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Opened 8 months ago
Closed 8 months ago
#16840 closed defect (limitation)
Restore session: MemoryError in grid_data_from_state
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250120-1 Receptor-
> Arrestin.cxs"
Log from Mon Jan 20 16:12:38 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/20250118-5 Receptor-
> Arrestin.cxs"
Log from Mon Jan 20 14:15:48 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/20250118-5 Receptor-
> Arrestin.cxs"
Log from Mon Jan 20 13:33:51 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/20250118-5 Receptor-
> Arrestin.cxs"
Log from Sun Jan 19 14:20:13 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/20250118-5 Receptor-
> Arrestin.cxs"
Log from Sat Jan 18 17:02:31 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/20240109-2.cxs"
Log from Tue Jan 9 15:58:33 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/20240106-7.cxs"
Opened J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc copy as #4,
grid size 440,440,440, pixel 0.73, shown at level 0.27, step 1, values float32
Opened cryosparc_P119_J938_003_volume_map_sharp.mrc as #5, grid size
360,360,360, pixel 0.73, shown at level 0.1, step 1, values float32
Log from Sat Jan 6 16:36:56 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/20240106-6.cxs"
Opened J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc copy as #4,
grid size 440,440,440, pixel 0.73, shown at level 0.27, step 1, values float32
Opened cryosparc_P119_J938_003_volume_map_sharp.mrc as #5, grid size
360,360,360, pixel 0.73, shown at level 0.1, step 1, values float32
Log from Sat Jan 6 16:28:40 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/20231204-16.cxs"
Opened J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc copy as #4,
grid size 440,440,440, pixel 0.73, shown at level 0.27, step 1, values float32
Opened cryosparc_P119_J938_003_volume_map_sharp.mrc as #5, grid size
360,360,360, pixel 0.73, shown at level 0.1, step 1, values float32
Log from Mon Dec 4 22:44:42 2023UCSF 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/20231204-13.cxs"
Opened J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc copy as #4,
grid size 440,440,440, pixel 0.73, shown at level 0.27, step 1, values float32
Opened cryosparc_P119_J938_003_volume_map_sharp.mrc as #5, grid size
360,360,360, pixel 0.73, shown at level 0.1, step 1, values float32
Log from Mon Dec 4 20:46:50 2023UCSF 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/20231204-10.cxs"
Opened J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc copy as #4,
grid size 440,440,440, pixel 0.73, shown at level 0.27, step 1, values float32
Opened cryosparc_P119_J938_003_volume_map_sharp.mrc as #5, grid size
360,360,360, pixel 0.73, shown at level 0.1, step 1, values float32
Log from Mon Dec 4 17:18:04 2023UCSF 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/20231204-6.cxs"
Opened J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc copy as #4,
grid size 440,440,440, pixel 0.73, shown at level 0.27, step 1, values float32
Opened cryosparc_P119_J938_003_volume_map_sharp.mrc as #5, grid size
360,360,360, pixel 0.73, shown at level 0.1, step 1, values float32
Log from Mon Dec 4 15:32:57 2023UCSF 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/20231202-1.cxs"
Opened J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc copy as #4,
grid size 440,440,440, pixel 0.73, shown at level 0.27, step 1, values float32
Opened cryosparc_P119_J938_003_volume_map_sharp.mrc as #5, grid size
360,360,360, pixel 0.73, shown at level 0.1, step 1, values float32
Log from Sat Dec 2 16:19:50 2023UCSF 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/20231129-2.cxs"
Opened J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc as #2, grid
size 440,440,440, pixel 0.73, shown at level 0.121, step 1, values float32
Opened J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc copy as #4,
grid size 440,440,440, pixel 0.73, shown at level 0.27, step 1, values float32
Opened cryosparc_P119_J938_003_volume_map_sharp.mrc as #5, grid size
360,360,360, pixel 0.73, shown at level 0.1, step 1, values float32
Log from Wed Nov 29 13:39:51 2023UCSF 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/20231129-1.cxs"
Opened J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc as #2, grid
size 440,440,440, pixel 0.73, shown at level 0.121, step 1, values float32
Opened J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc copy as #4,
grid size 440,440,440, pixel 0.73, shown at level 0.27, step 1, values float32
Opened cryosparc_P119_J938_003_volume_map_sharp.mrc as #5, grid size
360,360,360, pixel 0.73, shown at level 0.1, step 1, values float32
Log from Wed Nov 29 12:06:41 2023UCSF 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/20231128-11.cxs"
Opened J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc as #2, grid
size 440,440,440, pixel 0.73, shown at level 0.121, step 1, values float32
Opened J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc copy as #4,
grid size 440,440,440, pixel 0.73, shown at level 0.27, step 1, values float32
Opened cryosparc_P119_J938_003_volume_map_sharp.mrc as #5, grid size
360,360,360, pixel 0.73, shown at level 0.1, step 1, values float32
Log from Wed Nov 29 00:17:11 2023UCSF 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/20231128-7.cxs"
Opened J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc as #2, grid
size 440,440,440, pixel 0.73, shown at level 0.121, step 1, values float32
Opened J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc copy as #4,
grid size 440,440,440, pixel 0.73, shown at level 0.27, step 1, values float32
Opened cryosparc_P119_J938_003_volume_map_sharp.mrc as #5, grid size
360,360,360, pixel 0.73, shown at level 0.1, step 1, values float32
Log from Tue Nov 28 18:00:22 2023UCSF 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/20231128.cxs"
