> turn Y 180 #2
Expected 'forever' or an integer >= 1 or a keyword
> turn Y 180 models #2
> turn Y 180 models #4
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.30233,0.94375,-0.13391,205.67,-0.9488,-0.28445,0.13735,468.28,0.091536,0.16858,0.98143,45.982
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = 0.1112, steps = 56
shifted from previous position = 1.29
rotated from previous position = 0.932 degrees
atoms outside contour = 5989, contour level = 0.14997
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
0.31067244 -0.95050198 -0.00534926 336.48146076
0.95051204 0.31068413 -0.00149291 -58.37310027
0.00308094 -0.00462073 0.99998458 69.21561965
Axis -0.00164532 -0.00443453 0.99998881
Axis point 208.33279332 203.03515759 0.00000000
Rotation angle (degrees) 71.90035310
Shift along axis 68.92008127
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = 0.1112, steps = 44
shifted from previous position = 0.0465
rotated from previous position = 0.272 degrees
atoms outside contour = 5969, contour level = 0.14997
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
0.31512544 -0.94903089 -0.00602697 335.40603021
0.94904371 0.31514017 -0.00164808 -58.92602745
0.00346342 -0.00520050 0.99998048 69.21377407
Axis -0.00187157 -0.00499993 0.99998575
Axis point 208.35736802 203.19284118 0.00000000
Rotation angle (degrees) 71.63175797
Shift along axis 68.87967967
> select clear
> select #2/D
165 atoms, 169 bonds, 21 residues, 1 model selected
> hide #!4 models
> show #!4 models
> turn Y 180 models #4
> turn Y 180 models #2
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = 0.07842, steps = 244
shifted from previous position = 1.95
rotated from previous position = 2.66 degrees
atoms outside contour = 6463, contour level = 0.14997
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
0.34888028 -0.93651631 -0.03492488 328.60844734
0.93712243 0.34898589 0.00322283 -67.91590773
0.00917006 -0.03385326 0.99938474 75.79764746
Axis -0.01977893 -0.02352327 0.99952761
Axis point 212.73954587 204.47168378 0.00000000
Rotation angle (degrees) 69.59673503
Shift along axis 70.85992114
> select #3
2 models selected
> select clear
[Repeated 1 time(s)]
> select add #2
7704 atoms, 7856 bonds, 1011 residues, 1 model selected
> view matrix models
> #2,0.34661,-0.93526,-0.071752,458.38,0.93791,0.3467,0.011579,-26.633,0.014047,-0.07131,0.99736,109.73
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = 0.4447, steps = 96
shifted from previous position = 1.3
rotated from previous position = 3.58 degrees
atoms outside contour = 1537, contour level = 0.14997
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
0.29979670 -0.95400298 -0.00050516 339.63880334
0.95400258 0.29979705 -0.00090240 -51.86226408
0.00101234 -0.00021138 0.99999946 68.21248699
Axis 0.00036217 -0.00079533 0.99999962
Axis point 205.10029518 205.45232969 0.00000000
Rotation angle (degrees) 72.55461297
Shift along axis 68.37671501
> select clear
> hide #!3 models
> show #!3 models
> view
> select add #2
7704 atoms, 7856 bonds, 1011 residues, 1 model selected
> select add #4
7704 atoms, 7856 bonds, 1011 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.65685,0.74803,0.094901,23.687,-0.75234,0.64177,0.14871,242.19,0.050333,-0.16908,0.98432,123.77,#4,-0.51675,0.85081,0.095408,236.81,-0.83788,-0.52547,0.14781,489.43,0.17589,-0.0035593,0.9844,-3.298
> view matrix models
> #2,0.079899,0.99364,0.079378,94.194,-0.99415,0.073628,0.07902,418.8,0.072673,-0.085227,0.99371,100.59,#4,-0.92402,0.37404,0.079249,422.02,-0.36832,-0.92642,0.077998,490.54,0.10259,0.042883,0.9938,0.17557
> view matrix models
> #2,0.27529,0.9609,0.029752,67.757,-0.94099,0.26299,0.21303,349.81,0.19688,-0.086643,0.97659,77.734,#4,-0.83419,0.55068,0.029828,377.6,-0.5331,-0.81905,0.21203,473.93,0.14119,0.16097,0.97681,-28.501
> view matrix models
> #2,0.77947,0.62243,-0.070707,47.863,-0.60229,0.77567,0.18862,178.05,0.17225,-0.10444,0.9795,86.053,#4,-0.36008,0.93029,-0.070049,223.19,-0.92066,-0.34221,0.18785,460.18,0.15078,0.13213,0.9797,-25.132
> view matrix models
> #2,0.85885,0.50331,-0.095134,59.501,-0.47568,0.85259,0.21636,132.2,0.19001,-0.14057,0.97167,90.945,#4,-0.22263,0.97032,-0.094371,191.88,-0.95609,-0.19839,0.2157,431.92,0.19058,0.13825,0.97189,-32.908
> view matrix models
> #2,0.63547,0.7713,-0.035675,41.904,-0.76856,0.63629,0.066738,258.34,0.074175,-0.014991,0.99713,85.338,#4,-0.5453,0.8375,-0.035195,272.94,-0.83747,-0.54251,0.065825,510.15,0.036035,0.065369,0.99721,8.4675
> view matrix models
> #2,0.80471,0.59287,-0.030632,43.037,-0.56029,0.77552,0.29094,154.86,0.19625,-0.21696,0.95625,107.57,#4,-0.32434,0.94547,-0.029943,204.27,-0.90797,-0.30228,0.29021,427.76,0.26533,0.12131,0.95649,-41.498
> view matrix models
> #2,0.5415,0.84058,0.014289,39.887,-0.83945,0.53969,0.06369,293.24,0.045825,-0.046483,0.99787,97.551,#4,-0.63958,0.76858,0.014659,295.97,-0.76656,-0.6391,0.062726,516.17,0.057579,0.028882,0.99792,11.422
> view matrix models
> #2,0.69991,0.71403,0.017078,32.9,-0.70025,0.68129,0.21329,214.13,0.14066,-0.16124,0.97684,104.62,#4,-0.47137,0.88176,0.017636,237.52,-0.86,-0.46398,0.21244,467.66,0.1955,0.08497,0.97702,-24.014
> view matrix models
> #2,0.68612,0.7224,-0.085867,48.683,-0.69724,0.68668,0.20575,213.48,0.2076,-0.081297,0.97483,74.678,#4,-0.48343,0.87121,-0.085326,263.88,-0.86423,-0.45949,0.2049,469.2,0.1393,0.17279,0.97506,-30.184
> view matrix models
> #2,0.99321,0.083055,-0.081454,116.34,-0.066548,0.97996,0.18777,25.811,0.095417,-0.18108,0.97883,117.74,#4,0.21857,0.9725,-0.080466,98.031,-0.95493,0.23013,0.1875,349.29,0.20086,0.035858,0.97896,-15.398
> view matrix models
> #2,0.68117,0.73212,-0.0039144,36.028,-0.71975,0.67062,0.1795,225.12,0.13404,-0.11945,0.98375,96.409,#4,-0.49423,0.86932,-0.0033795,249.2,-0.85565,-0.48576,0.17863,478.36,0.15365,0.091176,0.98391,-18.161
> view matrix models
> #2,-0.45208,0.88491,0.11201,221.48,-0.8638,-0.46565,0.19238,486.72,0.2224,-0.0097813,0.97491,56.908,#4,-0.9798,-0.1661,0.11136,538.05,0.18517,-0.96385,0.19161,360.77,0.075513,0.20836,0.97513,-24.449
> view matrix models
> #2,-0.38883,0.91544,0.10381,203.34,-0.89349,-0.40216,0.19986,478.71,0.22471,-0.015041,0.97431,57.6,#4,-0.98996,-0.096586,0.10322,527.51,0.1157,-0.97314,0.19904,375.37,0.081224,0.20898,0.97454,-25.624
> select clear
> select add #4
2 models selected
> set transparency 80 #4
Expected a keyword
> transparency 80 #4
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 80 #4 s
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 80 #4 all
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> ui tool show "Volume Viewer"
> transparency sel 50
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> volume sel style mesh
[Repeated 1 time(s)]
> volume sel style surface
> volume sel style image
> volume sel style mesh
> volume sel style surface
> volume sel show
> volume sel hide
> volume #!3 style surface
[Repeated 1 time(s)]
> volume #!3 step 1
> volume #!3 step 2
> volume #!3 style image
> volume #!3 style mesh
> volume #!3 style surface
> show #!4 models
> volume sel style surface
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> transparency sel 40
> transparency sel 70
> color #4 darkgrey models
> select clear
> save /Users/wang/Downloads/Fim_Mfa_colour.cxs
——— End of log from Wed Aug 14 16:39:39 2024 ———
opened ChimeraX session
> select add #3
3 models selected
> select add #4
6 models selected
> transparency sel 80
> select add #2
7704 atoms, 7856 bonds, 1011 residues, 7 models selected
> select subtract #4
7704 atoms, 7856 bonds, 1011 residues, 4 models selected
> select subtract #3
7704 atoms, 7856 bonds, 1011 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.38883,0.91544,0.10381,101.08,-0.89349,-0.40216,0.19986,425.96,0.22471,-0.015041,0.97431,3.0313
> view matrix models
> #2,-0.38883,0.91544,0.10381,91.694,-0.89349,-0.40216,0.19986,427.97,0.22471,-0.015041,0.97431,2.5238
> ui tool show Matchmaker
> matchmaker #2/B to #1/B pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Mfa1_noH-coot-15-1.pdb, chain B (#1) with real_space_refin_FimA-
coot-0_real_space_refined_018.pdb, chain B (#2), sequence alignment score =
111.9
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: Mfa1_noH-coot-15-1.pdb #1/B,
real_space_refin_FimA-coot-0_real_space_refined_018.pdb #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 17 pruned atom pairs is 1.324 angstroms; (across all 283 pairs:
25.765)
> view matrix models
> #2,-0.96568,0.22749,0.12538,452.65,0.18669,0.94345,-0.27394,67.267,-0.1806,-0.24113,-0.95354,472.22
> view matrix models
> #2,-0.96568,0.22749,0.12538,458.23,0.18669,0.94345,-0.27394,71.483,-0.1806,-0.24113,-0.95354,534.22
> view matrix models
> #2,-0.96568,0.22749,0.12538,452.02,0.18669,0.94345,-0.27394,73.039,-0.1806,-0.24113,-0.95354,536.92
> select subtract #2
Nothing selected
> select add #4
3 models selected
> view matrix models
> #4,-0.98996,-0.096586,0.10322,526.35,0.1157,-0.97314,0.19904,375.54,0.081224,0.20898,0.97454,-22.061
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.84302,-0.49423,0.21226,555.21,0.45511,-0.86574,-0.20825,369.67,0.28668,-0.078957,0.95477,-0.65623
> view matrix models
> #4,-0.8873,-0.46115,0.0063509,600.89,0.45091,-0.87033,-0.198,369.32,0.096837,-0.17283,0.98018,52.265
> view matrix models
> #4,-0.22302,-0.95147,0.21203,522.4,0.97328,-0.20513,0.10322,61.559,-0.054717,0.22939,0.9718,2.184
> view matrix models
> #4,-0.060225,-0.96958,0.23727,487.44,0.99743,-0.049194,0.052148,35.227,-0.038889,0.2398,0.97004,-2.8383
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.060225,-0.96958,0.23727,477.45,0.99743,-0.049194,0.052148,28.994,-0.038889,0.2398,0.97004,-6.4629
> view matrix models
> #4,-0.060225,-0.96958,0.23727,482.46,0.99743,-0.049194,0.052148,23.232,-0.038889,0.2398,0.97004,43.055
> view matrix models
> #4,-0.060225,-0.96958,0.23727,492.95,0.99743,-0.049194,0.052148,32.229,-0.038889,0.2398,0.97004,49.275
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.85893,0.39922,0.32073,356.92,-0.20235,-0.83993,0.50357,346.08,0.47042,0.36763,0.80222,-46.126
> view matrix models
> #4,-0.014786,0.95211,0.30541,73.072,-0.38039,-0.28784,0.87889,189.63,0.92471,-0.10318,0.36643,49.674
> view matrix models
> #4,-0.36962,0.88351,-0.28775,285.03,-0.75381,-0.10405,0.6488,276.82,0.54328,0.45671,0.70446,-58.819
> view matrix models
> #4,0.82065,0.51565,-0.24625,108.07,-0.38589,0.81792,0.42673,58.119,0.42146,-0.25517,0.87021,77.98
> view matrix models
> #4,0.98055,0.049632,-0.18988,159.48,0.031799,0.91454,0.40325,-42.494,0.19367,-0.40145,0.89517,149.58
> view matrix models
> #4,0.906,0.38529,-0.17528,102.48,-0.26917,0.84399,0.46392,20.969,0.32668,-0.37313,0.86836,122.12
> view matrix models
> #4,0.91384,0.34444,-0.21507,117.69,-0.34055,0.93855,0.056106,102.09,0.22118,0.021971,0.97499,39.817
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.91384,0.34444,-0.21507,99.383,-0.34055,0.93855,0.056106,118.8,0.22118,0.021971,0.97499,45.926
> view matrix models
> #4,0.91384,0.34444,-0.21507,98.905,-0.34055,0.93855,0.056106,119.4,0.22118,0.021971,0.97499,53.502
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.63836,0.75132,-0.16738,61.448,-0.74994,0.65606,0.08473,255.55,0.17347,0.071433,0.98225,51.557
> view matrix models
> #4,0.10216,0.94559,-0.30891,161.18,-0.99184,0.12065,0.04129,424.69,0.076313,0.30217,0.95019,30.664
> view matrix models
> #4,-0.097568,0.97172,-0.21504,176.95,-0.97891,-0.054728,0.19685,425.4,0.17951,0.22971,0.95656,23.102
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.097568,0.97172,-0.21504,177.87,-0.97891,-0.054728,0.19685,424.4,0.17951,0.22971,0.95656,16.86
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.88996,0.45404,-0.042653,410.73,-0.42703,-0.79687,0.42738,415.64,0.16006,0.39856,0.90307,-2.6854
> view matrix models
> #4,-0.94121,0.33135,-0.065757,451.4,-0.31958,-0.81028,0.49124,382.91,0.10949,0.48337,0.86854,-2.5231
> view matrix models
> #4,-0.91707,0.39485,-0.055486,431.19,-0.37277,-0.79962,0.4708,395.93,0.14153,0.45244,0.88049,-5.2354
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.91707,0.39485,-0.055486,449.19,-0.37277,-0.79962,0.4708,383.91,0.14153,0.45244,0.88049,-65.05
> view matrix models
> #4,-0.91707,0.39485,-0.055486,448.04,-0.37277,-0.79962,0.4708,381.75,0.14153,0.45244,0.88049,-67.351
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.95157,0.25184,-0.17632,510.08,-0.30376,-0.85852,0.41313,391.91,-0.047328,0.44668,0.89344,-30.168
> view matrix models
> #4,-0.97307,0.18579,-0.13642,519.69,-0.2189,-0.93026,0.29446,414.32,-0.072203,0.31639,0.94588,-9.2621
> view matrix models
> #4,-0.99463,0.06421,0.081208,503.29,-0.051544,-0.98743,0.14944,422.36,0.089783,0.14445,0.98543,-15.367
> view matrix models
> #4,-0.74792,0.66377,-0.0046658,347.2,-0.65422,-0.73594,0.17432,488.84,0.11228,0.13343,0.98468,-17.548
> view matrix models
> #4,-0.2232,0.97223,-0.070311,189.85,-0.96235,-0.2083,0.17464,443.17,0.15514,0.10664,0.98212,-20.275
> view matrix models
> #4,0.16626,0.97436,-0.1516,126.7,-0.9812,0.17875,0.072714,388.73,0.097946,0.13666,0.98576,-15.505
