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Opened 7 months ago
Closed 7 months ago
#17236 closed defect (duplicate)
MemoryError saving session
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "F:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250201-J6703
> interaction Cloop width 1.2 thick 0.3 Trans 5.cxs"
Opened 20250117 cryosparc_P119_J6703_008_volume_map_sharp (1).mrc as #1, grid
size 440,440,440, pixel 0.73, shown at level 0.264, step 1, values float32
Opened 20250119 P119_J6703_max_resample_map_sharp_local.mrc as #2, grid size
440,440,440, pixel 0.73, shown at level 0.206, step 1, values float32
Log from Sat Feb 1 19:38:51 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Fri Jan 24 23:31:29 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250124-J6703
> interaction.cxs"
Opened 20250117 cryosparc_P119_J6703_008_volume_map_sharp (1).mrc as #1, grid
size 440,440,440, pixel 0.73, shown at level 0.192, step 1, values float32
Opened 20250119 P119_J6703_max_resample_map_sharp_local.mrc as #2, grid size
440,440,440, pixel 0.73, shown at level 0.25, step 1, values float32
Log from Fri Jan 24 13:24:45 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250123 WT-1
> interaction.cxs"
Opened 20250117 cryosparc_P119_J6703_008_volume_map_sharp (1).mrc as #1, grid
size 440,440,440, pixel 0.73, shown at level 0.149, step 1, values float32
Opened 20250119 P119_J6703_max_resample_map_sharp_local.mrc as #2, grid size
440,440,440, pixel 0.73, shown at level 0.295, step 1, values float32
Log from Thu Jan 23 22:46:13 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250122 WT-1
> interaction.cxs"
Opened 20250117 cryosparc_P119_J6703_008_volume_map_sharp (1).mrc as #1, grid
size 440,440,440, pixel 0.73, shown at level 0.197, step 1, values float32
Opened 20250119 P119_J6703_max_resample_map_sharp_local.mrc as #2, grid size
440,440,440, pixel 0.73, shown at level 0.295, step 1, values float32
Log from Thu Jan 23 14:30:39 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250120 WT-1
> interaction.cxs"
Opened 20250117 cryosparc_P119_J6703_008_volume_map_sharp (1).mrc as #1, grid
size 440,440,440, pixel 0.73, shown at level 0.197, step 1, values float32
Opened 20250119 P119_J6703_max_resample_map_sharp_local.mrc as #2, grid size
440,440,440, pixel 0.73, shown at level 0.295, step 1, values float32
Log from Wed Jan 22 21:18:32 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250120 WT-2 interaction
> figerloop.cxs"
Opened 20250117 cryosparc_P119_J6703_008_volume_map_sharp (1).mrc as #1, grid
size 440,440,440, pixel 0.73, shown at level 0.197, step 1, values float32
Opened 20250119 P119_J6703_max_resample_map_sharp_local.mrc as #2, grid size
440,440,440, pixel 0.73, shown at level 0.295, step 1, values float32
Log from Tue Jan 21 13:32:42 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250120 WT-2 interaction
> figerloop.cxs"
Opened 20250117 cryosparc_P119_J6703_008_volume_map_sharp (1).mrc as #1, grid
size 440,440,440, pixel 0.73, shown at level 0.25, step 1, values float32
Opened 20250119 P119_J6703_max_resample_map_sharp_local.mrc as #2, grid size
440,440,440, pixel 0.73, shown at level 0.255, step 1, values float32
Log from Mon Jan 20 23:43:34 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250120-2 WT-1.cxs"
Opened 20250117 cryosparc_P119_J6703_008_volume_map_sharp (1).mrc as #1, grid
size 440,440,440, pixel 0.73, shown at level 0.298, step 1, values float32
Opened 20250119 P119_J6703_max_resample_map_sharp_local.mrc as #2, grid size
440,440,440, pixel 0.73, shown at level 0.316, step 1, values float32
Log from Mon Jan 20 13:53:21 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-3 WT-1.cxs"
Opened 20250117 cryosparc_P119_J6703_008_volume_map_sharp (1).mrc as #1, grid
size 440,440,440, pixel 0.73, shown at level 0.28, step 1, values float32
Log from Sat Jan 18 22:24:15 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-3 WT-1.cxs"
Opened 20250117 cryosparc_P119_J6703_008_volume_map_sharp (1).mrc as #1, grid
size 440,440,440, pixel 0.73, shown at level 0.28, step 1, values float32
Log from Sat Jan 18 17:41:24 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-3 WT-1.cxs"
Opened 20250117 cryosparc_P119_J6703_008_volume_map_sharp (1).mrc as #1, grid
size 440,440,440, pixel 0.73, shown at level 0.28, step 1, values float32
Log from Sat Jan 18 17:19:35 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-3 WT-1.cxs"
Opened 20250117 cryosparc_P119_J6703_008_volume_map_sharp (1).mrc as #1, grid
size 440,440,440, pixel 0.73, shown at level 0.28, step 1, values float32
Log from Sat Jan 18 16:30:36 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-3.cxs"
Opened 20250117 cryosparc_P119_J6703_008_volume_map_sharp (1).mrc as #1, grid
size 440,440,440, pixel 0.73, shown at level 0.298, step 1, values float32
Log from Sat Jan 18 15:02:23 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:\PTH1R-Arrestin paper\2024年1月16日投稿\2025New\20250118-2.cxs" format
> session
Opened 20250117 cryosparc_P119_J6703_008_volume_map_sharp (1).mrc as #4, grid
size 440,440,440, pixel 0.73, shown at level 0.23, step 1, values float32
Opened 20250117 WT_P119_J6710_resample_map_sharp_local.mrc as #6, grid size
440,440,440, pixel 0.73, shown at level 0.299, step 1, values float32
Log from Sat Jan 18 14:41:15 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-1.cxs"
Opened P119_J4383_009 20241123.mrc as #1, grid size 440,440,440, pixel 0.73,
shown at level 0.24, step 1, values float32
Opened P119_J4383_009 20241123.mrc as #3, grid size 440,440,440, pixel 0.73,
shown at level 0.106, step 2, values float32
Opened 20250117 cryosparc_P119_J6703_008_volume_map_sharp (1).mrc as #4, grid
size 440,440,440, pixel 0.73, shown at level 0.194, step 1, values float32
Opened 20250117 WT_P119_J6710_resample_map_sharp_local.mrc as #6, grid size
440,440,440, pixel 0.73, shown at level 0.299, step 1, values float32
Log from Sat Jan 18 13:19:19 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:/PTH1R-Arrestin paper/figs20231123/cxc/20241201-1.cxs"
Opened P119_J4383_009 20241123.mrc as #1, grid size 440,440,440, pixel 0.73,
shown at level 0.24, step 1, values float32
Opened P119_J4383_009 20241123.mrc as #3, grid size 440,440,440, pixel 0.73,
shown at level 0.106, step 2, values float32
Log from Sun Dec 1 21:41:24 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:\PTH1R-Arrestin paper\figs20231123\cxc\20241201-1.cxs" format
> session
Opened P119_J4383_009 20241123.mrc as #1, grid size 440,440,440, pixel 0.73,
shown at level 0.106, step 2, values float32
Log from Sun Dec 1 20:42:31 2024 Startup Messages
---
warnings | Data format provider 'LAMMPS coordinates' supplied unknown keywords
with format description: {'default_for': '.data'}
Data format provider 'LAMMPS trajectory' supplied unknown keywords with format
description: {'default_for': '.dump'}
Data format provider 'LAMMPS coordinates' supplied unknown keywords with
format description: {'default_for': '.data'}
Data format provider 'LAMMPS trajectory' supplied unknown keywords with format
description: {'default_for': '.dump'}
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:/PTH1R-Arrestin paper/map/P119_J4383_009 20241123.mrc"
Opened P119_J4383_009 20241123.mrc as #1, grid size 440,440,440, pixel 0.73,
shown at level 0.106, step 2, values float32
> open "D:/PTH1R-Arrestin paper/map/arrestin_R_lig_4383-coot-1 241129.pdb"
