MemoryError saving session

[chimerax-bug-report@…]

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.  
  

> 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/20250329-2-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.  
  

> save "F:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250329-2-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.  
  




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