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.16626,0.97436,-0.1516,115.25,-0.9812,0.17875,0.072714,393.22,0.097946,0.13666,0.98576,-17.316
> view matrix models
> #4,0.16626,0.97436,-0.1516,124.5,-0.9812,0.17875,0.072714,404.71,0.097946,0.13666,0.98576,-17.47
> view matrix models
> #4,0.16626,0.97436,-0.1516,123.98,-0.9812,0.17875,0.072714,405.9,0.097946,0.13666,0.98576,-20.695
> view matrix models
> #4,0.16626,0.97436,-0.1516,123.19,-0.9812,0.17875,0.072714,405.64,0.097946,0.13666,0.98576,-20.472
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.68967,-0.72339,0.03249,327.08,0.72406,0.68951,-0.017647,-30.267,-0.0096363,0.035695,0.99932,19.546
> view matrix models
> #4,0.61332,-0.78944,-0.024905,368.45,0.77013,0.60473,-0.203,16.847,0.17532,0.10533,0.97886,-28.421
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.61332,-0.78944,-0.024905,355.79,0.77013,0.60473,-0.203,20.305,0.17532,0.10533,0.97886,-31.719
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.30861,-0.94525,0.10615,549.32,0.94621,-0.31648,-0.067253,145.5,0.097165,0.079686,0.99207,-13.194
> view matrix models
> #4,-0.44159,-0.89157,0.10048,566.72,0.89615,-0.43281,0.097986,144.91,-0.043873,0.13332,0.9901,5.0843
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.17552,-0.97093,0.16277,443.41,0.97872,0.18995,0.077635,3.879,-0.1063,0.14568,0.98361,16.704
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.17552,-0.97093,0.16277,431.35,0.97872,0.18995,0.077635,-6.3581,-0.1063,0.14568,0.98361,21.392
> view matrix models
> #4,0.17552,-0.97093,0.16277,432.99,0.97872,0.18995,0.077635,-21.317,-0.1063,0.14568,0.98361,23.116
> view matrix models
> #4,0.17552,-0.97093,0.16277,442.27,0.97872,0.18995,0.077635,-18.166,-0.1063,0.14568,0.98361,22.552
> ui tool show "Fit in Map"
> fitmap #4 inMap #3
Fit map EMhancer_J306.mrc in map Mfa1_volmax_EMhancer.mrc using 99766 points
correlation = -0.04413, correlation about mean = 0.01005, overlap = -0.6367
steps = 232, shift = 1.89, angle = 1.57 degrees
Position of EMhancer_J306.mrc (#4) relative to Mfa1_volmax_EMhancer.mrc (#3)
coordinates:
Matrix rotation and translation
0.19042263 -0.97158208 0.14059690 444.64610932
0.97573783 0.20307777 0.08182364 -19.39808091
-0.10805049 0.12160464 0.98668008 27.44721204
Axis 0.02025991 0.12663263 0.99174277
Axis point 236.51137965 259.87267329 0.00000000
Rotation angle (degrees) 79.04194949
Shift along axis 33.77263227
> select subtract #4
Nothing selected
> select add #2
7704 atoms, 7856 bonds, 1011 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #3
3 models selected
> select subtract #3
Nothing selected
> select add #4
3 models selected
> view matrix models
> #4,0.19042,-0.97158,0.1406,350.09,0.97574,0.20308,0.081824,6.8126,-0.10805,0.1216,0.98668,34.018
> view matrix models
> #4,0.19042,-0.97158,0.1406,312.46,0.97574,0.20308,0.081824,-21.044,-0.10805,0.1216,0.98668,42.471
> fitmap #4 inMap #3
Fit map EMhancer_J306.mrc in map Mfa1_volmax_EMhancer.mrc using 99766 points
correlation = 0.2093, correlation about mean = 0.01989, overlap = 1136
steps = 552, shift = 22.3, angle = 2.76 degrees
Position of EMhancer_J306.mrc (#4) relative to Mfa1_volmax_EMhancer.mrc (#3)
coordinates:
Matrix rotation and translation
0.18009297 -0.97358227 0.14037127 326.17375405
0.97153109 0.19838512 0.12950166 -48.11042850
-0.15392809 0.11305271 0.98159330 53.12812949
Axis -0.00836110 0.14959403 0.98871215
Axis point 196.36500962 170.02048607 0.00000000
Rotation angle (degrees) 79.62816123
Shift along axis 42.60422445
> view matrix models
> #4,0.18009,-0.97358,0.14037,345.46,0.97153,0.19839,0.1295,-60.416,-0.15393,0.11305,0.98159,60.336
> view matrix models
> #4,0.18009,-0.97358,0.14037,348.47,0.97153,0.19839,0.1295,-68.307,-0.15393,0.11305,0.98159,1.9476
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.076676,-0.80081,0.59399,238.42,0.82503,0.38548,0.4132,-136.66,-0.55987,0.45837,0.69025,75.416
> view matrix models
> #4,0.17902,-0.97823,0.105,357.11,0.97621,0.18989,0.10471,-62.288,-0.12237,0.083752,0.98894,-0.031657
> view matrix models
> #4,0.98335,0.18022,0.023544,-29.472,-0.18066,0.95506,0.23498,-10.301,0.019861,-0.23532,0.97172,40.22
> view matrix models
> #4,0.85573,0.51597,0.038769,-75.737,-0.50868,0.8252,0.24553,81.507,0.094693,-0.22983,0.96861,24.398
> fitmap #4 inMap #3
Fit map EMhancer_J306.mrc in map Mfa1_volmax_EMhancer.mrc using 99766 points
correlation = 0.2633, correlation about mean = 0.01087, overlap = 2036
steps = 492, shift = 7.24, angle = 5.26 degrees
Position of EMhancer_J306.mrc (#4) relative to Mfa1_volmax_EMhancer.mrc (#3)
coordinates:
Matrix rotation and translation
0.86832607 0.49520587 0.02794593 -76.17842701
-0.49287063 0.85517484 0.16048218 92.99536178
0.05557305 -0.15312456 0.98664313 17.55336553
Axis -0.30241187 -0.02664091 -0.95280497
Axis point 133.91183265 187.09677899 0.00000000
Rotation angle (degrees) 31.23231073
Shift along axis 3.83484556
> view matrix models
> #4,0.87,0.49087,0.046341,-79.506,-0.4904,0.85175,0.18447,88.136,0.05108,-0.18322,0.98174,25.711
> view matrix models
> #4,0.76935,0.62934,0.10968,-100.77,-0.63836,0.76395,0.094256,155.6,-0.024467,-0.14253,0.98949,31.181
> fitmap #4 inMap #3
Fit map EMhancer_J306.mrc in map Mfa1_volmax_EMhancer.mrc using 99766 points
correlation = 0.2905, correlation about mean = 0.02647, overlap = 2430
steps = 672, shift = 9.84, angle = 10 degrees
Position of EMhancer_J306.mrc (#4) relative to Mfa1_volmax_EMhancer.mrc (#3)
coordinates:
Matrix rotation and translation
0.85952125 0.50846778 0.05180474 -85.10894873
-0.51053900 0.85890379 0.04042536 130.17265572
-0.02394030 -0.06119478 0.99783878 14.52018167
Axis -0.09896214 0.07376384 -0.99235346
Axis point 193.60161334 220.16748134 0.00000000
Rotation angle (degrees) 30.89252692
Shift along axis 3.61544612
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.85952,0.50847,0.051805,13.564,-0.51054,0.8589,0.040425,178.91,-0.02394,-0.061195,0.99784,19.917
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = 0.08184, steps = 168
shifted from previous position = 11.6
rotated from previous position = 3.13 degrees
atoms outside contour = 6392, contour level = 0.14997
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
-0.91773594 -0.30226718 0.25767286 415.02635524
-0.34785873 0.92479622 -0.15409819 123.30433950
-0.19171605 -0.23105519 -0.95386501 534.26233795
Axis -0.16795340 0.98076058 -0.09950045
Axis point 249.68059126 0.00000000 248.84128760
Rotation angle (degrees) 166.75577683
Shift along axis -1.93239573
> select subtract #4
Nothing selected
> select add #2
7704 atoms, 7856 bonds, 1011 residues, 1 model selected
> view matrix models
> #2,-0.97562,0.19845,0.093707,456.46,0.16201,0.93929,-0.30247,88.565,-0.14804,-0.27991,-0.94854,478.98
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = 0.0851, steps = 192
shifted from previous position = 3.4
rotated from previous position = 6.73 degrees
atoms outside contour = 6363, contour level = 0.14997
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
-0.91426562 -0.36660158 0.17239970 445.68029235
-0.38601060 0.91747451 -0.09610581 117.81511659
-0.12293978 -0.15441435 -0.98032751 450.15564405
Axis -0.19328881 0.97903006 -0.06433956
Axis point 251.90866675 0.00000000 211.68280271
Rotation angle (degrees) 171.32481457
Shift along axis 0.23671103
> view matrix models
> #2,-0.98847,0.1434,0.048529,484.06,0.13025,0.96894,-0.21019,72.71,-0.077164,-0.20145,-0.97645,446.79
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.24993,0.94664,-0.2035,214.21,0.94942,0.19832,-0.24347,64.211,-0.19012,-0.25405,-0.94832,475.76
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = 0.08049, steps = 80
shifted from previous position = 6.22
rotated from previous position = 0.638 degrees
atoms outside contour = 6430, contour level = 0.14997
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
-0.69818069 0.71570521 -0.01760038 218.22183580
0.69533870 0.67205032 -0.25466144 -30.23967354
-0.17043417 -0.19003791 -0.96687010 459.08607428
Axis 0.38655055 0.91418687 -0.12182379
Axis point 126.01899773 0.00000000 222.53799458
Rotation angle (degrees) 175.20504978
Shift along axis 0.78145130
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.25537,0.94703,-0.1947,209.74,0.94679,0.20415,-0.24883,61.353,-0.1959,-0.24789,-0.94878,472.46
> view matrix models
> #2,-0.25537,0.94703,-0.1947,145.48,0.94679,0.20415,-0.24883,67.867,-0.1959,-0.24789,-0.94878,450.5
> view matrix models
> #2,-0.25537,0.94703,-0.1947,194.76,0.94679,0.20415,-0.24883,74.481,-0.1959,-0.24789,-0.94878,434.22
> view matrix models
> #2,-0.25537,0.94703,-0.1947,204.54,0.94679,0.20415,-0.24883,67.811,-0.1959,-0.24789,-0.94878,435.36
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.96808,0.20055,0.1503,440.91,0.18361,0.97573,-0.11933,47.247,-0.17058,-0.087923,-0.98141,403.72
> view matrix models
> #2,-0.63999,-0.75691,0.13225,569.17,-0.76541,0.64312,-0.02327,293.83,-0.067439,-0.11612,-0.99094,389.73
> view matrix models
> #2,-0.31577,-0.94867,-0.017566,567.48,-0.94701,0.31396,0.067779,381.51,-0.058785,0.038038,-0.99755,358.04
> view matrix models
> #2,0.46167,-0.88477,-0.063605,401.67,-0.88502,-0.46428,0.034517,531.53,-0.06007,0.040356,-0.99738,357.81
> view matrix models
> #2,0.54364,-0.83742,-0.056463,373.85,-0.83874,-0.54453,0.00051542,544.22,-0.031177,0.047077,-0.9984,350.65
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.54364,-0.83742,-0.056463,362.29,-0.83874,-0.54453,0.00051542,540.92,-0.031177,0.047077,-0.9984,354.4
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.6337,-0.77171,-0.053704,329.88,-0.77313,-0.63417,-0.0099942,547.27,-0.026345,0.047854,-0.99851,353.26
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = 0.08571, steps = 1224
shifted from previous position = 9.16
rotated from previous position = 29.5 degrees
atoms outside contour = 6322, contour level = 0.14997
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
0.65255981 -0.74879397 -0.11607444 244.14135598
-0.74987876 -0.66017473 0.04302508 482.38660653
-0.10884630 0.05896530 -0.99230820 363.29528292
Axis 0.90899671 -0.41218715 -0.06186065
Axis point 0.00000000 295.67042003 191.11890125
Rotation angle (degrees) 179.49762250
Shift along axis 0.61644631
> select subtract #2
Nothing selected
> select add #4
3 models selected
> transparency sel 0
> select clear
> hide #!4 models
> show #!4 models
> select add #2
7704 atoms, 7856 bonds, 1011 residues, 1 model selected
> hide #!3 models
> hide #1 models
> view
> view matrix models
> #2,0.17013,-0.96782,-0.18544,496.68,-0.94726,-0.21248,0.23989,449.25,-0.27157,0.13485,-0.95292,376.9
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.17013,-0.96782,-0.18544,491.66,-0.94726,-0.21248,0.23989,445.66,-0.27157,0.13485,-0.95292,386.33
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = 0.08844, steps = 208
shifted from previous position = 3.36
rotated from previous position = 5.63 degrees
atoms outside contour = 6317, contour level = 0.14997
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
0.70018867 -0.66858622 -0.25045618 238.45663968
-0.66708004 -0.73765806 0.10423432 465.97273203
-0.25444060 0.09409060 -0.96250035 387.99907265
Axis -0.92200699 0.36216105 0.13690322
Axis point 0.00000000 280.39713838 211.00908565
Rotation angle (degrees) 179.68482038
Shift along axis 2.01680703
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.24877,-0.88304,0.39793,456.95,0.96273,-0.27046,0.0016865,106.53,0.10614,0.38352,0.91741,-79.813
> view matrix models
> #2,-0.937,-0.13255,0.32321,461.73,0.16503,-0.98342,0.075126,402.49,0.30789,0.12373,0.94334,-73.919
> view matrix models
> #2,0.12883,0.98722,0.093765,56.153,-0.94583,0.093908,0.3108,373.32,0.29802,-0.12873,0.94584,-21.421
> view matrix models
> #2,0.67213,0.74041,0.0049003,9.2121,-0.74019,0.67173,0.030096,264.54,0.018992,-0.023856,0.99954,5.6543
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = 0.113, steps = 292
shifted from previous position = 3.93
rotated from previous position = 9.41 degrees
atoms outside contour = 5917, contour level = 0.14997
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
0.98740749 0.15453962 0.03382227 -34.83692406
-0.15488833 0.98790016 0.00792926 30.12351209
-0.03218761 -0.01306808 0.99939641 12.84720145
Axis -0.06621960 0.20817626 -0.97584712
Axis point 180.91225130 241.86177499 0.00000000
Rotation angle (degrees) 9.12235155
Shift along axis -3.95901742
> view matrix models
> #2,0.78478,0.61737,0.05452,5.0744,-0.6196,0.77942,0.092729,205.83,0.014754,-0.10655,0.9942,25.305
> view matrix models
> #2,0.64483,0.75629,0.1105,-3.9612,-0.76299,0.62841,0.15149,255.47,0.045136,-0.182,0.98226,36.357
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.64483,0.75629,0.1105,-3.7726,-0.76299,0.62841,0.15149,255.41,0.045136,-0.182,0.98226,34.765
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.75035,0.64964,0.12221,-6.2484,-0.66067,0.74318,0.10583,219.24,-0.022069,-0.16015,0.98685,43.471
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = 0.4481, steps = 168
shifted from previous position = 3.62
rotated from previous position = 11.7 degrees