Chain information for arrestin_R_lig_4383-coot-1 241129.pdb #2
---
Chain | Description
B | No description available
C | No description available
E | No description available
L | No description available
R | No description available
> set bgColor white
> hide atoms
> show cartoons
> hide #!1 models
> select /B
2656 atoms, 2710 bonds, 2 pseudobonds, 334 residues, 2 models selected
> ui tool show "Color Actions"
> color sel salmon
> lighting simple
> lighting soft
> lighting full
> lighting simple
> select /L
278 atoms, 283 bonds, 33 residues, 1 model selected
> ui tool show "Color Actions"
> color sel goldenrod
> select /E
1587 atoms, 1621 bonds, 1 pseudobond, 207 residues, 2 models selected
> color sel pink
> select /E
1587 atoms, 1621 bonds, 1 pseudobond, 207 residues, 2 models selected
> select /R
2780 atoms, 2850 bonds, 4 pseudobonds, 342 residues, 2 models selected
> color sel forest green
> select /L
278 atoms, 283 bonds, 33 residues, 1 model selected
> select /B
2656 atoms, 2710 bonds, 2 pseudobonds, 334 residues, 2 models selected
> select /C
1551 atoms, 1591 bonds, 1 pseudobond, 205 residues, 2 models selected
> color sel plum
> select clear
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20241201-1.cxs"
——— End of log from Sun Dec 1 20:42:31 2024 ———
opened ChimeraX session
> select /R
2780 atoms, 2850 bonds, 4 pseudobonds, 342 residues, 2 models selected
> ui tool show "Color Actions"
> color sel lime green
> hide #2.1 models
> lighting shadows true
> lighting flat
[Repeated 1 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting full
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> cartoon style width 1.5 thickness 0.3
> cartoon style width 2 thickness 0.5
> show #!1 models
> volume #1 step 1
> color zone #2 near all distance 7
color zone: No surfaces specified.
> color zone #1 near all distance 7
> volume #1 level 0.1968
> color zone #1 near all distance 7
> volume #1 level 0.2467
> hide #!2 models
> surface dust #1 size 20
> volume #1 level 0.2059
> volume #1 level 0.2195
> volume #1 level 0.2467
> volume #1 level 0.2
> volume #1 level 0.22
> volume #1 level 0.23
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #1 level 0.1394
> volume #1 level 0.2
> volume #1 level 0.22
> hide #!2 models
> volume #1 level 0.24
> volume #1 level 0.23
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20241201-1.cxs"
> volume #1 level 0.24
> volume #1 level 0.25
> volume #1 level 0.23
> volume #1 level 0.26
> volume #1 level 0.24
> hide #!1 models
> show #!2 models
> select clear
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #1 level 0.25
> volume #1 level 0.23
> volume #1 level 0.235
> volume #1 level 0.24
> open "D:/PTH1R-Arrestin paper/map/P119_J4383_009 20241123.mrc"
Opened P119_J4383_009 20241123.mrc as #3, grid size 440,440,440, pixel 0.73,
shown at level 0.106, step 2, values float32
> volume #3 step 1
> volume #3 step 8
> volume #3 step 4
> volume #3 step 2
> hide #!3 models
> hide #!1 models
> show #!2 models
> open "D:/PTH1R-Arrestin paper/map/arrestin_R_lig_4383-coot-2 20241201.pdb"
Chain information for arrestin_R_lig_4383-coot-2 20241201.pdb #4
---
Chain | Description
B | No description available
C | No description available
E | No description available
L | No description available
R | No description available
> hide atoms
> show cartoons
> hide #!2 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!2 models
> show #!4 models
> select add #4
8860 atoms, 9063 bonds, 9 pseudobonds, 1122 residues, 2 models selected
> close #4
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!1 models
> save "D:/PTH1R-Arrestin paper/figs20231123/20240120/20241201-1.png" width
> 2000 height 1245 supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> save "D:/PTH1R-Arrestin paper/figs20231123/20240120/20241201-2.png" width
> 2000 height 1245 supersample 3 transparentBackground true
> show #!3 models
> hide #!2 models
> color #3 light gray
[Repeated 1 time(s)]
> transparency #3 50
> save "D:/PTH1R-Arrestin paper/figs20231123/20240120/20241201-3.png" width
> 2000 height 1245 supersample 3 transparentBackground true
> hide #!3 models
> show #!1 models
> save "D:/PTH1R-Arrestin paper/figs20231123/20240120/20241201-1.png" width
> 2000 height 1245 supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> save "D:/PTH1R-Arrestin paper/figs20231123/20240120/20241201-2.png" width
> 2000 height 1245 supersample 3 transparentBackground true
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20241201-1.cxs"
——— End of log from Sun Dec 1 21:41:24 2024 ———
opened ChimeraX session
> show #!3 models
> hide #!3 models
> show #!1 models
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250117
> cryosparc_P119_J6703_008_volume_map_sharp (1).mrc"
Opened 20250117 cryosparc_P119_J6703_008_volume_map_sharp (1).mrc as #4, grid
size 440,440,440, pixel 0.73, shown at level 0.0973, step 2, values float32
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250117
> WT_P119_J6703_arrestin_R-Fab-coot-0.pdb"
Chain information for 20250117 WT_P119_J6703_arrestin_R-Fab-coot-0.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
E | No description available
L | No description available
R | No description available
> hide #!2 models
> hide #!1 models
> surface dust #4 size 7.3
> volume #4 step 1
> volume #4 level 0.3605
> hide #!5 atoms
> show #!5 cartoons
> volume #4 level 0.2903
> hide #!5 models
> volume #4 level 0.264
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!5 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-1.cxs"
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-1.cxs"
> includeMaps true
> show #!4 models
> hide #!4 models
> show #!4 models
> transparency #4-5 30
> show #!2 models
> hide #!4 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #!1 models
> show #!5 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> hide #!1 models
> show #!4 models
> show #!5 models
> hide #!4 models
> show #!2 models
> hide #!5 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!4 models
> show #!2 models
> hide #!4 models
> show #!5 models
> hide #!2 models
> show #!4 models
> volume #4 level 0.1938
> hide #!5 models
> hide #!4 models
> show #!5 models
> select add #5/R:505
16 atoms, 15 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 3 residues, 1 model selected
> select add #5/R:503
64 atoms, 62 bonds, 4 residues, 1 model selected
> select up
111 atoms, 111 bonds, 7 residues, 1 model selected
> select add #5/R:507
125 atoms, 124 bonds, 8 residues, 1 model selected
> select add #5/R:508
132 atoms, 130 bonds, 9 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 132 atom styles
> color sel byhetero
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> select add #5/B:14
143 atoms, 140 bonds, 10 residues, 1 model selected
> select add #5/B:13
154 atoms, 150 bonds, 11 residues, 1 model selected
> select add #5/B:12
164 atoms, 159 bonds, 12 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 164 atom styles
> select add #5/B:164
180 atoms, 174 bonds, 13 residues, 1 model selected
> select add #5/B:165
204 atoms, 197 bonds, 14 residues, 1 model selected
> select add #5/B:163
215 atoms, 207 bonds, 15 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 215 atom styles
> show #!4 models
> select clear
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250117
> WT_P119_J6710_resample_map_sharp_local.mrc"
Opened 20250117 WT_P119_J6710_resample_map_sharp_local.mrc as #6, grid size