atoms outside contour = 1491, contour level = 0.14997
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
0.99998217 0.00585173 -0.00119050 -0.88118719
-0.00585076 0.99998255 0.00081321 1.02462109
0.00119525 -0.00080622 0.99999896 -0.09519842
Axis -0.13436465 -0.19794659 -0.97095998
Axis point 174.94707317 150.93479331 0.00000000
Rotation angle (degrees) 0.34528078
Shift along axis 0.00801401
> select clear
> volume #3 change image level -5.647e-05,0 level 0.1913,0.8 level 1.914,1
> volume #3 level 0.1237
> volume #3 level 0.1178
> volume #4 level 0.12
> volume #4 change image level 8.541e-06,0 level 0.1654,0.8 level 1.654,1
> hide #!3 models
> select add #2
7704 atoms, 7856 bonds, 1011 residues, 1 model selected
> select add #4
7704 atoms, 7856 bonds, 1011 residues, 4 models selected
> turn Y 180 models #2
> turn Y 180 models #4
> select subtract #2
3 models selected
> transparency sel 80
> show #!3 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> select #2/D
165 atoms, 169 bonds, 21 residues, 1 model selected
> turn Y 180 models #4
> turn Y 180 models #2
> turn X 180 models #2
> turn X 180 models #4
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> select #1/D
167 atoms, 172 bonds, 20 residues, 1 model selected
> show #!4 models
> hide #2 models
> show #!3 models
> show #2 models
> hide #1 models
> show #1 models
> select add #1
11812 atoms, 12099 bonds, 1546 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #2
7704 atoms, 7856 bonds, 1011 residues, 1 model selected
> select add #3
7704 atoms, 7856 bonds, 1011 residues, 4 models selected
> select subtract #3
7704 atoms, 7856 bonds, 1011 residues, 1 model selected
> select add #4
7704 atoms, 7856 bonds, 1011 residues, 4 models selected
> view matrix models
> #2,-0.17611,0.96713,-0.18343,189.49,0.97689,0.14878,-0.15346,2.3828,-0.12112,-0.20621,-0.97098,484.63,#4,-0.17023,0.96799,-0.18442,188.33,0.97793,0.14294,-0.15241,3.0836,-0.12117,-0.20629,-0.97096,484.64
> view matrix models
> #2,-0.54278,0.8386,-0.046366,262.22,0.83887,0.53861,-0.078696,-65.427,-0.041021,-0.08161,-0.99582,447.77,#4,-0.53781,0.84172,-0.047691,260.88,0.8421,0.53363,-0.078128,-65.239,-0.040312,-0.082178,-0.9958,447.72
> view matrix models
> #2,-0.33656,0.9416,-0.010819,191.22,0.93924,0.33484,-0.075598,-44.67,-0.06756,-0.035605,-0.99708,444,#4,-0.33103,0.94354,-0.011981,189.96,0.94127,0.32928,-0.074745,-44.185,-0.06658,-0.03602,-0.99713,443.88
> view matrix models
> #2,-0.3775,0.92528,0.036828,192.92,0.92524,0.37851,-0.025805,-61.306,-0.037817,0.024333,-0.99899,425.95,#4,-0.37212,0.9275,0.035631,191.64,0.92747,0.37307,-0.025005,-60.874,-0.036485,0.023741,-0.99905,425.8
> view matrix models
> #2,-0.82582,0.5572,0.086877,350.12,0.54983,0.82979,-0.095524,-62.616,-0.12532,-0.031117,-0.99163,453.76,#4,-0.82265,0.56209,0.085441,348.83,0.55479,0.82648,-0.095535,-62.983,-0.12432,-0.03119,-0.99175,453.59
> view matrix models
> #2,-0.89525,0.43177,0.10998,385.33,0.43368,0.90104,-0.0071751,-72.128,-0.1022,0.041274,-0.99391,434.59,#4,-0.89284,0.43709,0.10856,384.1,0.43895,0.89848,-0.0073832,-72.662,-0.10077,0.041063,-0.99406,434.36
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.89525,0.43177,0.10998,399.92,0.43368,0.90104,-0.0071751,-71.156,-0.1022,0.041274,-0.99391,408.61,#4,-0.89284,0.43709,0.10856,398.69,0.43895,0.89848,-0.0073832,-71.69,-0.10077,0.041063,-0.99406,408.38
> select subtract #4
7704 atoms, 7856 bonds, 1011 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #3
3 models selected
> select add #1
11812 atoms, 12099 bonds, 1546 residues, 4 models selected
> view matrix models
> #1,1,0.00033116,9.1466e-05,-4.8315,-0.00033116,1,2.0297e-06,0.68988,-9.1465e-05,-2.06e-06,1,-2.4034,#3,1,0,0,-4.7814,0,1,0,0.58862,0,0,1,-2.4493
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.92976,0.36809,0.0073485,-67.216,-0.36776,0.92949,-0.028255,99.59,-0.017231,0.023568,0.99957,-3.5171,#3,0.92988,0.36779,0.0072627,-67.207,-0.36746,0.92961,-0.028224,99.479,-0.017132,0.023576,0.99958,-3.5662
> ui tool show "Side View"
> select clear
> color #3 #919191ff models
> color #4 #919191ff models
> select add #3
3 models selected
> select add #4
6 models selected
> transparency sel 80
> volume sel style mesh
> transparency sel 80
> volume sel step 1
> select clear
> select add #3
3 models selected
> select subtract #3
Nothing selected
> select add #4
3 models selected
> select add #2
7704 atoms, 7856 bonds, 1011 residues, 4 models selected
> view matrix models
> #2,-0.93593,0.33591,0.10585,428.88,0.33435,0.94188,-0.032646,-53.832,-0.11066,0.0048358,-0.99385,417.84,#4,-0.93407,0.34147,0.10446,427.72,0.3399,0.93988,-0.033006,-54.499,-0.10945,0.0046749,-0.99398,417.65
> select clear
> volume step 2
> volume step 1
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> lighting simple
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> lighting full
[Repeated 1 time(s)]
> set bgColor gray
> set bgColor black
> set bgColor white
> color #4 #212121ff models
> color #4 white models
> color #4 #008f00ff models
> color #4 #d4fb79ff models
> color #4 #797979ff models
> color #4 #929292ff models
> select add #3
3 models selected
> color #3 #929292ff models
> select add #4
6 models selected
> transparency sel 70
> volume sel style surface
> select clear
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
[Repeated 1 time(s)]
> lighting soft
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting simple
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting soft
> lighting flat
[Repeated 1 time(s)]
> graphics silhouettes false
> lighting soft
> lighting full
> lighting simple
> select #2/D
165 atoms, 169 bonds, 21 residues, 1 model selected
> select #2/C
2568 atoms, 2619 bonds, 337 residues, 1 model selected
> ui tool show "Color Actions"
> color sel plum
> color sel violet
> color sel plum
> color sel thistle
> color sel plum
> select #2/B
2568 atoms, 2619 bonds, 337 residues, 1 model selected
> color sel light pink
> select #2/A
2403 atoms, 2449 bonds, 316 residues, 1 model selected
> color sel peach puff
> color sel burly wood
> color sel pink
> color sel moccasin
> color sel peach puff
> select clear
> select #2/D
165 atoms, 169 bonds, 21 residues, 1 model selected
> color sel #f1e6b2ff
> select #2/C
2568 atoms, 2619 bonds, 337 residues, 1 model selected
> color sel #f7e7ceff
> select clear
> select #2/C
2568 atoms, 2619 bonds, 337 residues, 1 model selected
> color sel #f7e7ceff
[Repeated 1 time(s)]
> color sel #b2ac88ff
[Repeated 1 time(s)]
> color sel #50c878ff
[Repeated 1 time(s)]
> select #2/B
2568 atoms, 2619 bonds, 337 residues, 1 model selected
> color sel #228b22ff
[Repeated 1 time(s)]
> select #2/C
2568 atoms, 2619 bonds, 337 residues, 1 model selected
> color sel #01796fff
> select #2/B
2568 atoms, 2619 bonds, 337 residues, 1 model selected
> color sel #556b2fff
[Repeated 1 time(s)]
> select #2/C
2568 atoms, 2619 bonds, 337 residues, 1 model selected
> color sel #556b2fff
> select #2/B
2568 atoms, 2619 bonds, 337 residues, 1 model selected
> color sel #00a36cff
[Repeated 1 time(s)]
> color sel #228b22ff
[Repeated 1 time(s)]
> select #2/A
2403 atoms, 2449 bonds, 316 residues, 1 model selected
> color sel #50c878ff
[Repeated 1 time(s)]
> select #2/B
2568 atoms, 2619 bonds, 337 residues, 1 model selected
> color sel #50c878ff
> select #2/A
2403 atoms, 2449 bonds, 316 residues, 1 model selected
> color sel #ace1afff
[Repeated 2 time(s)]
> select #2/D
165 atoms, 169 bonds, 21 residues, 1 model selected
> color sel #ace1afff
> select clear
> transparency sel 60
> select add #4
3 models selected
> select add #3
6 models selected
> transparency sel 60
> select clear
> select #2/A
2403 atoms, 2449 bonds, 316 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pale green
> color sel light green
[Repeated 2 time(s)]
> color sel lime
> color sel yellow green
> color sel lawn green
[Repeated 1 time(s)]
> color sel chartreuse
> select clear
> volume #3 level 0.12
> volume #4 level 0.1
> volume #4 level 0.12
> volume #3 level 0.1016
> volume #4 level 0.1503
> volume #3 level 0.1047
> volume #3 level 0.1
> save /Users/wang/Desktop/image1.png supersample 3
> color midnight blue
> undo
> select add #3
3 models selected
> select add #4
6 models selected
> color #4 darkgrey models
> transparency sel 70
> color #4 #212121ff models
> transparency sel 70
> color #4 #5e5e5eff models
> color #3 #5e5e5eff models
> transparency sel 80
> select clear
> save /Users/wang/Desktop/image2.png supersample 3
> save /Users/wang/Desktop/FimA_colored.cxs
> save /Users/wang/Documents/FimA_Mfa.cxs
——— End of log from Wed Aug 14 18:37:43 2024 ———
opened ChimeraX session
> ui tool show "Fit in Map"
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = 0.4482, steps = 28
shifted from previous position = 0.00795
rotated from previous position = 0.14 degrees
atoms outside contour = 1496, contour level = 0.15033
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
0.99999353 0.00342788 -0.00108436 -0.42179243
-0.00342728 0.99999397 0.00055802 0.56640951
0.00108629 -0.00055430 0.99999925 -0.11677244
Axis -0.15287172 -0.29832389 -0.94214282
Axis point 165.52929931 123.11334619 0.00000000
Rotation angle (degrees) 0.20844641
Shift along axis 0.00552296
> fitmap #2 inMap #4
Fit molecule real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2) to
map EMhancer_J306.mrc (#4) using 7704 atoms
average map value = 0.4482, steps = 40
shifted from previous position = 0.01
rotated from previous position = 0.019 degrees
atoms outside contour = 1499, contour level = 0.15033
Position of real_space_refin_FimA-coot-0_real_space_refined_018.pdb (#2)
relative to EMhancer_J306.mrc (#4) coordinates:
Matrix rotation and translation
0.99999247 0.00374673 -0.00100544 -0.49447821
-0.00374621 0.99999285 0.00051517 0.63443312
0.00100738 -0.00051140 0.99999936 -0.11472527
Axis -0.13117017 -0.25718962 -0.95741730
Axis point 169.89302404 131.91340981 0.00000000
Rotation angle (degrees) 0.22420485
Shift along axis 0.01153113
> ui tool show "Color Zone"
> color zone #3 near #2 distance 4.05
> color zone #4 near #2 distance 5.13
> color zone #3 near #1 distance 4.05
> select #1/A
3781 atoms, 3872 bonds, 496 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium turquoise
> ui tool show "Color Zone"
> color zone #3 near #1 distance 4.05
> select clear
> select #1/A
3781 atoms, 3872 bonds, 496 residues, 1 model selected
> color sel light sea green
> color zone #3 near #1 distance 4.05
> select #1/A
3781 atoms, 3872 bonds, 496 residues, 1 model selected
> color sel medium turquoise
> color zone #3 near #1 distance 4.05
> select clear
> turn X 90 models #2 #4
> save /Users/wang/Desktop/image12.png supersample 3
> save /Users/wang/Documents/FimA_Mfa_map_colour.cxs
——— End of log from Thu Aug 15 06:35:57 2024 ———
opened ChimeraX session
> select #1/A
3781 atoms, 3872 bonds, 496 residues, 1 model selected
> color sel #296bc5ff
> ui tool show "Color Zone"
> color zone #3 near #1 distance 4.05
> select clear
> hide #2 models
> save /Users/wang/Desktop/image16.png supersample 3
> save /Users/wang/Documents/Mfa_blue_theme.cxs
——— End of log from Mon Aug 19 12:29:48 2024 ———
opened ChimeraX session
> select #1/B
3935 atoms, 4030 bonds, 516 residues, 1 model selected
> select #1/A
3781 atoms, 3872 bonds, 496 residues, 1 model selected
> color sel #1f5298ff
> ui tool show "Color Zone"
> select add #1
11812 atoms, 12099 bonds, 1546 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
11812 atoms, 12099 bonds, 1546 residues, 1 model selected
> color #3 white models
> color #3 #ffffff00 models
> color zone #3 near sel distance 4.05
> select clear
> select #1/D
167 atoms, 172 bonds, 20 residues, 1 model selected
> color sel #8facd5ff
[Repeated 1 time(s)]
> select add #1
11812 atoms, 12099 bonds, 1546 residues, 1 model selected
> color zone #3 near sel distance 4.05
> select #1/A
3781 atoms, 3872 bonds, 496 residues, 1 model selected
> color sel #2b70cfff
> color zone #3 near sel distance 4.05
> undo
> select add #1
11812 atoms, 12099 bonds, 1546 residues, 1 model selected
> color zone #3 near sel distance 4.05
> select #3
3 models selected
> select clear
> select #1/C
3929 atoms, 4025 bonds, 514 residues, 1 model selected
> color sel #14335fff
[Repeated 1 time(s)]
> select add #1
11812 atoms, 12099 bonds, 1546 residues, 1 model selected
> color zone #3 near sel distance 4.05
> select clear
> select #1/D
167 atoms, 172 bonds, 20 residues, 1 model selected
> color sel #3992ffff
[Repeated 1 time(s)]
> select add #1
11812 atoms, 12099 bonds, 1546 residues, 1 model selected
> color zone #3 near sel distance 4.05
> select clear
> select #1/D
167 atoms, 172 bonds, 20 residues, 1 model selected
> color sel #378fffff
[Repeated 1 time(s)]
> select add #1
11812 atoms, 12099 bonds, 1546 residues, 1 model selected
> color zone #3 near sel distance 4.05
[Repeated 1 time(s)]
> select clear
> save /Users/wang/Documents/Mfa_blue_theme.cxs
——— End of log from Mon Aug 19 12:50:52 2024 ———
opened ChimeraX session
> open /Users/wang/Downloads/RealSpaceRefine_19/coot-fit-
> chimeraX_real_space_refined_019.pdb
Chain information for coot-fit-chimeraX_real_space_refined_019.pdb #4
---
Chain | Description
A | No description available
B C | No description available
D | No description available
> hide #4 models
> show #4 models
> hide #1 models
> show #1 models
> hide #!3 models
> ui tool show "Fit in Map"
> volume #3 step 4
> volume #3 step 1
> fitmap #4 inMap #3
Fit molecule coot-fit-chimeraX_real_space_refined_019.pdb (#4) to map
Mfa1_volmax_EMhancer.mrc (#3) using 11787 atoms
average map value = 0.09259, steps = 308
shifted from previous position = 2.74
rotated from previous position = 6.49 degrees
atoms outside contour = 9170, contour level = 0.1
Position of coot-fit-chimeraX_real_space_refined_019.pdb (#4) relative to
Mfa1_volmax_EMhancer.mrc (#3) coordinates:
Matrix rotation and translation
0.96545445 -0.26046357 -0.00751248 64.94209756
0.26056457 0.96524211 0.02034129 -50.36916301
0.00195320 -0.02159607 0.99976487 8.48062388
Axis -0.08021700 -0.01810576 0.99661297
Axis point 222.51267076 221.10013140 0.00000000
Rotation angle (degrees) 15.15311582
Shift along axis 4.15441143
> show #!3 models
> select add #4
11787 atoms, 12073 bonds, 1543 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.9936,0.11265,0.0077566,-24.829,-0.1126,0.99362,-0.0065469,29.79,-0.0084446,0.0056317,0.99995,-2.4738
> view matrix models
> #4,0.9936,0.11265,0.0077566,-25.173,-0.1126,0.99362,-0.0065469,28.513,-0.0084446,0.0056317,0.99995,-2.5986
> view matrix models
> #4,0.9936,0.11265,0.0077566,-30.434,-0.1126,0.99362,-0.0065469,27.457,-0.0084446,0.0056317,0.99995,-1.8156
> view matrix models
> #4,0.9936,0.11265,0.0077566,-30.014,-0.1126,0.99362,-0.0065469,29.424,-0.0084446,0.0056317,0.99995,-2.1162
> view matrix models
> #4,0.9936,0.11265,0.0077566,-26.653,-0.1126,0.99362,-0.0065469,28.415,-0.0084446,0.0056317,0.99995,-0.59886
> fitmap #4 inMap #3
Fit molecule coot-fit-chimeraX_real_space_refined_019.pdb (#4) to map
Mfa1_volmax_EMhancer.mrc (#3) using 11787 atoms
average map value = 0.4025, steps = 144
shifted from previous position = 2.07
rotated from previous position = 15.3 degrees
atoms outside contour = 2547, contour level = 0.1
Position of coot-fit-chimeraX_real_space_refined_019.pdb (#4) relative to
Mfa1_volmax_EMhancer.mrc (#3) coordinates:
Matrix rotation and translation
0.99999298 0.00245098 -0.00283569 0.09304369
-0.00244223 0.99999225 0.00308640 -0.06886701
0.00284324 -0.00307945 0.99999122 0.24103730
Axis -0.63524492 -0.58507902 -0.50412937
Axis point 0.00000000 55.16027329 49.05277058
Rotation angle (degrees) 0.27806511
Shift along axis -0.14032687
> open
> /Users/wang/Documents/Zeytuni_lab/Mfa1_Krios/Mfa1_processing/Mfa1-chimerax-25-coot-0.pdb
Chain information for Mfa1-chimerax-25-coot-0.pdb #5
---
Chain | Description
A | No description available
B C | No description available
D | No description available
> close #4
> select add #5
11800 atoms, 12077 bonds, 1552 residues, 1 model selected
> view matrix models #5,1,0,0,-2.0725,0,1,0,5.8301,0,0,1,-3.4046
> view matrix models #5,1,0,0,1.4848,0,1,0,4.4749,0,0,1,-2.6356
> view matrix models #5,1,0,0,0.48828,0,1,0,0.82458,0,0,1,-1.8241
> fitmap #5 inMap #3
Fit molecule Mfa1-chimerax-25-coot-0.pdb (#5) to map Mfa1_volmax_EMhancer.mrc
(#3) using 11800 atoms
average map value = 0.4105, steps = 200
shifted from previous position = 2.79
rotated from previous position = 21.6 degrees
atoms outside contour = 2471, contour level = 0.1
Position of Mfa1-chimerax-25-coot-0.pdb (#5) relative to
Mfa1_volmax_EMhancer.mrc (#3) coordinates:
Matrix rotation and translation
0.99999989 -0.00044682 0.00011626 0.10159042
0.00044683 0.99999990 -0.00005316 -0.04868962
-0.00011624 0.00005321 0.99999999 0.05254312
Axis 0.11443061 0.25013474 0.96142511
Axis point 136.98509685 214.53468535 0.00000000
Rotation angle (degrees) 0.02662832
Shift along axis 0.04996236
> hide #1 models
> hide #5 models
> show #5 models
> hide #!3 models
> show #1 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> copycolor #1 to #5
Unknown command: copycolor #1 to #5
> copycolors #1 to #5
Unknown command: copycolors #1 to #5
> copycolours #1 to #5
Unknown command: copycolours #1 to #5
> ui tool show "Command Line Interface"
> defattr copy_chain_colors(session, from_atoms, to_atoms = None):
Missing or invalid "fileName" argument: File 'copy_chain_colors(session,' does
not exist
> from_res = from_atoms.residues
Unknown command: from_res = from_atoms.residues
> from chimerax.atomic import Residue
Unknown command: from chimerax.atomic import Residue
> from_res = from_res[from_res.polymer_types != Residue.PT_NONE]
Unknown command: from_res = from_res[from_res.polymer_types !=
Residue.PT_NONE]
> chain_colors = {cid:color for cid,color in zip(from_res.chain_ids,
> from_res.ribbon_colors)}
Unknown command: chain_colors = {cid:color for cid,color in
zip(from_res.chain_ids, from_res.ribbon_colors)}
> force s, s_to_atoms in to_atoms.by_structure:
force is provided by the uninstalled bundle SEQCROW versions 1.8.4 – 1.8.10
> force cid in set(s_to_atoms.chain_ids):
force is provided by the uninstalled bundle SEQCROW versions 1.8.4 – 1.8.10
> if cid in chain_colors:
Unknown command: if cid in chain_colors:
> from chimerax.core.commands import run
Unknown command: from chimerax.core.commands import run
> from chimerax.core.colors import hex_color
Unknown command: from chimerax.core.colors import hex_color
> run(session, 'color #%s/%s %s ribbon'
Unknown command: run(session, 'color #%s/%s %s ribbon'
> % (s.id_string, cid, hex_color(chain_colors[cid])))
Unknown command: % (s.id_string, cid, hex_color(chain_colors[cid])))
> defattr register_command(session):
Missing or invalid "fileName" argument: File 'register_command(session):' does
not exist
> from chimerax.core.commands import CmdDesc, register, FloatArg, BoolArg
Unknown command: from chimerax.core.commands import CmdDesc, register,
FloatArg, BoolArg
> from chimerax.atomic import AtomsArg
Unknown command: from chimerax.atomic import AtomsArg
> desc = CmdDesc(required= [('from_atoms', AtomsArg)],
Unknown command: desc = CmdDesc(required= [('from_atoms', AtomsArg)],
> keyword = [('to_atoms', AtomsArg)],
Unknown command: keyword = [('to_atoms', AtomsArg)],
> required_arguments = ['to_atoms'],
Unknown command: required_arguments = ['to_atoms'],
> synopsis = 'copy ribbon colors for chains')
Unknown command: synopsis = 'copy ribbon colors for chains')
> register('copycolors', desc, copy_chain_colors, logger=session.logger)
Unknown command: register('copycolors', desc, copy_chain_colors,
logger=session.logger)
> register_command(session)
Unknown command: register_command(session)
> register_command
Unknown command: register_command
> toolshed show
> copycolours #1 to #5
Unknown command: copycolours #1 to #5
> mcopy #1 toAtoms #5
> hide #1 models
> hide #!3 models
> select subtract #5
Nothing selected
> show #5 atoms
> hide #5 atoms
> select #5/A
3748 atoms, 3837 bonds, 493 residues, 1 model selected
> color sel bynucleotide
Alignment identifier is 5/A
> show ligand
> dssp
> show ions
> select ions
4 atoms, 4 residues, 2 models selected
> color (#5 & sel) orange
> ui tool show "Color Actions"
> color sel sandy brown
[Repeated 1 time(s)]
> ui tool show ViewDockX
No suitable models found for ViewDockX
> show (#5 & sel) target ab
> show (#5 & sel-residues & sidechain) target ab
> label (#5 & sel) atoms attribute name
> select ligand
30 atoms, 24 bonds, 6 residues, 2 models selected
> select ::name="SO4"
15 atoms, 12 bonds, 3 residues, 1 model selected
> label sel attribute name
> show #!3 models
> select add #5
11800 atoms, 12077 bonds, 1552 residues, 2 models selected
> select subtract #5
Nothing selected
> view
> view orient
> view
> turn x 90
> view
> view name p1
> zoom 1.5
> move y -70
> zoom 1.5
> move y 140
> volume #3 level 0.1229
> volume #3 level 0.1258
> view name p2
> move y 210
> move y -210
> move y 140
> move y 70
> move y -140
> view name p3
> view
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!3 models
> save
> /Users/wang/Documents/Zeytuni_lab/fimbriae_movies_chimeraX/movie_Mfa1_views_draft1.cxs
——— End of log from Tue Oct 8 14:51:28 2024 ———
opened ChimeraX session
> hide #!3 models
> show #!3 models
> hide #!3 models
> select ligand
30 atoms, 24 bonds, 6 residues, 2 models selected
> view select
Expected an objects specifier or a view name or a keyword
> view sel
> zoom 3
moved plane near 170.02179480690498 [-0.00000000e+00 -1.00000000e+00
-1.11022302e-16]
moved plane far 170.02179480690498 [-0.00000000e+00 -1.00000000e+00
-1.11022302e-16]
> cofr sel
> select sel :< 5
644 atoms, 630 bonds, 76 residues, 2 models selected
> show sel & #!5 atoms
> color (#!5 & sel) byhetero
> show (#!5 & sel) target ab
> ui tool show H-Bonds
> hbonds sel reveal true
208 hydrogen bonds found
> undo
[Repeated 4 time(s)]
> hide (#!5 & sel) target a
> undo
> select ~sel & ##selected
23582 atoms, 24152 bonds, 208 pseudobonds, 3092 residues, 3 models selected
> hide (#!5 & sel) target a
[Repeated 1 time(s)]
> ~hbonds
> select ~sel & ##selected
30 atoms, 24 bonds, 6 residues, 2 models selected
> view select
Expected an objects specifier or a view name or a keyword
> view
> view sel
[Repeated 1 time(s)]
> zoom 3
moved plane near 173.13296694590142 [ 0.27126448 -0.96046268 -0.06266591]
moved plane far 173.13296694590142 [ 0.27126448 -0.96046268 -0.06266591]
> zoom 3
moved plane near 57.710988965414174 [ 0.27126448 -0.96046268 -0.06266591]
moved plane far 57.710988965414174 [ 0.27126448 -0.96046268 -0.06266591]
> cofr sel
> select (#5/B & ::polymer_type>0 ) & ((#1/B & ::polymer_type>0 ) :<3.5)
3925 atoms, 4022 bonds, 513 residues, 1 model selected
> select ~sel & ##selected
7875 atoms, 8055 bonds, 1039 residues, 1 model selected
> select sel :< 3
16404 atoms, 16736 bonds, 2148 residues, 2 models selected
> select sel :< 2
17226 atoms, 17611 bonds, 2251 residues, 2 models selected
> select sel :< 1
17226 atoms, 17611 bonds, 2251 residues, 2 models selected
> select sel :< 1
17226 atoms, 17611 bonds, 2251 residues, 2 models selected
> select ligand
30 atoms, 24 bonds, 6 residues, 2 models selected
> select sel :< 2
30 atoms, 24 bonds, 6 residues, 2 models selected
> select sel :< 3
105 atoms, 92 bonds, 13 residues, 2 models selected
> select sel :< 3
266 atoms, 252 bonds, 34 residues, 2 models selected
> show sel & #!5 cartoons
> show sel & #!5 atoms
> color (#!5 & sel) byhetero
> select clear
[Repeated 1 time(s)]
> select ligand
30 atoms, 24 bonds, 6 residues, 2 models selected
> hbonds sel & #!5 reveal true
12 hydrogen bonds found
> select#5/B ARG 482
Unknown command: select#5/B ARG 482
> select#5/B ARG482
Unknown command: select#5/B ARG482
> select#5/B R482
Unknown command: select#5/B R482
> select#5/B:R482
Unknown command: select#5/B:R482
> select#5/B:arg482
Unknown command: select#5/B:arg482
> select#5/B:482
Unknown command: select#5/B:482
> select#5/B:ARG482
Unknown command: select#5/B:ARG482
> select #5/B:ARG482
Nothing selected
> select #5/B:R482
Nothing selected
> select model #5/B:R482
Expected an objects specifier or a keyword
> select model #5/B:ARG482
Expected an objects specifier or a keyword
> select model #5/B: ARG482
Expected an objects specifier or a keyword
> select model #5/B: ARG 482
Expected an objects specifier or a keyword
> select model #5/B: 482
Expected an objects specifier or a keyword
> select model #5/B:482
Expected an objects specifier or a keyword
> select model #5/B ARG482
Expected an objects specifier or a keyword
> select #5/B:482
11 atoms, 10 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #5/B:482, SO4
16 atoms, 14 bonds, 2 pseudobonds, 2 residues, 2 models selected
> select ~sel & ##selected
11784 atoms, 12063 bonds, 10 pseudobonds, 1550 residues, 2 models selected
> transparency select 0.8
Missing or invalid "percent" argument: Expected a number
> transparency select 0.8 target c
Missing or invalid "percent" argument: Expected a number
> transparency 0.8 select target c
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> undo
[Repeated 1 time(s)]
> redo
[Repeated 1 time(s)]
> hide #!3 models
> transparency 80 select target c
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency select 80 target c
Missing or invalid "percent" argument: Expected a number
> transparency select 0.8 target c
Missing or invalid "percent" argument: Expected a number
> transparency select 75 target c
Missing or invalid "percent" argument: Expected a number
> transparency 75 select, target c
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 75, select, target c
Missing or invalid "percent" argument: Expected a number
> transparency 75, select target c
Missing or invalid "percent" argument: Expected a number
> transparency 0.7, select target c
Missing or invalid "percent" argument: Expected a number
> transparency sel 70 target c
> select clear
> view name p4
> select ions
4 atoms, 4 residues, 2 models selected
> view
> view sel
No displayed objects specified.
> view sel
No displayed objects specified.
> zoom 6
> view ions
No displayed objects specified.