440,440,440, pixel 0.73, shown at level 0.151, step 2, values float32
> hide #!5 models
> hide #!4 models
> volume #6 step 1
> volume #6 level 0.4207
> surface dust #6 size 7.3
> show #!5 models
> transparency #5-6 30
> show #!4 models
> hide #!5 models
> hide #!4 models
> volume #6 level 0.3667
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!4 models
> hide #!4 models
> volume #6 level 0.2992
> hide #!6 models
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!6 models
> hide #!4 models
> show #!4 models
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-1.cxs"
——— End of log from Sat Jan 18 13:19:19 2025 ———
opened ChimeraX session
> volume #4 level 0.1666
> hide #!5 models
> show #!5 models
> hide #!4 models
> select add #5/B:294
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> show #!4 models
> surface dust #4 size 7.3
> select clear
> delete H
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-1.cxs"
> hide #!4 models
> show #!4 models
> volume #4 level 0.2481
> hide #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> select #5/B
2755 atoms, 2813 bonds, 2 pseudobonds, 346 residues, 2 models selected
> ui tool show "Color Actions"
> color sel salmon
> select clear
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!2 models
> cartoon style width 2 thickness 0.5
> undo
> hide #!5 models
> cartoon style width 2 thickness 0.5
> undo
> cartoon style width 2 thickness 0.3
> undo
> cartoon style width 1.5 thickness 0.3
> undo
> cartoon style width 2 thickness 0.5
> show #!5 models
> cartoon style width 2 thickness 0.5
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #5/L
279 atoms, 284 bonds, 33 residues, 1 model selected
> ui tool show "Color Actions"
> color sel goldenrod
> hide #!2 models
> show #!4 models
> volume #4 level 0.3929
> volume #4 level 0.3658
> show sel atoms
> style sel stick
Changed 279 atom styles
> color sel byhetero
> select add #5/A:429
291 atoms, 296 bonds, 34 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 291 atom styles
> select add #5/A:426
296 atoms, 300 bonds, 35 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 296 atom styles
> select add #5/A:428
303 atoms, 307 bonds, 36 residues, 1 model selected
> select clear
> select #4
2 models selected
> select clear
> hide #!4 models
> select add #5/A:427
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> show #!4 models
> hide #!4 models
> select add #5/A:361
21 atoms, 21 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 21 atom styles
> select add #5/A:365
28 atoms, 27 bonds, 3 residues, 1 model selected
> select add #5/A:364
37 atoms, 35 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 37 atom styles
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> select #5/C
1552 atoms, 1592 bonds, 1 pseudobond, 205 residues, 2 models selected
> ui tool show "Color Actions"
> color sel plum
> show #!2 models
> hide #!2 models
> select clear
> select #5/E
1588 atoms, 1622 bonds, 1 pseudobond, 207 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light pink
[Repeated 1 time(s)]
> select clear
> select #5/A
2403 atoms, 2469 bonds, 4 pseudobonds, 293 residues, 2 models selected
> ui tool show "Color Actions"
> color sel lime green
> color sel forest green
> color sel medium sea green
> color sel sea green
> color sel lime
> color sel dodger blue
> color sel cornflower blue
> color sel light sea green
> color sel medium turquoise
> color sel turquoise
> select clear
> select #5/A:199
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A
2403 atoms, 2469 bonds, 4 pseudobonds, 293 residues, 2 models selected
> color sel cadet blue
> color sel steel blue
> color sel teal
> color sel dark cyan
> color sel sea green
> color sel medium sea green
> color sel forest green
> select clear
> hide #!5 atoms
> select #5/A
2403 atoms, 2469 bonds, 4 pseudobonds, 293 residues, 2 models selected
> color sel indian red
> color sel medium violet red
> color sel deep sky blue
> color sel sea green
> color sel medium sea green
> color sel light sea green
> color sel medium turquoise
> color sel light sea green
[Repeated 1 time(s)]
> help help:user
> ui tool show "Color Actions"
[Repeated 1 time(s)]
> color (#!5 & sel) #00ced1ff
> select clear
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-1.cxs"
> hide #5.1 models
> select clear
> show #!4 models
> volume #4 level 0.23
> color zone #4 near all distance 7
> close #2
> close #1
> close #3
> color zone #4 near all distance 7
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-2.cxs"
> includeMaps true
——— End of log from Sat Jan 18 14:41:15 2025 ———
opened ChimeraX session
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250117
> cryosparc_P119_J6703_008_volume_map_sharp (1).mrc"
Opened 20250117 cryosparc_P119_J6703_008_volume_map_sharp (1).mrc as #1, grid
size 440,440,440, pixel 0.73, shown at level 0.0973, step 2, values float32
> hide #!1 models
> hide #!4 models
> hide #!5 models
> close #1
> show #!4 models
> show #!6 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> color zone #4 near all distance 7
> hide #!6 models
> volume #6 level 0.4039
> volume #4 level 0.3704
> hide #!4 models
> show #!5 models
> select add /R:505
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add /R:504
17 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 27 bonds, 3 residues, 1 model selected
> select add /R:507
36 atoms, 34 bonds, 4 residues, 1 model selected
> select down
36 atoms, 34 bonds, 4 residues, 1 model selected
> select up
40 atoms, 39 bonds, 5 residues, 1 model selected
> select add /R:503
51 atoms, 49 bonds, 6 residues, 1 model selected
> select up
78 atoms, 78 bonds, 9 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #21b6aaff
> ui tool show "Color Actions"
> color sel #0000ccff
> color sel #00ced1ff
> select clear
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> close #4
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250117
> cryosparc_P119_J6703_008_volume_map_sharp (1).mrc"
Opened 20250117 cryosparc_P119_J6703_008_volume_map_sharp (1).mrc as #1, grid
size 440,440,440, pixel 0.73, shown at level 0.0973, step 2, values float32
> hide #!6 models
> hide #!1 models
> show #!6 models
> close #6
> show #!1 models
> show #!5 models
> color zone #1 near all distance 7
> surface dust #1 size 7.3
> volume #1 step 1
> volume #1 level 0.4746
> hide #!1 models
> hide atoms
> show cartoons
> show #!1 models
> color zone #1 near all distance 7
> select /L
279 atoms, 284 bonds, 33 residues, 1 model selected
> color sel orange red
> select clear
> color zone #1 near all distance 7
> select /L
279 atoms, 284 bonds, 33 residues, 1 model selected
> ui tool show "Color Actions"
> color sel goldenrod
> color zone #1 near all distance 7
> select clear
> volume #1 level 0.3605
> hide #!5 models
> volume #1 level 0.2464
> volume #1 level 0.2
> volume #1 level 0.25
> volume #1 level 0.24
> volume #1 level 0.26
> surface dust #1 size 20
> volume #1 level 0.3214
> volume #1 level 0.25
> volume #1 level 0.26
> volume #1 level 0.27
> volume #1 level 0.2086
> volume #1 level 0.25
> volume #1 level 0.24
> surface dust #1 size 20
> volume #1 level 0.25
> volume #1 level 0.26
> volume #1 level 0.339
> volume #1 level 0.3
> volume #1 level 0.28
> show #!5 models
> volume #1 level 0.27
> hide #!5 models
> volume #1 level 0.28
> volume #1 level 0.4204
> volume #1 level 0.2975