> show ions
> view sel
[Repeated 1 time(s)]
> zoom 6
moved plane near 228.46863984016957 [-0.07299158 -0.96977592 -0.23282379]
moved plane far 228.46863984016957 [-0.07299158 -0.96977592 -0.23282379]
> select sel :< 3
202 atoms, 174 bonds, 28 residues, 2 models selected
> show sel & #!5 atoms
> color (#!5 & sel) byhetero
> label (#!5 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select up
2562 atoms, 2668 bonds, 333 residues, 2 models selected
> select up
23225 atoms, 23792 bonds, 3043 residues, 2 models selected
> select down
2562 atoms, 2668 bonds, 333 residues, 2 models selected
> undo
[Repeated 2 time(s)]
> transparency sel 0
> transparency sel 0 target c
> transparency sel 0 target a
> select ~sel & ##selected
23410 atoms, 24002 bonds, 12 pseudobonds, 3070 residues, 3 models selected
> transparency sel 80 target c
> select ~sel & ##selected
202 atoms, 174 bonds, 28 residues, 2 models selected
> cofr sel
> select clear
> select ions
4 atoms, 4 residues, 2 models selected
> ~label (#!5 & sel) atoms
> hbonds sel & #!5 reveal true
0 hydrogen bonds found
> select sel :< 3
202 atoms, 174 bonds, 28 residues, 2 models selected
> hbonds sel & #!5 reveal true
17 hydrogen bonds found
> ~hbonds
> select ions
4 atoms, 4 residues, 2 models selected
> hbonds sel & #!5 reveal true
0 hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel reveal true
0 hydrogen bonds found
> ui tool show ViewDockX
No suitable models found for ViewDockX
> show (#!5 & sel) target ab
> ui tool show Distances
> contacts :CA restrict #5@N*,O* distanceOnly 3.5 reveal true name metalbonds
> color gold
28 distances
> view matrix models
> #1,0.92976,0.36809,0.0073485,-67.216,-0.36776,0.92949,-0.028255,99.591,-0.017231,0.023568,0.99957,-3.5126,#5,0.93005,0.36737,0.0073513,-67.13,-0.36704,0.92977,-0.028316,99.396,-0.017237,0.023637,0.99957,-3.5121
> select #5/B:311
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/B:311
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> select #5/B:312
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select #5/B:600@CA
1 atom, 1 residue, 1 model selected
> cofr sel
> select sel :< 3.5
68 atoms, 58 bonds, 14 pseudobonds, 10 residues, 3 models selected
> style sel & #!5 stick
Changed 34 atom styles
> style sel & #!5 stick
Changed 34 atom styles
> style sel & #!5 ball
Changed 34 atom styles
> undo
[Repeated 2 time(s)]
> show sel & #!5 atoms
> show (#!5 & sel-residues & sidechain) target ab
> cartoon (#!5 & sel)
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> show sel & #!5 atoms
> show sel & #!5 cartoons
> show sel & #!5 atoms
[Repeated 1 time(s)]
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> show (#!5 & sel-residues & sidechain) target ab
> show sel & #!5 atoms
> show sel & #!5 cartoons
> hide sel & #!5 cartoons
> show sel & #!5 cartoons
> hide sel & #!5 cartoons
> show sel & #!5 cartoons
> hide sel & #!5 cartoons
> show sel & #!5 cartoons
> color (#!5 & sel) byelement
> hide sel & #!5 cartoons
> show sel & #!5 atoms
> show sel & #!5 cartoons
> show (#!5 & sel-residues & sidechain) target ab
> show (#!5 & sel) target ab
> style (#!5 & sel) stick
Changed 34 atom styles
> show (#!5 & sel) target ab
> undo
[Repeated 1 time(s)]
> color (#!5 & sel) byhetero
> style sel & #!5 stick
Changed 34 atom styles
> undo
> nucleotides sel & #!5 atoms
> style nucleic & sel & #!5 stick
Changed 0 atom styles
> hide sel & #!5 cartoons
> show sel & #!5 cartoons
> hide sel & #!5 cartoons
> show sel & #!5 cartoons
> hide sel & #!5 cartoons
> show sel & #!5 cartoons
> select clear
> view name p6
> zoom 0.25
moved plane near -149.60044019684986 [ 0.05060681 -0.92733226 0.37080163]
moved plane far -149.60044019684986 [ 0.05060681 -0.92733226 0.37080163]
> select
31316 atoms, 32032 bonds, 28 pseudobonds, 4109 residues, 8 models selected
> transparency 0 sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 0 sel target c
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency sel 0 target c
> select clear
> undo
> select clear
> view name p7
> zoom 1.5
moved plane near 125.35638857478115 [-0.56243864 -0.8132286 0.14940559]
moved plane far 125.35638857478115 [-0.56243864 -0.8132286 0.14940559]
> zoom 1.5
moved plane near 83.57092538531644 [-0.56243864 -0.8132286 0.14940559]
moved plane far 83.57092538531644 [-0.56243864 -0.8132286 0.14940559]
> zoom 0.8
moved plane near -41.785462527056055 [-0.56243864 -0.8132286 0.14940559]
moved plane far -41.785462527056055 [-0.56243864 -0.8132286 0.14940559]
> zoom 0.8
moved plane near -52.23182824162114 [-0.56243864 -0.8132286 0.14940559]
moved plane far -52.23182824162114 [-0.56243864 -0.8132286 0.14940559]
> view name p8
> fly p1 p2
> select subtract #4
Nothing selected
> show #!3 models
> fly p1 p2
[Repeated 2 time(s)]
> fly p1 p2 2
> fly p1 p2 1
> fly p1 p2 2
> wait
> roll y 2 180
> fly p1 p2
> roll y 2 180
> select subtract #4
Nothing selected
> show #1 models
> view
> hide #1 models
> show #1 models
> hide #1 models
> fly p1 p2
> roll y 2 180
> view
> fly p1 p2
> roll y 2 180
> fly p1 p2
> roll y 2 180
> fly p1 p2
> roll y 2 360
> fly p1 p2
> roll y 2 360
> fly p1 p2
> roll y 2 360
> view
[Repeated 1 time(s)]
> view orient
> fly p1 p2
> roll y 2 360
> view orient
> fly p1 p2
> roll x 2 360
> fly p1 p2
> roll z 2 360
> fly p1 p2
> roll y 2 360
> view orient
> ui tool show "Side View"
> view
[Repeated 1 time(s)]
> turn x 90
> view
> fly p1 p2
> roll y 360
> fly p1 p2
> roll y 360
> fly p1 p2
> roll y 2 360
> fly p1 p2
> roll y 2 360
> fly p1 p2
> roll y 2 180
> fly p1 p2
> roll y 4 360
> fly p1 p2
> roll y 1 360
> fly p1 p2
> roll y 1 360
> view
> zoom 3
> view name p2
> fly p1 p2
> roll y 1 360
> ui tool show "Volume Viewer"
> volume #3 level 0.1604
> volume #3 level 0.1397
> hide #!5 models
> fly p1 p2
> roll y 1 360
> p1 wait; fly p1 p2; roll y 1 360
Unknown command: p1 wait; fly p1 p2; roll y 1 360
> roll p1 wait; fly p1 p2; roll y 1 360
Expected an axis vector or a keyword
> roll p1; wait; fly p1 p2; roll y 1 360
Expected an axis vector or a keyword
> roll y 360 p1; wait; fly p1 p2; roll y 1 360
Expected 'forever' or an integer >= 1 or a keyword
> view orient
> turn x 90
> view
> roll y 360 p1; wait; fly p1 p2; roll y 1 360
Expected 'forever' or an integer >= 1 or a keyword
> roll y 1 360
> wait
> fly p1 p2
> roll y 1 360
> view
> fly p1 p2
> roll y 1 360
> view
> fly p1 p2
> roll y 1 360
> view p1
> zoom 2.5
> view p1
> stop
> view p1
> zoom 3
> view name p2
> fly p1 p2
> roll y 1 540
> fly p1 p2
> roll y 1 360
> fly p1 p2
> roll y 1 450
> view p3
> view p4
> view p5
Expected an objects specifier or a view name or a keyword
> view p3
> view p2
> move y 70
> view name p3
> move y -140
> view name p4
> fly p1 p2
> roll y 1 450
> crossfade
> fly p3 60 p4 60 p1
> fly p1 p2
> roll y 1 450
> crossfade
> fly p3 60 p4 60 p1
> fly p1 p2
> roll y 1 450
> wait
> crossfade
> fly p3 60 p4 60 p1
> fly p1 p2
> roll y 1 450
> wait
> fly p3 60 p4 60 p1
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> view p5
Expected an objects specifier or a view name or a keyword
> view p6
> hide #!3 models
> show #!5 models
> view p4
> show #!3 models
> view p1
> hide #!3 models
> zoom 1.5
> view p1
> show #!3 models
> hide #!3 models
> select ~sel & ##selected
Nothing selected
> view name p5
> zoom 2
> zoom 0.5
> view
> view name p6
> view p7
> select #5/B:ions
Nothing selected
> view
[Repeated 2 time(s)]
> select #5/B:600
1 atom, 1 residue, 1 model selected
> view sel
> view
> view p6
> select #5/B:600
1 atom, 1 residue, 1 model selected
> cofr sel
> zoom 6
> view p6
> zoom 3
> view name p7
> roll y 360
> roll y 1 360
> select #5/B:600
1 atom, 1 residue, 1 model selected
> select #5/B:601
5 atoms, 4 bonds, 1 residue, 1 model selected
> zoom 3
> view sel
> select clear
> view name p8
> hbonds #!5 reveal true
2915 hydrogen bonds found
> ~hbonds
> select #5/B:601@S
1 atom, 1 residue, 1 model selected
> select #5/B:601@S
1 atom, 1 residue, 1 model selected
> select #5/B:601@S
1 atom, 1 residue, 1 model selected
> select #5/B:601@S
1 atom, 1 residue, 1 model selected
> select sel :< 3
10 atoms, 8 bonds, 2 residues, 2 models selected
> select sel :< 3
32 atoms, 28 bonds, 4 residues, 2 models selected
> show (#!5 & sel) target ab
> ui tool show Distances
> ui tool show Contacts
> ui tool show Distances
> ui tool show H-Bonds
> hbonds sel reveal true
17 hydrogen bonds found
> ~hbonds
> ui tool show H-Bonds
> select #5/B:482
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select #5/B:601@S
1 atom, 1 residue, 1 model selected
> view name p8
> select #5/B:601
5 atoms, 4 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel reveal true
4 hydrogen bonds found
> hbonds sel reveal true
4 hydrogen bonds found
> select clear
> view name p8
> view p7
> hide #!5 cartoons
> show #!5 cartoons
> hide #!5 atoms
> view p7
> select #5/B:601
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/B:482, 601, 511, 513, 508, 506, 600
50 atoms, 43 bonds, 9 pseudobonds, 7 residues, 3 models selected
> select ~sel & ##selected
11750 atoms, 12034 bonds, 23 pseudobonds, 1545 residues, 3 models selected
> hide sel atoms
> select clear
> select #5/B:601
5 atoms, 4 bonds, 1 residue, 1 model selected
> view sel
> select clear
> view name p8
> view p8
> zoom 0.25
moved plane near -87.56386402118895 [-1.32335333e-12 -1.00000000e+00
-1.11022302e-16]
moved plane far -87.56386402118895 [-1.32335333e-12 -1.00000000e+00
-1.11022302e-16]
> view p7
> select #5/B:600
1 atom, 1 residue, 1 model selected
> view sel
> view
> view p7
> select #5/B:600
1 atom, 1 residue, 1 model selected
> view
> select #5/B:600
1 atom, 1 residue, 1 model selected
> cofr sel
> select #5/B:482, 601, 511, 513, 508, 506, 600
50 atoms, 43 bonds, 9 pseudobonds, 7 residues, 3 models selected
> view sel
> select #5/B:511, 513, 508, 506, 600
34 atoms, 29 bonds, 7 pseudobonds, 5 residues, 2 models selected
> view sel
> select clear
> view name p9
> view p9
> view p7
> view p1
> view p3
> view p4
> view p5
> show #!3 models
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> view p5
> hide #!3 models
> show #!3 models
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> hide #3
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait
> hide #3
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #3.2 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait
> hide #3.1
> fly p4 p5
> view p4
> view p5
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait
> hide #3.1
> fly p5 p6
> show #3.1 models
> view p7
> hide #3.1 models
> view p8
> show #3.1 models
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait
> hide #3.1
> fly p5 60 p6 60 p7
> view
> show #3.1 models
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait
> hide #3.1
> fly p5 60 p6 60 p7
> show #3.1 models
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 30
> hide #3.1
> fly p5 60 p6 60 p7 60 p8
> view p8
> view p6
> view p7
> view p9
> view p7
> show #3.1 models
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 30
> hide #3.1
> fly p5 60 p6 60 p7 120 p8 360 p7
> wait
> p9 360 p7; wait; roll y 1 360
Unknown command: p9 360 p7; wait; roll y 1 360
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 30
> hide #3.1
> fly p5 p6 60 p7 120 p8 360 p7
> wait
> fly p9 180 p7
> wait
> roll y 1 360
> show #3.1 models
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 30
> hide #3.1
> fly p5 p6 60 p7 120 p8 360 p7
> wait
> fly p7 60 p9 180 p7
> wait
> fly p7 180
> show #3.1 models
> view p9
> hide #!3 models
> view p8
> view p9
> view name p9
> view name p10
> view p7
> view p6
[Repeated 1 time(s)]
> hide #3.1 models
> show #3.1 models
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 30
> hide #3.1
> wait
> fly p5 p6 60 p7 120 p8 360 p7
> wait
> fly p7 60 p9 180 p10 180 p7 p6
> show #3.1 models
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 180
> hide #3.1
> wait
> fly p5 p6 60 p7 120 p8 360 p7
> wait 180
> fly p7 60 p9 360 p10 360 p7 p6
> view p5
> view p6
> view p7
> view p8
> view p9
> show #3.1 models
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 180
> hide #3.1
> wait
> fly p5 p6 p7 120 p8 360
> fly p7 180 p9 360 p10 360 p7 p6
> view
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 180
> hide #3.1
> wait
> fly p5 p6 p7 120 p8 360
> fly p7 180 p9 360 p10 360 p7 p6
> view p8
> show #3.1 models
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 180
> hide #3.1
> wait
> fly p5 p6 p7 360 p8 360
> fly p7 180 p9 360 p10 360 p7 p6
> view
> show #3.1 models
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 180
> hide #3.1
> wait
> fly p5 p6 p7 360 p8 360
> fly p7 180 p9 360 p10 360 p7 p6
> show #3.1 models
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 360
> hide #3.1
> wait
> fly p5 p6 p7 p8 360
> wait
> fly p7 180 p9 360 p10 360 p7 p6
> view p8
> view p7
> show #3.1 models
> view
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 360
> hide #3.1
> wait
> fly p5 p6 p7 180 p8 360
> wait 180
> fly p7 180 p9 360 p10 360 p7 p6
> show #3.1 models
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 360
> hide #3.1
> wait
> fly p5 p6 p7 360 p8
> fly p7 180 p9 360 p10 360 p7 p6
> show #3.1 models
> hide #!5 models
> view name p1
> show #!5 models
> hide #5
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 360
> hide #3.1
> show #5
> wait
> fly p5 p6 p7 360 p8
> fly p7 180 p9 360 p10 360 p7 p6
> hide #!5 models
> show #5 cartoons
> show #5
> show #5 cartoons
> show models #5 cartoon
Expected ',' or a keyword
> show models #5, cartoon
Expected ',' or a keyword
> show #5/c
> show #5
> show #5 target c
> show #5 target m
> hide #!5 cartoons
> show #!5 cartoons
> hide #!5 atoms
> view p1
> show #3.1 models
> hide #5
> hide #5 target c
> hide #5/c
> hide #3.1 models
> show #3.1 models
> show #5/c
> hide #3.1 models
> show #3.1 models
> select add #5
11800 atoms, 12077 bonds, 23 pseudobonds, 1552 residues, 4 models selected
> show sel cartoons
> hide sel atoms
> select subtract #5
Nothing selected
> hide #5/c
> hide #3.1 models
> show #3.1 models
> hide #5/c
[Repeated 1 time(s)]
> hide #3.1 models
> show #3.1 models
> view p8
> hide #!3.1 models
> select #5/B:601
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel target ab
> select sel :< 3
32 atoms, 28 bonds, 4 pseudobonds, 4 residues, 3 models selected
> show sel & #!5 atoms
> view p8
> select clear
> select #5/B:600
1 atom, 1 residue, 1 model selected
> view sel
No displayed objects specified.
> view
> select #5/B:600
1 atom, 1 residue, 1 model selected
> show sel target ab
> ui tool show H-Bonds
> hbonds sel reveal true
0 hydrogen bonds found
> hbonds sel reveal true
0 hydrogen bonds found
> select #5/B:511,513,508,506
33 atoms, 29 bonds, 4 residues, 1 model selected
> view sel
> show sel atoms
> select clear
> hide #!5 models
> show #!5 models
> hide #5
> select clear
> hide #5/m
> hide #!3 models
> show #!3 models
> undo
> show #3.2 models
> select subtract #4
Nothing selected
> select add #4
Nothing selected
> view
> hide #!3 models
> hide #5/m
> hide #5 target acs
> show #5 target acs
> hide #5 target acs
> show #5 target ac
> redo
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #5 target m
> hide #5 target m
> show #5 target m
> show #3.1 models
> view
> hide #5 target m
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 360
> hide #3.1
> hide #5 target m
> wait 60
> fly p5 p6 p7 360 p8
> fly p7 180 p9 360 p10 360 p7 p6
> show #3.1 models
> show #!5 models
> hide #!3 models
> show #5 target m
> select #5/B:600
1 atom, 1 residue, 1 model selected
> view sel
> select #5/B:511,513,508,506
33 atoms, 29 bonds, 4 residues, 1 model selected
> show #5 target m
> hide #5 target m
> show #5 target m
> view sel
> view
> select subtract #4
33 atoms, 29 bonds, 4 residues, 2 models selected
> select add #5
11800 atoms, 12077 bonds, 21 pseudobonds, 1552 residues, 4 models selected
> show #!3 models
> select subtract #4
11800 atoms, 12077 bonds, 21 pseudobonds, 1552 residues, 7 models selected
> select subtract #5
4 models selected
> select add #6
28 pseudobonds, 1 model selected
> select subtract #4
28 pseudobonds, 1 model selected
> select subtract #6
Nothing selected
> select subtract #4
Nothing selected
> hide #5 target m
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 360
> hide #3.1
> show #5 target m
> wait 60
> fly p5 p6 p7 360 p8
> fly p7 180 p9 360 p10 360 p7 p6
> stop
> view p8
> view p7
> view
> show #3.1 models
> hide #5 target m
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 360
> hide #3.1
> show #5 target m
> wait 60
> fly p5 p6 p7 360 p8 360 p7 180 p9 360 p10 360 p7 p6
> select #5/B:601
5 atoms, 4 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel reveal true
4 hydrogen bonds found
> hbonds sel reveal true
4 hydrogen bonds found
> select #3
3 models selected
> view p6
> view p7
> show #3.1 models
> view
> select subtract #3.1
2 models selected
> select add #3.2
2 models selected
> select add #3
3 models selected
> select add #3
3 models selected
> select subtract #3.1
2 models selected
> hide #5 target m
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 360
> hide #3.1
> show #5 target m
> wait 60
> fly p5 p6 p7 360 p8 360 p7 180 p9 360 p10 360 p7
> roll y 1 -180; view p6
Missing or invalid "frames" argument: Must be greater than or equal to 1
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> select #5/B:601
5 atoms, 4 bonds, 1 residue, 1 model selected
> view sel
> show #3.1 models
> hide #!3.1 models
> select #5/B:601,482
16 atoms, 14 bonds, 2 pseudobonds, 2 residues, 2 models selected
> view sel
> show sel surfaces
> view sel
> surface style #5.3 mesh
> view sel
> view
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> surface style #5.3 solid
> view sel
> split #3
> hide #3.2 models
> show #3.2 models
> hide #!3.1 models
> show #3.1 models
> volume style mesh
> view
> view sel
> view
[Repeated 1 time(s)]
> hide sel surfaces
> view
> view p1
> view sel
> volume step 1
> volume step 2
> volume step 1
> volume show
> volume hide
> volume show
> volume style mesh
> volume style image
[Repeated 1 time(s)]
> volume style mesh
> ui tool show "Show Volume Menu"
> view name p8
> view name p10
> view name p8
> view p9
> hide #3.1 models
> view name p10
> show #3.1 models
> view
> view p1
> show #3.1 target m
> volume style mesh
> volume style surface
> hide #3.1
> show #3.1
> hide #3.1
> show #3.1 mesh
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #3.1 target m
> volume #3 style mesh level 0.8
> volume #3 style mesh level 0.14
> volume #3 style mesh level 0.2
> volume #3 style surface
> view 1
Expected an objects specifier or a view name or a keyword
> view p1
> fly p1 p2
> volume #3 style mesh level, 0.2
Expected a keyword
> fly p1 p2
> show volume #3 style mesh level, 0.2
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> fly p1 p2
> show #3 style mesh level, 0.2
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> fly p1 p2
> view show #3 style mesh level, 0.2
Expected an objects specifier or a view name or a keyword
> view
> select ~sel & ##selected
11784 atoms, 12063 bonds, 23 pseudobonds, 1550 residues, 3 models selected
> select add #4
11784 atoms, 12063 bonds, 25 pseudobonds, 1550 residues, 7 models selected
> select add #5
11800 atoms, 12077 bonds, 25 pseudobonds, 1552 residues, 8 models selected
> select add #6
11800 atoms, 12077 bonds, 32 pseudobonds, 1552 residues, 8 models selected
> select subtract #4
11800 atoms, 12077 bonds, 28 pseudobonds, 1552 residues, 7 models selected
> select subtract #5
4 models selected
> select add #6
28 pseudobonds, 1 model selected
> select subtract #6
Nothing selected
> hide #5 target m
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 180
> hide #3.1
> show #5 target m
> wait 60
> fly p5 p6 p7 360 p8 360 p7 180 p9 360 p10 360 p7
> roll y 1 -180; view p6
Missing or invalid "frames" argument: Must be greater than or equal to 1
> view p9
> view p10
> view p9
> view p10
> view p9
> view name p10
> fly p9 p10
> view p9
[Repeated 2 time(s)]
> view name p10
> view name p11
> show #3.1 models
> view
> hide #5 target m
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 180
> hide #3.1
> show #5 target m
> wait 180
> fly p5 p6 p7 360 p8 360 p7 180 p9 180 p10 p11 180 p7
> wait
> roll y 1 -180; view p6 p5
Missing or invalid "frames" argument: Must be greater than or equal to 1
> show #3.1 models
> view
> view orient
> turn x 90
> view
> hide #5 target m
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 180
> hide #3.1
> show #5 target m
> wait 240
> fly p5 p6 p7 360 p8 360 p7 180 p9 180 p10 60 p11 180 p7 p6
> roll y 1 180
> select #5/B:50
4 atoms, 3 bonds, 1 residue, 1 model selected
> view sel
> view
> select #5/B:50-60
82 atoms, 83 bonds, 11 residues, 1 model selected
> view sel
> view
> view p1
> select clear
> view p1
> view name p12
> move y -30
> view name p13
> move y -30
> view name p14
> fly p11 p12 p13 p14
> view name p15
> fly p11-15
fly: Unknown position name "p11-15"
> fly p11-p15
fly: Unknown position name "p11-p15"
> fly p11 to p15
fly: Unknown position name "to"
> fly p11 p12 p13 p14 p15
> fly p11 180 p12 p13 p14 p15
> fly p11 180 p12 180 p13 p14 p15
> fly p11 180 p12 240 p13 120 p14 120 p15
[Repeated 1 time(s)]
> view p12
> show #3.1 models
> show #3.2 models
> hide #3.2 models
> view
> hide #5 target m
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 180
> hide #3.1
> show #5 target m
> wait 240
> fly p5 p6 p7 360 p8 360 p7 180 p9 180 p10 60 p11 180 p7 p6 600 p11 180 p12
> 240 p13 120 p14 120 p15
> wait
> roll y 1 180
> view p1
> show #3.1 models
> hide #5 target m
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 360
> hide #3.1
> show #5 target m
> wait 240
> fly p5 p6 p7 360 p8 360 p7 180 p9 180 p10 60 p11 180 p7 600 p12 240 p13 120
> p14 120 p15
> view p1
> show #3.1 models
> hide #5 target m
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 360
> hide #3.1
> show #5 target m
> wait 60
> fly p5 p6 p7 360 p8 360 p7 180 p9 180 p10 60 p11 180 p7 600 p12 240 p13 120
> p14 120 p15
> view p4
> view p2
> view p1
> show #3.1 models
> view
> hide #5 target m
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 360
> hide #3.1
> show #5 target m
> fly p5 p6 p7 360 p8 360 p7 180 p9 180 p10 180 p11 180 p7 600 p12 240 p13 120
> p14 120 p15
> view
> show #3.1 models
> hide #5 target m
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180
> wait 360
> hide #3.1
> show #5 target m
> fly p1 p5 p6 p7 360 p8 360 p7 180 p9 180 p10 180 p11 180 p7 600 p12 240 p13
> 120 p14 120 p15
> show #3.1 models
> view
> stop
> view
> hide #5 target m
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 360
> hide #3.1
> show #5 target m
> wait
> fly p1 p5 p6 p7 360 p8 360 p7 180 p9 180 p10 180 p11 180 p7 600 p12 240 p13
> 120 p14 120 p15
> stop
> view p1
> show #3.1 models
> hide #5 target m
> fly p1 p2
> roll y 1 450
> wait 120
> fly p3 180 p4 180 p1
> wait 480
> hide #3.1
> show #5 target m
> wait
wait requires a frame count argument unless motion is in progress
> fly p1 p5 p6 p7 360 p8 360 p7 180 p9 180 p10 180 p11 180 p7 600 p12 240 p13
> 120 p14 120 p15
> show #3.1 models
> hide #5 target m
> fly p1 p2
> roll y 1 450
> wait 120
> fly p3 180 p4 180 p1
> wait 480
> hide #3.1
> show #5 target m
> wait
wait requires a frame count argument unless motion is in progress
> fly p1 p5 p6 p7 360 p8 360 p7 180 p9 180 p10 180 p11 180 p7 600 p12 240 p13
> 120 p14 120 p15
> stop
> hide #5 target m
> fly p1 p2
fly: Nothing displayed to calculate center of rotation
> show #3.1 models
> hide #5 target m
> fly p1 p2
> roll y 1 450
> fly p3 180 p4 180 p1
> wait 480
> hide #3.1
> show #5 target m
> wait
wait requires a frame count argument unless motion is in progress
> fly p1 p5 p6 p7 360 p8 360 p7 180 p9 180 p10 180 p11 180 p7 600 p12 240 p13
> 120 p14 120 p15
> show #3.1 models
> stop
> hide #5 target m
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 480
> hide #3.1
> show #5 target m
> wait
wait requires a frame count argument unless motion is in progress
> fly p1 p5 p6 p7 360 p8 360 p7 180 p9 180 p10 180 p11 180 p7 600 p12 240 p13
> 120 p14 120 p15
> view p1
> show #3.1 models
> movie record
Already recording a movie
> hide #5 target m
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 480
> hide #3.1
> show #5 target m
> wait
wait requires a frame count argument unless motion is in progress
> fly p1 p5 p6 p7 360 p8 360 p7 180 p9 180 p10 180 p11 180 p7 600 p12 240 p13
> 120 p14 120 p15
> movie encode
> /Users/wang/Documents/Zeytuni_lab/fimbriae_movies_chimeraX/Mfa_turn.mp4
Movie saved to /Users/wang/.../fimbriae_movies_chimeraX/Mfa_turn.mp4
> close #1
> close #2
> show #3.1 models
> view p1
> view name p1
> movie record
> hide #5 target m
> fly p1 p2
> roll y 1 450
> wait
> fly p3 180 p4 180 p1
> wait 480
> hide #3.1
> show #5 target m
> wait
wait requires a frame count argument unless motion is in progress
> fly p1 p5 p6 p7 360 p8 360 p7 180 p9 180 p10 180 p11 180 p7 600 p12 240 p13
> 120 p14 120 p15
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/movie.py", line 176, in capture_image
i.save(save_path, self.img_fmt)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 2439, in save
save_handler(self, fp, filename)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/PpmImagePlugin.py", line 329, in _save
ImageFile._save(im, fp, [("raw", (0, 0) + im.size, 0, (rawmode, 0, 1))])
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/ImageFile.py", line 538, in _save
_encode_tile(im, fp, tile, bufsize, fh)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/ImageFile.py", line 565, in _encode_tile
errcode = encoder.encode_to_file(fh, bufsize)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: [Errno 28] No space left on device
Error processing trigger "frame drawn":
OSError: [Errno 28] No space left on device
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/ImageFile.py", line 565, in _encode_tile
errcode = encoder.encode_to_file(fh, bufsize)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> movie encode
> /Users/wang/Documents/Zeytuni_lab/fimbriae_movies_chimeraX/Mfa_turn.mp4
/Applications/ChimeraX-1.7.1.app/Contents/bin/ffmpeg -r 25 -i
/var/folders/p0/2fhrggzd43l1mhh6082h4r100000gn/T/chimovie_Zkq1-%05d.ppm -vf
crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt
yuv420p -crf 20
/Users/wang/Documents/Zeytuni_lab/fimbriae_movies_chimeraX/Mfa_turn.mp4
stdout:
stderr:
ffmpeg version 6.0 Copyright (c) 2000-2023 the FFmpeg developers
built with Apple clang version 13.1.6 (clang-1316.0.21.2.5)
configuration: --prefix=/Volumes/tempdisk/sw --extra-cflags=-fno-stack-check
--arch=arm64 --cc=/usr/bin/clang --enable-gpl --enable-libvmaf --enable-
libbluray --enable-libopenjpeg --enable-libopus --enable-libmp3lame --enable-
libx264 --enable-libx265 --enable-libvpx --enable-libwebp --enable-libass
--enable-libfreetype --enable-fontconfig --enable-libtheora --enable-libvorbis
--enable-libsnappy --enable-libaom --enable-libvidstab --enable-libzimg
--enable-libsvtav1 --enable-libkvazaar --enable-version3 --pkg-config-
flags=--static --enable-ffplay --enable-postproc --enable-nonfree --enable-
neon --enable-runtime-cpudetect --disable-indev=qtkit --disable-
indev=x11grab_xcb
libavutil 58. 2.100 / 58. 2.100
libavcodec 60. 3.100 / 60. 3.100
libavformat 60. 3.100 / 60. 3.100
libavdevice 60. 1.100 / 60. 1.100
libavfilter 9. 3.100 / 9. 3.100
libswscale 7. 1.100 / 7. 1.100
libswresample 4. 10.100 / 4. 10.100
libpostproc 57. 1.100 / 57. 1.100
Input #0, image2, from
'/var/folders/p0/2fhrggzd43l1mhh6082h4r100000gn/T/chimovie_Zkq1-%05d.ppm':
Duration: 00:01:10.76, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 1340x1338, 25 fps, 25 tbr, 25 tbn
Stream mapping:
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))
Press [q] to stop, [?] for help
[libx264 @ 0x158e06690] using cpu capabilities: ARMv8 NEON
[libx264 @ 0x158e06690] profile High, level 4.0, 4:2:0, 8-bit
[libx264 @ 0x158e06690] 264 - core 164 r3075 66a5bc1 - H.264/MPEG-4 AVC codec
- Copyleft 2003-2021 - http://www.videolan.org/x264.html - options: cabac=1
ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00
mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11
fast_pskip=1 chroma_qp_offset=-2 threads=12 lookahead_threads=2
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to
'/Users/wang/Documents/Zeytuni_lab/fimbriae_movies_chimeraX/Mfa_turn.mp4':
Metadata:
encoder : Lavf60.3.100
Stream #0:0: Video: h264 (avc1 / 0x31637661), yuv420p(tv, progressive),
1340x1338, q=2-31, 25 fps, 12800 tbn
Metadata:
encoder : Lavc60.3.100 libx264
Side data:
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: N/A
frame= 0 fps=0.0 q=0.0 size= 0kB time=-577014:32:22.77 bitrate= -0.0kbits/s
speed=N/A frame= 23 fps=0.0 q=25.0 size= 256kB time=00:00:00.84
bitrate=2497.1kbits/s speed=1.62x frame= 87 fps= 85 q=25.0 size= 1792kB
time=00:00:03.36 bitrate=4369.2kbits/s speed=3.27x frame= 135 fps= 88 q=25.0
size= 3328kB time=00:00:05.32 bitrate=5124.7kbits/s speed=3.48x frame= 183
fps= 90 q=25.0 size= 4864kB time=00:00:07.24 bitrate=5503.6kbits/s speed=3.56x
av_interleaved_write_frame(): No space left on device
[out#0/mp4 @ 0x6000021dc300] Error muxing a packet
[out#0/mp4 @ 0x6000021dc300] Error writing trailer: No space left on device
frame= 183 fps= 74 q=-1.0 Lsize= 4864kB time=00:00:09.60 bitrate=4150.7kbits/s
speed=3.89x
video:5139kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: unknown
[libx264 @ 0x158e06690] frame I:1 Avg QP: 7.79 size: 79345
[libx264 @ 0x158e06690] frame P:61 Avg QP:22.26 size: 56228
[libx264 @ 0x158e06690] frame B:181 Avg QP:29.22 size: 21710
[libx264 @ 0x158e06690] consecutive B-frames: 0.4% 0.8% 0.0% 98.8%
[libx264 @ 0x158e06690] mb I I16..4: 78.4% 10.3% 11.3%
[libx264 @ 0x158e06690] mb P I16..4: 0.5% 0.5% 2.2% P16..4: 4.7% 8.0% 11.9%
0.0% 0.0% skip:72.2%
[libx264 @ 0x158e06690] mb B I16..4: 0.0% 0.1% 0.0% B16..8: 6.9% 7.1% 7.3%
direct: 3.1% skip:75.4% L0:36.2% L1:40.5% BI:23.2%
[libx264 @ 0x158e06690] 8x8 transform intra:15.8% inter:18.4%
[libx264 @ 0x158e06690] coded y,uvDC,uvAC intra: 48.6% 52.9% 51.1% inter: 9.8%
6.3% 2.6%
[libx264 @ 0x158e06690] i16 v,h,dc,p: 92% 5% 3% 0%
[libx264 @ 0x158e06690] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 15% 5% 70% 1% 2% 2% 2%
2% 2%
[libx264 @ 0x158e06690] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 17% 14% 14% 7% 11% 11%
9% 9% 8%
[libx264 @ 0x158e06690] i8c dc,h,v,p: 66% 12% 14% 7%
[libx264 @ 0x158e06690] Weighted P-Frames: Y:0.0% UV:0.0%
[libx264 @ 0x158e06690] ref P L0: 52.1% 24.4% 15.8% 7.7%
[libx264 @ 0x158e06690] ref B L0: 86.9% 10.5% 2.6%
[libx264 @ 0x158e06690] ref B L1: 93.8% 6.2%
[libx264 @ 0x158e06690] kb/s:6122.39
Conversion failed!