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-3.cxs"
> includeMaps true
——— End of log from Sat Jan 18 15:02:23 2025 ———
opened ChimeraX session
> show #!5 models
> hide #!1 models
> select /A
2403 atoms, 2469 bonds, 4 pseudobonds, 293 residues, 2 models selected
> ui tool show "Color Actions"
> color sel deep sky blue
> select clear
> show #!1 models
> color zone #1 near all distance 7
> hide #!1 models
> select add /R:506
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
28 atoms, 27 bonds, 3 residues, 1 model selected
> select down
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
28 atoms, 27 bonds, 3 residues, 1 model selected
> select add /R:507
36 atoms, 34 bonds, 4 residues, 1 model selected
> select down
36 atoms, 34 bonds, 4 residues, 1 model selected
> select up
40 atoms, 39 bonds, 5 residues, 1 model selected
> select add /R:503
51 atoms, 49 bonds, 6 residues, 1 model selected
> select up
78 atoms, 78 bonds, 9 residues, 1 model selected
> ui tool show "Color Actions"
> color sel deep sky blue
> select clear
> show #!1 models
> color zone #1 near all distance 7
> hide #!1 models
> show #!1 models
> hide #!5 models
> volume #1 level 0.3
> volume #1 level 0.26
> volume #1 level 0.27
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-3 WT-1.cxs"
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting full
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting full
[Repeated 1 time(s)]
> lighting flat
[Repeated 2 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting full
> graphics silhouettes false
> ui tool show "Side View"
> lighting shadows false
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> volume #1 level 0.26
> volume #1 level 0.28
> volume #1 level 0.29
> volume #1 level 0.28
> hide #!1 models
> show #!5 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-3 WT-1.cxs"
> show #!1 models
> hide #!5 models
> graphics silhouettes false
> lighting simple
> lighting soft
> hide #!1 models
> show #!5 models
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting full
> lighting shadows false
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> show #!1 models
> hide #!5 models
> lighting simple
> lighting soft
> lighting flat
[Repeated 2 time(s)]
> lighting full
> lighting shadows false
> lighting simple
> lighting full
> lighting shadows false
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-3 WT-1.cxs"
——— End of log from Sat Jan 18 16:30:36 2025 ———
opened ChimeraX session
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting simple
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-WT-1.png" width
> 2000 height 1245 supersample 3 transparentBackground true
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-3 WT-1.cxs"
——— End of log from Sat Jan 18 17:19:35 2025 ———
opened ChimeraX session
> volume #1 level 0.27
> volume #1 level 0.28
> volume #1 level 0.29
> hide #!1 models
> show #!5 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> volume #1 level 0.28
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!1 models
> lighting full
> hide #!1 models
> show #!5 models
> lighting shadows false
> hide #!5 models
> show #!1 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-3 WT-1.cxs"
——— End of log from Sat Jan 18 17:41:24 2025 ———
opened ChimeraX session
> ui tool show "Side View"
> show #!5 models
> hide #!5 models
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-WT-1-1.png"
> width 2000 height 1245 supersample 3 transparentBackground true
> hide #!1 models
> show #!5 models
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-WT-2-1.png"
> width 2000 height 1245 supersample 3 transparentBackground true
> show #!1 models
> hide #!1 models
> hide #!5 models
> show #!1 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-WT-1-1.png"
> width 2000 height 1245 supersample 3 transparentBackground true
> hide #!1 models
> show #!5 models
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-WT-1-2.png"
> width 2000 height 1245 supersample 3 transparentBackground true
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-3 WT-1.cxs"
——— End of log from Sat Jan 18 22:24:15 2025 ———
opened ChimeraX session
> show #!1 models
> transparency #1#!5 30
> transparency #1#!5 50
> show atoms
> style stick
Changed 8655 atom styles
> hide atoms
> hide #!5 models
> show #!5 models
> hide #!1 models
> select add /A:384
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> style sel stick
Changed 7 atom styles
> select add /A:385
15 atoms, 13 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 15 atom styles
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> select add /A:387
22 atoms, 19 bonds, 3 residues, 1 model selected
> select add /A:388
31 atoms, 27 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 31 atom styles
> show #!1 models
> select clear
> volume #1 level 0.473
> volume #1 level 0.3063
> volume #1 level 0.1308
> volume #1 level 0.2975
> transparency #1#!5 30
> hide #!1 models
> show #!1 models
> volume #1 level 0.201
> volume #1 level 0.2975
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250119
> P119_J6703_max_resample_map_sharp_local.mrc"
Opened 20250119 P119_J6703_max_resample_map_sharp_local.mrc as #2, grid size
440,440,440, pixel 0.73, shown at level 0.121, step 2, values float32
> volume #2 step 1
> volume #2 level 0.3164
> hide #!1 models
> transparency #2#!5 50
> surface dust #2 size 7.3
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select clear
> hide #!2 models
> select add /A:388
9 atoms, 8 bonds, 1 residue, 3 models selected
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250120-2 WT-1.cxs"
——— End of log from Mon Jan 20 13:53:21 2025 ———
opened ChimeraX session
> hide #!2 models
> hide #!5 models
> show #!5 models
> select clear
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250120
> WT_P119_J6703_arrestin_R-Fab-coot-5.pdb"
Chain information for 20250120 WT_P119_J6703_arrestin_R-Fab-coot-5.pdb #3
---
Chain | Description
B | No description available
C | No description available
E | No description available
L | No description available
R | No description available
> hide atoms
> show cartoons
> hide #!3 models
> show #!3 models
> hide #!5 models
> hide #3.1 models
> select #3/C
1552 atoms, 1592 bonds, 1 pseudobond, 205 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> select #3/E
1588 atoms, 1623 bonds, 1 pseudobond, 207 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250120 WT-2
> interaction.cxs"
> cartoon style width 1.5 thickness 0.3
> cartoon suppressBackboneDisplay false
> select #3/R
2481 atoms, 2547 bonds, 5 pseudobonds, 302 residues, 2 models selected
> ui tool show "Color Actions"
> color sel deep sky blue
> select #3/B
2755 atoms, 2813 bonds, 2 pseudobonds, 346 residues, 2 models selected
> color sel salmon
> select #3/L
279 atoms, 284 bonds, 33 residues, 1 model selected
> color sel goldenrod
> cartoon style width 1.5 thickness 0.5
> cartoon style width 1.5 thickness 0.3
> transparency 5 ribbons
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250120 WT-2
> interaction.cxs"
> show #!2 models
> hide #!2 models
> select #3/B:77
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> show #!2 models
> select clear
> hide #!3 models
> transparency #2 30
> transparency #2 50
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!3 atoms
> select #3/B:66
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #3/B:67
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #3/B:69
25 atoms, 22 bonds, 3 residues, 1 model selected
> select add #3/B:70
32 atoms, 28 bonds, 4 residues, 1 model selected
> select add #3/B:71
40 atoms, 35 bonds, 5 residues, 1 model selected
> select add #3/B:72
44 atoms, 38 bonds, 6 residues, 1 model selected
> select add #3/B:73
52 atoms, 45 bonds, 7 residues, 1 model selected
> select add #3/B:75
63 atoms, 56 bonds, 8 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 63 atom styles
> color sel byhetero
> select clear
> show #!2 models
> volume #1 level 0.25
> volume #2 level 0.25
> color #2#!3 light gray
> undo
> transparency #2#!3 80
> transparency #2#!3 30
> volume #2 level 0.27
> volume #2 level 0.29
> volume #2 level 0.27
> hide #!3 models
> show #!3 models
> hide #!2 models
> select #3/B:65
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> show #!2 models
> hide #!2 models
> show #!2 models
> transparency sel 70
> select clear
> transparency #2#!3 60
> select clear
> color #2 #ffffffb3 models
> transparency #2#!3 90
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> transparency #2#!3 10
[Repeated 1 time(s)]
> hide #!2 models
> select #3/B:65@CA
1 atom, 1 residue, 1 model selected
> select subtract #3/B:65@CA
Nothing selected
> select #3/B:65
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/B:72
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #3/B:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #3/B:70
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #3.1 models
> select #3/R:408
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> show #!2 models
> volume #2 level 0.1952
> volume #2 level 0.255
> hide #!2 models
> select clear
> select add #3/R:459
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #3/R:412
19 atoms, 18 bonds, 2 residues, 1 model selected
> select add #3/R:409
25 atoms, 23 bonds, 3 residues, 1 model selected
> select add #3/R:385
33 atoms, 30 bonds, 4 residues, 1 model selected
> select add #3/R:384
40 atoms, 36 bonds, 5 residues, 1 model selected
> select add #3/R:310
48 atoms, 43 bonds, 6 residues, 1 model selected
> select add #3/R:388
57 atoms, 51 bonds, 7 residues, 1 model selected
> select add #3/R:309
65 atoms, 58 bonds, 8 residues, 1 model selected
> select add #3/R:314
76 atoms, 69 bonds, 9 residues, 1 model selected
> select add #3/R:465
85 atoms, 77 bonds, 10 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 85 atom styles
> color sel byhetero
> select add #3/R:219
96 atoms, 87 bonds, 11 residues, 1 model selected
> show (sel-residues & sidechain) target ab
[Repeated 1 time(s)]
> style sel stick
Changed 96 atom styles
> color sel byhetero
> select clear
> select #3/R:314@CA
1 atom, 1 residue, 1 model selected
> select #3/R:314
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> color #3 byhetero
> select #3/R:465
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select add #3/R:408
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> show (sel-residues & sidechain) target ab
> select clear
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250120 WT-2 interaction
> figerloop.cxs"
——— End of log from Mon Jan 20 23:43:34 2025 ———
opened ChimeraX session
> show #!2 models
> color #2 #9a9a9ae6 models
> transparency #2-3 30
> transparency #2-3 60
> hide #!2 models
> close #2
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250119
> P119_J6703_max_resample_map_sharp_local.mrc"
Opened 20250119 P119_J6703_max_resample_map_sharp_local.mrc as #2, grid size
440,440,440, pixel 0.73, shown at level 0.121, step 2, values float32
> volume #2 step 1
> surface dust #2 size 7.3
> volume #2 level 0.3817
> transparency #2-3 50
> hide #!2 models
> show #!2 models
> volume #1 level 0.2939
> volume #1 level 0.1974
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> transparency 0 ribbons
> show #!2 models
> transparency #2-3 40
> volume #2 level 0.2947
> hide #!2 models
> select add #3/B:244
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #3/B:243
16 atoms, 15 bonds, 2 residues, 1 model selected
> select add #3/B:246
23 atoms, 21 bonds, 3 residues, 1 model selected
> select add #3/B:245
31 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 31 atom styles
> show #!2 models
> hide #!2 models
> select add #3/B:77
40 atoms, 36 bonds, 5 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 40 atom styles
> show #!2 models
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250120 WT-2 interaction
> figerloop.cxs"
——— End of log from Tue Jan 21 13:32:42 2025 ———
opened ChimeraX session
> hide #!3 models
> hide #!2 models
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250122 phenix
> WT_P119_J6703_arrestin_R-Fab-coot-15(1).pdb"
Chain information for 20250122 phenix WT_P119_J6703_arrestin_R-Fab-
coot-15(1).pdb #4
---
Chain | Description
B | No description available
C | No description available
E | No description available
L | No description available
R | No description available
> hide #!4 atoms
> show #!4 cartoons
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> cartoon style width 1.5 thickness 0.3
> hide #!5 models
> show #!5 models
> hide #4.1 models
> hide #!5 models
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250122 phenix
> WT_P119_J6703_arrestin_R-Fab-coot-16.pdb"
Chain information for 20250122 phenix WT_P119_J6703_arrestin_R-Fab-coot-16.pdb
#6
---
Chain | Description
B | No description available
C | No description available
E | No description available
L | No description available
R | No description available
> hide #!4,6 atoms
> show #!4,6 cartoons
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!6 models
> show #!6 models
> hide #!4 models
> hide #!6 models
> show #!6 models
> hide #!2 models
> select #6/B:75
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> show #!2 models
> hide #!6 models
> close #5
> close #4
> close #3
> show #!6 models
> hide #!6 models
> show #!6 models
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250120 WT-1
> interaction.cxs"
——— End of log from Wed Jan 22 21:18:32 2025 ———
opened ChimeraX session
> hide #!2 models
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> hide #6.1 models
> cartoon style width 1.5 thickness 0.3
> cartoon suppressBackboneDisplay false
> select clear
> select /C
1552 atoms, 1592 bonds, 1 pseudobond, 205 residues, 2 models selected
> hide sel cartoons
> select /E
1588 atoms, 1623 bonds, 1 pseudobond, 207 residues, 2 models selected
> hide sel cartoons
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250122 WT-1
> interaction.cxs"
> select /R
2470 atoms, 2536 bonds, 5 pseudobonds, 301 residues, 2 models selected
> ui tool show "Color Actions"
> color sel deep sky blue
> select /L
279 atoms, 284 bonds, 33 residues, 1 model selected
> color sel goldenrod
> select /B
2755 atoms, 2813 bonds, 2 pseudobonds, 346 residues, 2 models selected
> color sel salmon
> select clear
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250122 WT-1
> interaction.cxs"
[Repeated 1 time(s)]
——— End of log from Thu Jan 23 14:30:39 2025 ———
opened ChimeraX session
> show #!1 models
> hide #!1 models
> select /R:388
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> show #!1 models
> volume #1 level 0.1491
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide atoms
> show atoms
> hide atoms
> show atoms
> style stick
Changed 8644 atom styles
> hide atoms
> select #6/R:412
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #6/R:413