An error occurred during encoding. See Reply Log for details.
Error during MPEG encoding:
\-----------------------------
Exit value: 228
Error message:
stdout:
stderr:
ffmpeg version 6.0 Copyright (c) 2000-2023 the FFmpeg developers
built with Apple clang version 13.1.6 (clang-1316.0.21.2.5)
configuration: --prefix=/Volumes/tempdisk/sw --extra-cflags=-fno-stack-check
--arch=arm64 --cc=/usr/bin/clang --enable-gpl --enable-libvmaf --enable-
libbluray --enable-libopenjpeg --enable-libopus --enable-libmp3lame --enable-
libx264 --enable-libx265 --enable-libvpx --enable-libwebp --enable-libass
--enable-libfreetype --enable-fontconfig --enable-libtheora --enable-libvorbis
--enable-libsnappy --enable-libaom --enable-libvidstab --enable-libzimg
--enable-libsvtav1 --enable-libkvazaar --enable-version3 --pkg-config-
flags=--static --enable-ffplay --enable-postproc --enable-nonfree --enable-
neon --enable-runtime-cpudetect --disable-indev=qtkit --disable-
indev=x11grab_xcb
libavutil 58. 2.100 / 58. 2.100
libavcodec 60. 3.100 / 60. 3.100
libavformat 60. 3.100 / 60. 3.100
libavdevice 60. 1.100 / 60. 1.100
libavfilter 9. 3.100 / 9. 3.100
libswscale 7. 1.100 / 7. 1.100
libswresample 4. 10.100 / 4. 10.100
libpostproc 57. 1.100 / 57. 1.100
Input #0, image2, from
'/var/folders/p0/2fhrggzd43l1mhh6082h4r100000gn/T/chimovie_Zkq1-%05d.ppm':
Duration: 00:01:10.76, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 1340x1338, 25 fps, 25 tbr, 25 tbn
Stream mapping:
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))
Press [q] to stop, [?] for help
[libx264 @ 0x158e06690] using cpu capabilities: ARMv8 NEON
[libx264 @ 0x158e06690] profile High, level 4.0, 4:2:0, 8-bit
[libx264 @ 0x158e06690] 264 - core 164 r3075 66a5bc1 - H.264/MPEG-4 AVC codec
- Copyleft 2003-2021 - http://www.videolan.org/x264.html - options: cabac=1
ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00
mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11
fast_pskip=1 chroma_qp_offset=-2 threads=12 lookahead_threads=2
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to
'/Users/wang/Documents/Zeytuni_lab/fimbriae_movies_chimeraX/Mfa_turn.mp4':
Metadata:
encoder : Lavf60.3.100
Stream #0:0: Video: h264 (avc1 / 0x31637661), yuv420p(tv, progressive),
1340x1338, q=2-31, 25 fps, 12800 tbn
Metadata:
encoder : Lavc60.3.100 libx264
Side data:
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: N/A
frame= 0 fps=0.0 q=0.0 size= 0kB time=-577014:32:22.77 bitrate= -0.0kbits/s
speed=N/A frame= 23 fps=0.0 q=25.0 size= 256kB time=00:00:00.84
bitrate=2497.1kbits/s speed=1.62x frame= 87 fps= 85 q=25.0 size= 1792kB
time=00:00:03.36 bitrate=4369.2kbits/s speed=3.27x frame= 135 fps= 88 q=25.0
size= 3328kB time=00:00:05.32 bitrate=5124.7kbits/s speed=3.48x frame= 183
fps= 90 q=25.0 size= 4864kB time=00:00:07.24 bitrate=5503.6kbits/s speed=3.56x
av_interleaved_write_frame(): No space left on device
[out#0/mp4 @ 0x6000021dc300] Error muxing a packet
[out#0/mp4 @ 0x6000021dc300] Error writing trailer: No space left on device
frame= 183 fps= 74 q=-1.0 Lsize= 4864kB time=00:00:09.60 bitrate=4150.7kbits/s
speed=3.89x
video:5139kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: unknown
[libx264 @ 0x158e06690] frame I:1 Avg QP: 7.79 size: 79345
[libx264 @ 0x158e06690] frame P:61 Avg QP:22.26 size: 56228
[libx264 @ 0x158e06690] frame B:181 Avg QP:29.22 size: 21710
[libx264 @ 0x158e06690] consecutive B-frames: 0.4% 0.8% 0.0% 98.8%
[libx264 @ 0x158e06690] mb I I16..4: 78.4% 10.3% 11.3%
[libx264 @ 0x158e06690] mb P I16..4: 0.5% 0.5% 2.2% P16..4: 4.7% 8.0% 11.9%
0.0% 0.0% skip:72.2%
[libx264 @ 0x158e06690] mb B I16..4: 0.0% 0.1% 0.0% B16..8: 6.9% 7.1% 7.3%
direct: 3.1% skip:75.4% L0:36.2% L1:40.5% BI:23.2%
[libx264 @ 0x158e06690] 8x8 transform intra:15.8% inter:18.4%
[libx264 @ 0x158e06690] coded y,uvDC,uvAC intra: 48.6% 52.9% 51.1% inter: 9.8%
6.3% 2.6%
[libx264 @ 0x158e06690] i16 v,h,dc,p: 92% 5% 3% 0%
[libx264 @ 0x158e06690] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 15% 5% 70% 1% 2% 2% 2%
2% 2%
[libx264 @ 0x158e06690] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 17% 14% 14% 7% 11% 11%
9% 9% 8%
[libx264 @ 0x158e06690] i8c dc,h,v,p: 66% 12% 14% 7%
[libx264 @ 0x158e06690] Weighted P-Frames: Y:0.0% UV:0.0%
[libx264 @ 0x158e06690] ref P L0: 52.1% 24.4% 15.8% 7.7%
[libx264 @ 0x158e06690] ref B L0: 86.9% 10.5% 2.6%
[libx264 @ 0x158e06690] ref B L1: 93.8% 6.2%
[libx264 @ 0x158e06690] kb/s:6122.39
Conversion failed!
\-----------------------------
> movie encode
> /Users/wang/Documents/Zeytuni_lab/fimbriae_movies_chimeraX/Mfa_turn.mp4
/Applications/ChimeraX-1.7.1.app/Contents/bin/ffmpeg -r 25 -i
/var/folders/p0/2fhrggzd43l1mhh6082h4r100000gn/T/chimovie_Zkq1-%05d.ppm -vf
crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt
yuv420p -crf 20
/Users/wang/Documents/Zeytuni_lab/fimbriae_movies_chimeraX/Mfa_turn.mp4
stdout:
stderr:
ffmpeg version 6.0 Copyright (c) 2000-2023 the FFmpeg developers
built with Apple clang version 13.1.6 (clang-1316.0.21.2.5)
configuration: --prefix=/Volumes/tempdisk/sw --extra-cflags=-fno-stack-check
--arch=arm64 --cc=/usr/bin/clang --enable-gpl --enable-libvmaf --enable-
libbluray --enable-libopenjpeg --enable-libopus --enable-libmp3lame --enable-
libx264 --enable-libx265 --enable-libvpx --enable-libwebp --enable-libass
--enable-libfreetype --enable-fontconfig --enable-libtheora --enable-libvorbis
--enable-libsnappy --enable-libaom --enable-libvidstab --enable-libzimg
--enable-libsvtav1 --enable-libkvazaar --enable-version3 --pkg-config-
flags=--static --enable-ffplay --enable-postproc --enable-nonfree --enable-
neon --enable-runtime-cpudetect --disable-indev=qtkit --disable-
indev=x11grab_xcb
libavutil 58. 2.100 / 58. 2.100
libavcodec 60. 3.100 / 60. 3.100
libavformat 60. 3.100 / 60. 3.100
libavdevice 60. 1.100 / 60. 1.100
libavfilter 9. 3.100 / 9. 3.100
libswscale 7. 1.100 / 7. 1.100
libswresample 4. 10.100 / 4. 10.100
libpostproc 57. 1.100 / 57. 1.100
Input #0, image2, from
'/var/folders/p0/2fhrggzd43l1mhh6082h4r100000gn/T/chimovie_Zkq1-%05d.ppm':
Duration: 00:01:10.76, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 1340x1338, 25 fps, 25 tbr, 25 tbn
Stream mapping:
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))
Press [q] to stop, [?] for help
[libx264 @ 0x11de07620] using cpu capabilities: ARMv8 NEON
[libx264 @ 0x11de07620] profile High, level 4.0, 4:2:0, 8-bit
[libx264 @ 0x11de07620] 264 - core 164 r3075 66a5bc1 - H.264/MPEG-4 AVC codec
- Copyleft 2003-2021 - http://www.videolan.org/x264.html - options: cabac=1
ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00
mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11
fast_pskip=1 chroma_qp_offset=-2 threads=12 lookahead_threads=2
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to
'/Users/wang/Documents/Zeytuni_lab/fimbriae_movies_chimeraX/Mfa_turn.mp4':
Metadata:
encoder : Lavf60.3.100
Stream #0:0: Video: h264 (avc1 / 0x31637661), yuv420p(tv, progressive),
1340x1338, q=2-31, 25 fps, 12800 tbn
Metadata:
encoder : Lavc60.3.100 libx264
Side data:
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: N/A
frame= 0 fps=0.0 q=0.0 size= 0kB time=-577014:32:22.77 bitrate= -0.0kbits/s
speed=N/A frame= 29 fps=0.0 q=25.0 size= 512kB time=00:00:01.08
bitrate=3884.0kbits/s speed=2.16x frame= 87 fps= 86 q=25.0 size= 1792kB
time=00:00:03.40 bitrate=4317.8kbits/s speed=3.37x frame= 139 fps= 92 q=25.0
size= 3328kB time=00:00:05.44 bitrate=5011.6kbits/s speed=3.59x frame= 187
fps= 93 q=25.0 size= 5120kB time=00:00:07.40 bitrate=5668.0kbits/s speed=3.66x
av_interleaved_write_frame(): No space left on device
[out#0/mp4 @ 0x6000021ac3c0] Error muxing a packet
[out#0/mp4 @ 0x6000021ac3c0] Error writing trailer: No space left on device
frame= 190 fps= 77 q=-1.0 Lsize= 5120kB time=00:00:09.88 bitrate=4245.3kbits/s
speed=4.02x
video:5398kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: unknown
[libx264 @ 0x11de07620] frame I:1 Avg QP: 7.79 size: 79345
[libx264 @ 0x11de07620] frame P:63 Avg QP:22.33 size: 56385
[libx264 @ 0x11de07620] frame B:186 Avg QP:29.22 size: 21853
[libx264 @ 0x11de07620] consecutive B-frames: 0.8% 0.0% 0.0% 99.2%
[libx264 @ 0x11de07620] mb I I16..4: 78.4% 10.3% 11.3%
[libx264 @ 0x11de07620] mb P I16..4: 0.5% 0.5% 2.3% P16..4: 4.8% 8.1% 11.9%
0.0% 0.0% skip:72.0%
[libx264 @ 0x11de07620] mb B I16..4: 0.0% 0.1% 0.0% B16..8: 7.0% 7.2% 7.3%
direct: 3.2% skip:75.3% L0:36.1% L1:40.6% BI:23.4%
[libx264 @ 0x11de07620] 8x8 transform intra:15.9% inter:18.6%
[libx264 @ 0x11de07620] coded y,uvDC,uvAC intra: 49.3% 53.6% 51.7% inter: 9.9%
6.3% 2.6%
[libx264 @ 0x11de07620] i16 v,h,dc,p: 91% 5% 3% 0%
[libx264 @ 0x11de07620] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 15% 5% 70% 1% 2% 2% 2%
2% 2%
[libx264 @ 0x11de07620] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 16% 14% 14% 7% 11% 11%
9% 9% 8%
[libx264 @ 0x11de07620] i8c dc,h,v,p: 66% 13% 14% 7%
[libx264 @ 0x11de07620] Weighted P-Frames: Y:0.0% UV:0.0%
[libx264 @ 0x11de07620] ref P L0: 52.3% 24.5% 15.7% 7.6%
[libx264 @ 0x11de07620] ref B L0: 87.2% 10.3% 2.6%
[libx264 @ 0x11de07620] ref B L1: 93.9% 6.1%
[libx264 @ 0x11de07620] kb/s:6157.01
Conversion failed!
An error occurred during encoding. See Reply Log for details.