15 atoms, 13 bonds, 2 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> select add #6/R:408
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add #6/R:409
30 atoms, 26 bonds, 4 residues, 1 model selected
> select add #6/R:381
38 atoms, 33 bonds, 5 residues, 1 model selected
> select add #6/R:384
45 atoms, 39 bonds, 6 residues, 1 model selected
> select add #6/R:385
53 atoms, 46 bonds, 7 residues, 1 model selected
> select add #6/R:388
62 atoms, 54 bonds, 8 residues, 1 model selected
> select add #6/R:405
71 atoms, 62 bonds, 9 residues, 1 model selected
> select add #6/R:408
71 atoms, 62 bonds, 9 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> color sel byhetero
> select add #6/R:219
82 atoms, 72 bonds, 10 residues, 1 model selected
> select add #6/R:310
90 atoms, 79 bonds, 11 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> color sel byhetero
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250123 WT-1
> interaction.cxs"
> show (sel-residues & sidechain) target ab
[Repeated 1 time(s)]
> color sel byhetero
> select clear
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250123 WT-1
> interaction.cxs"
——— End of log from Thu Jan 23 22:46:13 2025 ———
opened ChimeraX session
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250124
> WT_P119_J6703_arrestin_R-Fab-coot-16(1).pdb"
Chain information for 20250124 WT_P119_J6703_arrestin_R-Fab-coot-16(1).pdb #3
---
Chain | Description
B | No description available
C | No description available
E | No description available
L | No description available
R | No description available
> hide #!3 models
> hide #!6 models
> show #!3 models
> hide #!3 atoms
> show #!3 cartoons
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250124-J6703
> interaction.cxs"
> cartoon style width 1.5 thickness 0.3
> show #!6 models
> hide #!6 models
> hide #3.1 models
> select #6/C
1552 atoms, 1592 bonds, 1 pseudobond, 205 residues, 2 models selected
> hide #!3 atoms
> delete atoms #!3
> delete bonds #!3
> undo
Undo failed, probably because structures have been modified.
> undo
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250124
> WT_P119_J6703_arrestin_R-Fab-coot-16(1).pdb"
Chain information for 20250124 WT_P119_J6703_arrestin_R-Fab-coot-16(1).pdb #3
---
Chain | Description
B | No description available
C | No description available
E | No description available
L | No description available
R | No description available
> show #!6 models
> hide #!3 models
> hide #!6 models
> show #!3 models
> hide #!3 atoms
> show #!3 cartoons
> close #6.1
> hide #3.1 models
> cartoon style width 1.5 thickness 0.3
> show #6 models
> hide #6 models
> select #3/C
1552 atoms, 1592 bonds, 1 pseudobond, 205 residues, 2 models selected
> hide (#!3 & sel) target a
> cartoon hide (#!3 & sel)
> select #3/E
1588 atoms, 1623 bonds, 1 pseudobond, 207 residues, 2 models selected
> hide sel cartoons
> select clear
> select #3/R
2470 atoms, 2536 bonds, 5 pseudobonds, 301 residues, 2 models selected
> ui tool show "Color Actions"
> color sel deep sky blue
> select #3/B
2755 atoms, 2813 bonds, 2 pseudobonds, 346 residues, 2 models selected
> ui tool show "Color Actions"
> color sel salmon
> select #3/L
279 atoms, 284 bonds, 33 residues, 1 model selected
> color sel goldenrod
> select clear
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250124-J6703
> interaction.cxs"
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #6 models
> show #!1 models
> hide #!1 models
> hide #6 models
> select add #3/R:310
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3/R:412
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #3/R:413
23 atoms, 20 bonds, 3 residues, 1 model selected
> select add #3/R:405
32 atoms, 28 bonds, 4 residues, 1 model selected
> select add #3/R:408
41 atoms, 36 bonds, 5 residues, 1 model selected
> select add #3/R:409
47 atoms, 41 bonds, 6 residues, 1 model selected
> select add #3/R:381
55 atoms, 48 bonds, 7 residues, 1 model selected
> select add #3/R:384
62 atoms, 54 bonds, 8 residues, 1 model selected
> select add #3/R:385
70 atoms, 61 bonds, 9 residues, 1 model selected
> select add #3/R:388
79 atoms, 69 bonds, 10 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 79 atom styles
> color sel byhetero
> select clear
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> select add #3/R:219
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select add #3/R:219
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> cartoon suppressBackboneDisplay false
> hide sel atoms
> show sel atoms
> style sel stick
Changed 11 atom styles
> hide sel atoms
> show (sel-residues & sidechain) target ab
> color sel byhetero
> select clear
> select add #3/R:459
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #3/R:463
20 atoms, 19 bonds, 2 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 20 atom styles
> color sel byhetero
> select clear
> show #!1 models
> volume #1 level 0.2134
> volume #1 level 0.1759
> volume #1 level 0.117
> volume #1 level 0.1652
> volume #1 level 0.1063
> hide #!1 models
> show #!2 models
> volume #2 level 0.2504
> hide #!3 models
> show #6 models
> hide #!2 models
> hide #6 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #6 models
> hide #6 models
> select #3/B:75
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> hide sel atoms
> show (sel-residues & sidechain) target ab
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> volume #1 level 0.192
> select clear
> show #6 models
> hide #6 models
> hide #!1 models
> show #6 models
> select #6/B:75
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!1 models
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250124-J6703
> interaction.cxs"
——— End of log from Fri Jan 24 13:24:45 2025 ———
opened ChimeraX session
> hide #!1 models
> hide #!3 models
> hide #6 models
> show #6 models
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250124-4
> WT_P119_J6703_arrestin_R-Fab-coot-18.pdb"
Chain information for 20250124-4 WT_P119_J6703_arrestin_R-Fab-coot-18.pdb #4
---
Chain | Description
B | No description available
C | No description available
E | No description available
L | No description available
R | No description available
> hide #6 models
> hide #!4 atoms
> show #!4 cartoons
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #4.1 models
> cartoon style width 1.5 thickness 0.3
> cartoon suppressBackboneDisplay false
> select #4/C
1552 atoms, 1592 bonds, 1 pseudobond, 205 residues, 2 models selected
> hide sel cartoons
> select #4/E
1588 atoms, 1623 bonds, 1 pseudobond, 207 residues, 2 models selected
> hide sel cartoons
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250124-J6703
> interaction.cxs"
> select #4/B
2755 atoms, 2813 bonds, 2 pseudobonds, 346 residues, 2 models selected
> ui tool show "Color Actions"
> color sel salmon
> select #4/R
2470 atoms, 2536 bonds, 5 pseudobonds, 301 residues, 2 models selected
> color sel deep sky blue
> select #4/L
279 atoms, 284 bonds, 33 residues, 1 model selected
> color sel goldenrod
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250124-J6703
> interaction.cxs"
> select clear
> select add #3/B:71
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #4/B:71
16 atoms, 14 bonds, 2 residues, 2 models selected
> select add #4/B:70
23 atoms, 20 bonds, 3 residues, 2 models selected
> select add #4/B:72
27 atoms, 23 bonds, 4 residues, 2 models selected
> select add #4/B:73
35 atoms, 30 bonds, 5 residues, 2 models selected
> select add #4/B:75
46 atoms, 41 bonds, 6 residues, 2 models selected
> select add #4/B:69
54 atoms, 48 bonds, 7 residues, 2 models selected
> select add #4/B:68
62 atoms, 55 bonds, 8 residues, 2 models selected
> select add #4/B:67
70 atoms, 62 bonds, 9 residues, 2 models selected
> select add #4/B:66
79 atoms, 70 bonds, 10 residues, 2 models selected
> select add #4/B:65
90 atoms, 80 bonds, 11 residues, 2 models selected
> select add #4/B:63
102 atoms, 92 bonds, 12 residues, 2 models selected
> show (#!4 & sel-residues & sidechain) target ab
> style sel & #!4 stick
Changed 94 atom styles
> color (#!4 & sel) byhetero
> show #!1 models
> volume #1 level 0.2644
> volume #1 level 0.201
> select clear
> hide #!1 models
> select add #4/R:309
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #4/R:310
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #4/R:405
25 atoms, 22 bonds, 3 residues, 1 model selected
> select add #4/R:408
34 atoms, 30 bonds, 4 residues, 1 model selected
> select add #4/R:412
41 atoms, 36 bonds, 5 residues, 1 model selected
> select add #4/R:413
49 atoms, 43 bonds, 6 residues, 1 model selected
> select add #4/R:384
56 atoms, 49 bonds, 7 residues, 1 model selected
> select add #4/R:385
64 atoms, 56 bonds, 8 residues, 1 model selected
> select add #4/R:381
72 atoms, 63 bonds, 9 residues, 1 model selected
> select add #4/R:388
81 atoms, 71 bonds, 10 residues, 1 model selected
> select add #4/R:219
92 atoms, 81 bonds, 11 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 92 atom styles
> color sel byhetero
> select clear
> show #!1 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!1 models
> show #!2 models
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250124-J6703
> interaction.cxs"
> hide #!2 models
> show #!2 models
> hide #!2 models
> select add #4/R:306
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select clear
> show #!2 models
> volume #2 level 0.3177
> volume #2 level 0.3626
> hide #!2 models
> select add #4/R:314
11 atoms, 11 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 11 atom styles
> color sel byhetero
> show #!2 models
> volume #2 level 0.3177
> volume #2 level 0.385
> select add #4/B:61
22 atoms, 22 bonds, 2 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 22 atom styles
> select clear
> hide #!4 models
> show #4.1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select add #4/R:459
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #4/R:463
20 atoms, 19 bonds, 2 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 20 atom styles
> color sel byhetero
> show #!2 models
> volume #2 level 0.3177
> volume #2 level 0.228
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250124-J6703
> interaction.cxs"
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> volume #1 level 0.4002
> volume #1 level 0.364
> volume #1 level 0.3006
> show #!2 models
> volume #2 level 0.3326
> volume #2 level 0.4972
> ui tool show "Side View"
> volume #2 level 0.4523
> hide #!2 models
> show #!2 models
> volume #2 level 0.3999
> volume #2 level 0.3326
> volume #2 level 0.2653
> hide #!2 models
> show #!1 models
> volume #1 level 0.201
> volume #2 level 0.2055
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> 、、、、、、、、、、、、、、、、、、、、、
Unknown command: 、、、、、、、、、、、、、、、、、、、、、
> hide #!2 models
> select #4/B:65@CA
1 atom, 1 residue, 1 model selected
> select #4/B:65
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4/B:61
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250124-J6703
> interaction.cxs"
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250124-J6703
> interaction fingerloop.cxs"
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250124-J6703
> interaction Cloop.cxs"
> hide #!4 atoms
> show #!1 models
> volume #1 level 0.3368
> select add #4/B:244
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #4/B:249
23 atoms, 23 bonds, 2 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 23 atom styles
> color sel byhetero
> volume #1 level 0.3097
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250124-J6703
> interaction Cloop.cxs"
> select #4/R:316
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #4/R:315
17 atoms, 16 bonds, 2 residues, 1 model selected
> select add #4/R:314
28 atoms, 27 bonds, 3 residues, 1 model selected
> select add #4/R:313
33 atoms, 31 bonds, 4 residues, 1 model selected
> select add #4/R:312
41 atoms, 38 bonds, 5 residues, 1 model selected
> select add #4/R:311
52 atoms, 49 bonds, 6 residues, 1 model selected
> select add #4/R:317
61 atoms, 57 bonds, 7 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 61 atom styles
> color sel byhetero
> hide #!1 models
> select subtract #4/R:311
50 atoms, 46 bonds, 6 residues, 1 model selected
> select clear
> select add #4/R:311
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!1 models
> select add #4/B:241
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #4/B:243
13 atoms, 11 bonds, 2 residues, 1 model selected
> select add #4/B:244
24 atoms, 22 bonds, 3 residues, 1 model selected
> select add #4/B:245
32 atoms, 29 bonds, 4 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 32 atom styles
> color sel byhetero
> select clear
> volume #1 level 0.5359
> volume #1 level 0.2644
> hide #!1 models
> select #4/B:61
11 atoms, 11 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250124-J6703
> interaction Cloop.cxs"
——— End of log from Fri Jan 24 23:31:29 2025 ———
opened ChimeraX session
> hide #!1 models
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250201-J6703
> interaction Cloop width 1.2 thick 0.3 Trans 5.cxs"
> cartoon style width 1.2 thickness 0.3
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250201-J6703
> interaction Cloop width 1.2 thick 0.3 Trans 5.cxs"
> show #!2 models
> ui tool show "Side View"
> hide #!2 models
> show #!1 models
> hide #!1 models
> select add #4/R:317@CA
1 atom, 1 residue, 1 model selected
> select subtract #4/R:317
Nothing selected
> select add #4/R:317
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select add #4/R:316
15 atoms, 13 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250201-J6703
> interaction Cloop width 1.2 thick 0.3 Trans 5.cxs"
> select add #4/R:312
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> show #!1 models
> ui tool show "Side View"
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250201-J6703
> interaction Cloop width 1.2 thick 0.3 Trans 5.cxs"
> select add #4/B:61
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
92 atoms, 93 bonds, 11 residues, 1 model selected
> select up
672 atoms, 685 bonds, 83 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
Drag select of 31 residues
> select up
1270 atoms, 1291 bonds, 162 residues, 1 model selected
> hide sel cartoons
> select add #4/B:316
1274 atoms, 1294 bonds, 163 residues, 1 model selected
> select up
1364 atoms, 1386 bonds, 174 residues, 1 model selected
> select down
1274 atoms, 1294 bonds, 163 residues, 1 model selected
> select down
1274 atoms, 1294 bonds, 163 residues, 1 model selected
> show sel cartoons
> select clear
Drag select of 9 residues
> select up
319 atoms, 323 bonds, 40 residues, 1 model selected
> hide sel cartoons
Drag select of 30 residues
> select up
737 atoms, 745 bonds, 95 residues, 1 model selected
> hide sel cartoons
> select add #4/B:63
749 atoms, 757 bonds, 96 residues, 1 model selected
> select up
773 atoms, 782 bonds, 99 residues, 1 model selected
> hide sel cartoons