Error during MPEG encoding:
\-----------------------------
Exit value: 228
Error message:
stdout:
stderr:
ffmpeg version 6.0 Copyright (c) 2000-2023 the FFmpeg developers
built with Apple clang version 13.1.6 (clang-1316.0.21.2.5)
configuration: --prefix=/Volumes/tempdisk/sw --extra-cflags=-fno-stack-check
--arch=arm64 --cc=/usr/bin/clang --enable-gpl --enable-libvmaf --enable-
libbluray --enable-libopenjpeg --enable-libopus --enable-libmp3lame --enable-
libx264 --enable-libx265 --enable-libvpx --enable-libwebp --enable-libass
--enable-libfreetype --enable-fontconfig --enable-libtheora --enable-libvorbis
--enable-libsnappy --enable-libaom --enable-libvidstab --enable-libzimg
--enable-libsvtav1 --enable-libkvazaar --enable-version3 --pkg-config-
flags=--static --enable-ffplay --enable-postproc --enable-nonfree --enable-
neon --enable-runtime-cpudetect --disable-indev=qtkit --disable-
indev=x11grab_xcb
libavutil 58. 2.100 / 58. 2.100
libavcodec 60. 3.100 / 60. 3.100
libavformat 60. 3.100 / 60. 3.100
libavdevice 60. 1.100 / 60. 1.100
libavfilter 9. 3.100 / 9. 3.100
libswscale 7. 1.100 / 7. 1.100
libswresample 4. 10.100 / 4. 10.100
libpostproc 57. 1.100 / 57. 1.100
Input #0, image2, from
'/var/folders/p0/2fhrggzd43l1mhh6082h4r100000gn/T/chimovie_Zkq1-%05d.ppm':
Duration: 00:01:10.76, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 1340x1338, 25 fps, 25 tbr, 25 tbn
Stream mapping:
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))
Press [q] to stop, [?] for help
[libx264 @ 0x11de07620] using cpu capabilities: ARMv8 NEON
[libx264 @ 0x11de07620] profile High, level 4.0, 4:2:0, 8-bit
[libx264 @ 0x11de07620] 264 - core 164 r3075 66a5bc1 - H.264/MPEG-4 AVC codec
- Copyleft 2003-2021 - http://www.videolan.org/x264.html - options: cabac=1
ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00
mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11
fast_pskip=1 chroma_qp_offset=-2 threads=12 lookahead_threads=2
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to
'/Users/wang/Documents/Zeytuni_lab/fimbriae_movies_chimeraX/Mfa_turn.mp4':
Metadata:
encoder : Lavf60.3.100
Stream #0:0: Video: h264 (avc1 / 0x31637661), yuv420p(tv, progressive),
1340x1338, q=2-31, 25 fps, 12800 tbn
Metadata:
encoder : Lavc60.3.100 libx264
Side data:
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: N/A
frame= 0 fps=0.0 q=0.0 size= 0kB time=-577014:32:22.77 bitrate= -0.0kbits/s
speed=N/A frame= 29 fps=0.0 q=25.0 size= 512kB time=00:00:01.08
bitrate=3884.0kbits/s speed=2.16x frame= 87 fps= 86 q=25.0 size= 1792kB
time=00:00:03.40 bitrate=4317.8kbits/s speed=3.37x frame= 139 fps= 92 q=25.0
size= 3328kB time=00:00:05.44 bitrate=5011.6kbits/s speed=3.59x frame= 187
fps= 93 q=25.0 size= 5120kB time=00:00:07.40 bitrate=5668.0kbits/s speed=3.66x
av_interleaved_write_frame(): No space left on device
[out#0/mp4 @ 0x6000021ac3c0] Error muxing a packet
[out#0/mp4 @ 0x6000021ac3c0] Error writing trailer: No space left on device
frame= 190 fps= 77 q=-1.0 Lsize= 5120kB time=00:00:09.88 bitrate=4245.3kbits/s
speed=4.02x
video:5398kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: unknown
[libx264 @ 0x11de07620] frame I:1 Avg QP: 7.79 size: 79345
[libx264 @ 0x11de07620] frame P:63 Avg QP:22.33 size: 56385
[libx264 @ 0x11de07620] frame B:186 Avg QP:29.22 size: 21853
[libx264 @ 0x11de07620] consecutive B-frames: 0.8% 0.0% 0.0% 99.2%
[libx264 @ 0x11de07620] mb I I16..4: 78.4% 10.3% 11.3%
[libx264 @ 0x11de07620] mb P I16..4: 0.5% 0.5% 2.3% P16..4: 4.8% 8.1% 11.9%
0.0% 0.0% skip:72.0%
[libx264 @ 0x11de07620] mb B I16..4: 0.0% 0.1% 0.0% B16..8: 7.0% 7.2% 7.3%
direct: 3.2% skip:75.3% L0:36.1% L1:40.6% BI:23.4%
[libx264 @ 0x11de07620] 8x8 transform intra:15.9% inter:18.6%
[libx264 @ 0x11de07620] coded y,uvDC,uvAC intra: 49.3% 53.6% 51.7% inter: 9.9%
6.3% 2.6%
[libx264 @ 0x11de07620] i16 v,h,dc,p: 91% 5% 3% 0%
[libx264 @ 0x11de07620] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 15% 5% 70% 1% 2% 2% 2%
2% 2%
[libx264 @ 0x11de07620] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 16% 14% 14% 7% 11% 11%
9% 9% 8%
[libx264 @ 0x11de07620] i8c dc,h,v,p: 66% 13% 14% 7%
[libx264 @ 0x11de07620] Weighted P-Frames: Y:0.0% UV:0.0%
[libx264 @ 0x11de07620] ref P L0: 52.3% 24.5% 15.7% 7.6%
[libx264 @ 0x11de07620] ref B L0: 87.2% 10.3% 2.6%
[libx264 @ 0x11de07620] ref B L1: 93.9% 6.1%
[libx264 @ 0x11de07620] kb/s:6157.01
Conversion failed!
\-----------------------------
> movie encode
> /Users/wang/Documents/Zeytuni_lab/fimbriae_movies_chimeraX/Mfa_turn.mp4
Movie saved to /Users/wang/.../fimbriae_movies_chimeraX/Mfa_turn.mp4
> stop
> movie record
> hide #5 target m
> fly p1 p2
fly: Nothing displayed to calculate center of rotation
> show #3.1 models
> show #!5 models
> show #3.2 models
> stop
[Repeated 2 time(s)]
> movie stop
> view p1
> fly p1 p2 4
> fly p1 p2
> fly p1 p 2 60
fly: Unknown position name "p"
> fly p1 p2 2 60
> fly p1 p2 4 60
> fly p1 p2 4 120
> fly p1 p2 8 120
> fly p1 10 p2
> fly p1 20 p2
> view p1
> movie record
> hide #5 target m
> fly p1 20 p2
> roll y 1 450
> wait
> fly p3 90 p4 90 p1
> wait 240
> hide #3.1
> show #5 target m
> wait
wait requires a frame count argument unless motion is in progress
> fly p1 30 p5 60 p6 60 p7 360 p8 360 p7 180 p9 180 p10 180 p11 180 p7 600 p12
> 240 p13 120 p14 120 p15
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/movie.py", line 176, in capture_image
i.save(save_path, self.img_fmt)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 2439, in save
save_handler(self, fp, filename)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/PpmImagePlugin.py", line 329, in _save
ImageFile._save(im, fp, [("raw", (0, 0) + im.size, 0, (rawmode, 0, 1))])
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/ImageFile.py", line 538, in _save
_encode_tile(im, fp, tile, bufsize, fh)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/ImageFile.py", line 565, in _encode_tile
errcode = encoder.encode_to_file(fh, bufsize)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: [Errno 28] No space left on device
Error processing trigger "frame drawn":
OSError: [Errno 28] No space left on device
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/ImageFile.py", line 565, in _encode_tile
errcode = encoder.encode_to_file(fh, bufsize)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> movie encode
> /Users/wang/Documents/Zeytuni_lab/fimbriae_movies_chimeraX/Mfa_turn.mp4
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 351, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 456, in add
self._history.enqueue((item, typed))
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 182, in enqueue
self.save()
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 212, in save
self._history.save(self._queue)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 119, in save
with SaveTextFile(self._filename) as f:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 191, in __init__
SaveFile.__init__(self, filename, open=open_text, critical=critical)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 85, in __init__
self._f = open(self._tmp_filename)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 190, in open_text
return open(filename, 'w', newline=newline, encoding=encoding)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: [Errno 28] No space left on device: '/Users/wang/Library/Application
Support/ChimeraX/commands.1749.tmp'
Error processing trigger "command started":
OSError: [Errno 28] No space left on device: '/Users/wang/Library/Application
Support/ChimeraX/commands.1749.tmp'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 190, in open_text
return open(filename, 'w', newline=newline, encoding=encoding)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
/Applications/ChimeraX-1.7.1.app/Contents/bin/ffmpeg -r 25 -i
/var/folders/p0/2fhrggzd43l1mhh6082h4r100000gn/T/chimovie_PT49-%05d.ppm -vf
crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt
yuv420p -crf 20
/Users/wang/Documents/Zeytuni_lab/fimbriae_movies_chimeraX/Mfa_turn.mp4
stdout:
stderr:
ffmpeg version 6.0 Copyright (c) 2000-2023 the FFmpeg developers
built with Apple clang version 13.1.6 (clang-1316.0.21.2.5)
configuration: --prefix=/Volumes/tempdisk/sw --extra-cflags=-fno-stack-check
--arch=arm64 --cc=/usr/bin/clang --enable-gpl --enable-libvmaf --enable-
libbluray --enable-libopenjpeg --enable-libopus --enable-libmp3lame --enable-
libx264 --enable-libx265 --enable-libvpx --enable-libwebp --enable-libass
--enable-libfreetype --enable-fontconfig --enable-libtheora --enable-libvorbis
--enable-libsnappy --enable-libaom --enable-libvidstab --enable-libzimg
--enable-libsvtav1 --enable-libkvazaar --enable-version3 --pkg-config-
flags=--static --enable-ffplay --enable-postproc --enable-nonfree --enable-
neon --enable-runtime-cpudetect --disable-indev=qtkit --disable-
indev=x11grab_xcb
libavutil 58. 2.100 / 58. 2.100
libavcodec 60. 3.100 / 60. 3.100
libavformat 60. 3.100 / 60. 3.100
libavdevice 60. 1.100 / 60. 1.100
libavfilter 9. 3.100 / 9. 3.100
libswscale 7. 1.100 / 7. 1.100
libswresample 4. 10.100 / 4. 10.100
libpostproc 57. 1.100 / 57. 1.100
Input #0, image2, from
'/var/folders/p0/2fhrggzd43l1mhh6082h4r100000gn/T/chimovie_PT49-%05d.ppm':
Duration: 00:01:22.68, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 1340x1338, 25 fps, 25 tbr, 25 tbn
/Users/wang/Documents/Zeytuni_lab/fimbriae_movies_chimeraX/Mfa_turn.mp4: No
space left on device
An error occurred during encoding. See Reply Log for details.
Error during MPEG encoding:
\-----------------------------
Exit value: 1
Error message:
stdout:
stderr:
ffmpeg version 6.0 Copyright (c) 2000-2023 the FFmpeg developers
built with Apple clang version 13.1.6 (clang-1316.0.21.2.5)
configuration: --prefix=/Volumes/tempdisk/sw --extra-cflags=-fno-stack-check
--arch=arm64 --cc=/usr/bin/clang --enable-gpl --enable-libvmaf --enable-
libbluray --enable-libopenjpeg --enable-libopus --enable-libmp3lame --enable-
libx264 --enable-libx265 --enable-libvpx --enable-libwebp --enable-libass
--enable-libfreetype --enable-fontconfig --enable-libtheora --enable-libvorbis
--enable-libsnappy --enable-libaom --enable-libvidstab --enable-libzimg
--enable-libsvtav1 --enable-libkvazaar --enable-version3 --pkg-config-
flags=--static --enable-ffplay --enable-postproc --enable-nonfree --enable-
neon --enable-runtime-cpudetect --disable-indev=qtkit --disable-
indev=x11grab_xcb
libavutil 58. 2.100 / 58. 2.100
libavcodec 60. 3.100 / 60. 3.100
libavformat 60. 3.100 / 60. 3.100
libavdevice 60. 1.100 / 60. 1.100
libavfilter 9. 3.100 / 9. 3.100
libswscale 7. 1.100 / 7. 1.100
libswresample 4. 10.100 / 4. 10.100
libpostproc 57. 1.100 / 57. 1.100
Input #0, image2, from
'/var/folders/p0/2fhrggzd43l1mhh6082h4r100000gn/T/chimovie_PT49-%05d.ppm':
Duration: 00:01:22.68, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 1340x1338, 25 fps, 25 tbr, 25 tbn
/Users/wang/Documents/Zeytuni_lab/fimbriae_movies_chimeraX/Mfa_turn.mp4: No
space left on device
\-----------------------------
> movie encode
> /Users/wang/Documents/Zeytuni_lab/fimbriae_movies_chimeraX/Mfa_turn.mp4
Movie saved to /Users/wang/.../fimbriae_movies_chimeraX/Mfa_turn.mp4
> save
> /Users/wang/Documents/Zeytuni_lab/fimbriae_movies_chimeraX/movie_Mfa1_views_draft1.cxs
——— End of log from Tue Oct 8 19:48:35 2024 ———
opened ChimeraX session
> view p1
> hide #!3 models
> show #!3 models
> volume #3
> volume #3 style surface
> hide #5.2 models
> show #5.2 models
> hide #5 target m
> fly p1 20 p2
> roll y 1 450
> wait
> fly p3 60 p4 60 p1
> wait 240
> hide #3.1
> show #5 target m
> wait
wait requires a frame count argument unless motion is in progress
> fly p1 30 p5 60 p6 60 p7 180 p8 180 p7 90 p9 90 p10 90 p11 90 p7 360 p12 120
> p13 60 p14 60 p15
> stop
> movie record
> hide #5 target m
> fly p1 20 p2
fly: Nothing displayed to calculate center of rotation
> movie stop
> show #3.1 models
> show #3.2 models
> show #!5 models
> show #5.1 models
> show #5.2 models
> show #5.3 models
> show #5.4 models
> show #5.5 models
> view p1
> movie record
> hide #5 target m
> fly p1 20 p2
> roll y 1 450
> wait
> fly p3 60 p4 60 p1
> wait 240
> hide #3.1
> show #5 target m
> wait
wait requires a frame count argument unless motion is in progress
> fly p1 30 p5 60 p6 60 p7 180 p8 180 p7 90 p9 90 p10 90 p11 90 p7 360 p12 120
> p13 60 p14 60 p15
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/movie.py", line 176, in capture_image
i.save(save_path, self.img_fmt)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/Image.py", line 2439, in save
save_handler(self, fp, filename)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/PpmImagePlugin.py", line 329, in _save
ImageFile._save(im, fp, [("raw", (0, 0) + im.size, 0, (rawmode, 0, 1))])
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/ImageFile.py", line 538, in _save
_encode_tile(im, fp, tile, bufsize, fh)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/ImageFile.py", line 565, in _encode_tile
errcode = encoder.encode_to_file(fh, bufsize)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: [Errno 28] No space left on device
Error processing trigger "frame drawn":
OSError: [Errno 28] No space left on device
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/PIL/ImageFile.py", line 565, in _encode_tile
errcode = encoder.encode_to_file(fh, bufsize)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> movie stop
> stop
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 351, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 456, in add
self._history.enqueue((item, typed))
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 182, in enqueue
self.save()
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 212, in save
self._history.save(self._queue)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/history.py", line 119, in save
with SaveTextFile(self._filename) as f:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 191, in __init__
SaveFile.__init__(self, filename, open=open_text, critical=critical)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 85, in __init__
self._f = open(self._tmp_filename)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 190, in open_text
return open(filename, 'w', newline=newline, encoding=encoding)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: [Errno 28] No space left on device: '/Users/wang/Library/Application
Support/ChimeraX/commands.7363.tmp'
Error processing trigger "command started":
OSError: [Errno 28] No space left on device: '/Users/wang/Library/Application
Support/ChimeraX/commands.7363.tmp'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 190, in open_text
return open(filename, 'w', newline=newline, encoding=encoding)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> view p1
> show #3.1 models
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: MGN63LL/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 9 hours, 2 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
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
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 13 months ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Movie recording: No space left on device |
comment:2 by , 13 months ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
Note:
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User ran out of disk space recording a movie.