> select add #4/B:67
781 atoms, 789 bonds, 100 residues, 1 model selected
> select up
797 atoms, 807 bonds, 102 residues, 1 model selected
> hide sel cartoons
Drag select of 7 residues
> hide sel cartoons
Drag select of 1 residues
> hide sel cartoons
> select #4/B:316
4 atoms, 3 bonds, 1 residue, 1 model selected
> select down
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> select down
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel cartoons
> select up
94 atoms, 94 bonds, 12 residues, 1 model selected
> select clear
Drag select of 3 residues
[Repeated 1 time(s)]
> hide sel cartoons
Drag select of 6 residues
> hide sel cartoons
Drag select of 1 residues
> hide sel cartoons
> select add #4/B:367
63 atoms, 8 bonds, 8 residues, 1 model selected
> select up
341 atoms, 344 bonds, 43 residues, 1 model selected
> hide sel cartoons
> select add #4/B:126
347 atoms, 349 bonds, 44 residues, 1 model selected
> hide sel cartoons
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250201-J6703
> interaction Cloop width 1.2 thick 0.3 Trans 5.cxs"
> cartoon style width 1.2 thickness 0.3
> transparency 5 ribbons
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250201-J6703
> interaction Cloop width 1.2 thick 0.3 Trans 5.cxs"
> select add #4/R:315
358 atoms, 360 bonds, 45 residues, 1 model selected
> select #4/R:315@CA
1 atom, 1 residue, 1 model selected
> select subtract #4/R:315@CA
Nothing selected
> select add #4/R:315@CA
1 atom, 1 residue, 1 model selected
> select subtract #4/R:315
Nothing selected
> select add #4/R:315
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #4/R:314
22 atoms, 22 bonds, 2 residues, 1 model selected
> show sel atoms
> select clear
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250201-J6703
> interaction Cloop width 1.2 thick 0.3 Trans 5.cxs"
——— End of log from Sat Feb 1 19:38:51 2025 ———
opened ChimeraX session
> save "F:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250329-J6703
> interaction C loop width 1.2 thick 0.3 Trans 5.cxs"
> hide #!4 models
> open "F:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/文章修改/20250329-3
> WT_P119_J6703_arrestin-changed-coot-3.pdb"
Chain information for 20250329-3 WT_P119_J6703_arrestin-changed-coot-3.pdb #5
---
Chain | Description
B | No description available
C | No description available
E | No description available
L | No description available
R | No description available
> hide #!5 atoms
> show #!5 cartoons
> cartoon style width 1.2 thickness 0.3
> cartoon suppressBackboneDisplay false
> select #6/B
2755 atoms, 2813 bonds, 346 residues, 1 model selected
> ui tool show "Color Actions"
> select #5/B
2758 atoms, 2816 bonds, 2 pseudobonds, 346 residues, 2 models selected
> ui tool show "Color Actions"
> color sel salmon
> select #5/R
2471 atoms, 2537 bonds, 5 pseudobonds, 301 residues, 2 models selected
> color sel deep sky blue
> select clear
> select add #5/R:316
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #5/R:315
17 atoms, 16 bonds, 2 residues, 1 model selected
> select add #5/R:314
28 atoms, 27 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 28 atom styles
> select clear
> select add #5/R:311
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select clear
> color #5 byhetero
> select clear
> select #5/B:249
12 atoms, 12 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 12 atom styles
> select #5/B:247
5 atoms, 4 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 5 atom styles
> select #5/B:247
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/B:247
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/B:246
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/B:241
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> select clear
> select #5/B:245
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 8 atom styles
> select clear
> select #5/B:243
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select clear
> select #5/B:244
11 atoms, 11 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 11 atom styles
> select clear
Drag select of 9 residues
> select up
462 atoms, 463 bonds, 56 residues, 1 model selected
> hide sel cartoons
Drag select of 5 residues
> select up
854 atoms, 857 bonds, 107 residues, 1 model selected
> hide sel cartoons
Drag select of 1 residues
> select up
875 atoms, 878 bonds, 110 residues, 1 model selected
> hide sel cartoons
Drag select of 3 residues
> select up
927 atoms, 930 bonds, 116 residues, 1 model selected
> hide sel cartoons
Drag select of 2 residues
> select up
1002 atoms, 1008 bonds, 127 residues, 1 model selected
> hide sel cartoons
Drag select of 2 residues
> select up
1166 atoms, 1178 bonds, 147 residues, 1 model selected
> hide sel cartoons
Drag select of 8 residues
> select up
1345 atoms, 1363 bonds, 168 residues, 1 model selected
> hide sel cartoons
Drag select of 2 residues
> select up
1367 atoms, 1387 bonds, 171 residues, 1 model selected
> hide sel cartoons
> select #5/R:313
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 5 atom styles
> select clear
> save "F:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250329-J6703
> interaction C loop width 1.2 thick 0.3 Trans 5.cxs"
Traceback (most recent call last):
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write
self._f.write(buf)
File "D:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 740, in write
compressed = self._compressor.compress(data)
File "D:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
MemoryError
MemoryError
File "D:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write
self._f.write(buf)
File "D:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 740, in write
compressed = self._compressor.compress(data)
File "D:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
MemoryError
MemoryError
File "D:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
See log for complete Python traceback.
> save "F:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250329-J6703
> interaction C loop width 1.2 thick 0.3 Trans 5.cxs"
Traceback (most recent call last):
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
MemoryError
MemoryError
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
MemoryError
MemoryError
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 538.78
OpenGL renderer: NVIDIA GeForce MX150/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows
Manufacturer: LENOVO
Model: 20L6A09YCD
OS: Microsoft Windows 10 家庭中文版 (Build 19045)
Memory: 17,027,555,328
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz
OSLanguage: zh-CN
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
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: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
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: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
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: 1.1.1
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: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
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: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
comtypes: 1.1.14
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pywin32: 305
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
WMI: 1.5.1
zipp: 3.15.0
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError saving session |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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