Opened J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc as #2, grid
size 440,440,440, pixel 0.73, shown at level 0.213, step 1, values float32
Log from Tue Nov 28 14:53:44 2023UCSF 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/20231128.cxs"
Log from Tue Nov 28 14:34:19 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:/PTH1R-Arrestin paper/R-Arr-fab-coot-refine20231127.pdb"
Chain information for R-Arr-fab-coot-refine20231127.pdb #1
---
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 #1.1 models
> select /B
2824 atoms, 2885 bonds, 357 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark salmon
> color sel salmon
> color sel tomato
> color sel brown
> color sel tomato
> color sel coral
> color sel indian red
> select /R
3009 atoms, 3086 bonds, 6 pseudobonds, 368 residues, 2 models selected
> help help:user
> color #1 royalblue
> select /B
2824 atoms, 2885 bonds, 357 residues, 1 model selected
> ui tool show "Color Actions"
> color sel indian red
> select clear
> lighting soft
[Repeated 1 time(s)]
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
[Repeated 2 time(s)]
> lighting full
[Repeated 1 time(s)]
> lighting flat
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> select /R
3009 atoms, 3086 bonds, 6 pseudobonds, 368 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!1 & sel) #00bfffff
> select clear
> select /L
292 atoms, 297 bonds, 35 residues, 1 model selected
> color sel olive
> color sel dark khaki
> color sel gold
> color sel orange
> color sel dark orange
> color sel goldenrod
> select /C
1694 atoms, 1738 bonds, 226 residues, 1 model selected
> color sel light blue
> color sel seashell
> color sel snow
> color sel old lace
> color sel light goldenrod yellow
> color sel sky blue
> color sel light sky blue
> color sel gray
> color sel dark sea green
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231128.cxs" includeMaps
> true
——— End of log from Tue Nov 28 14:34:19 2023 ———
opened ChimeraX session
> open "D:/PTH1R-Arrestin
> paper/J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc"
Opened J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc as #2, grid
size 440,440,440, pixel 0.73, shown at level 0.0179, step 2, values float32
> select clear
> volume #2 step 1
> volume #2 level 0.1313
> color zone #2 near all distance 7
> volume #2 level 0.5992
> volume #2 level 0.2057
> surface dust #2 size 20
> volume #2 level 0.1136
> volume #2 level 0.07458
> volume #2 level 0.2164
> volume #2 level 0.3865
> volume #2 level 0.2128
> select /C
1694 atoms, 1738 bonds, 226 residues, 1 model selected
> ui tool show "Color Actions"
> color sel rosy brown
> color sel tan
> color sel bisque
> color sel misty rose
> help help:user
> select /L
292 atoms, 297 bonds, 35 residues, 1 model selected
> color sel peru
> color sel dark orange
> color sel goldenrod
> color sel gold
> color sel dark orange
> select /C
1694 atoms, 1738 bonds, 226 residues, 1 model selected
> color sel misty rose
[Repeated 1 time(s)]
> select /E
1617 atoms, 1652 bonds, 2 pseudobonds, 218 residues, 2 models selected
> color sel blanched almond
> color sel lavender blush
> color sel light gray
> color sel snow
> color sel alice blue
> color sel linen
> color sel lavender
> color sel light cyan
> color sel gainsboro
> color sel purple
> color sel light steel blue
> color sel lavender
> color zone #2 near all distance 7
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231128.cxs"
——— End of log from Tue Nov 28 14:53:44 2023 ———
opened ChimeraX session
> color zone #2 near all distance 7
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231128.cxs"
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231128-1.cxs"
> ui mousemode right "map eraser"
> volume erase #2 center 142.77,212.68,140.21 radius 24.638
Opened J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc copy as #4,
grid size 440,440,440, pixel 0.73, shown at step 1, values float32
> volume erase #4 center 171.96,218.18,125.08 radius 24.572
> volume erase #4 center 197.14,198.6,125.64 radius 24.572
> volume erase #4 center 210.48,179.93,125.71 radius 24.572
> volume erase #4 center 210.43,150.16,143.46 radius 24.572
> volume erase #4 center 186.56,117.22,139.72 radius 24.572
> volume erase #4 center 136.5,112.1,149.27 radius 24.572
> volume erase #4 center 112.28,128.17,153.38 radius 24.572
> volume erase #4 center 111.95,157.57,150.24 radius 24.572
> volume erase #4 center 99.726,168.23,143.9 radius 24.572
[Repeated 1 time(s)]
> volume erase #4 center 106.52,181.61,146.36 radius 24.572
> volume erase #4 center 149.54,109.49,133.61 radius 24.572
> volume erase #4 center 136.41,118.69,126.7 radius 24.572
> volume erase #4 center 151.94,114.34,116.97 radius 24.572
> volume erase #4 center 183.48,118.69,120.86 radius 24.572
> volume erase #4 center 200.21,132.26,120.67 radius 24.572
> volume erase #4 center 206.71,144.19,122.18 radius 24.572
> volume erase #4 center 81.475,126.96,147.3 radius 24.572
> volume erase #4 center 114.9,191.14,164.18 radius 24.572
> volume erase #4 center 112.62,181.54,138.2 radius 20.236
> volume erase #4 center 112.92,168.41,135.16 radius 17.505
> volume erase #4 center 114.73,159.92,137.69 radius 17.505
> volume erase #4 center 115.38,146.27,126.12 radius 17.505
> volume #4 level 0.266
> volume erase #4 center 118.69,168.7,152.23 radius 17.505
> show #!2 models
> hide #!2 models
> color zone #4 near all distance 7
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231128-1.cxs"
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231128-1.cxs" includeMaps
> true
> volume erase #4 center 167.1,111.32,150.62 radius 17.505
> volume erase #4 center 166.95,113.56,149.2 radius 17.505
> volume erase #4 center 168.49,204.53,133.57 radius 17.505
> volume erase #4 center 168.54,202.55,126.8 radius 17.505
> volume erase #4 center 146.54,189.46,160.54 radius 11.403
> volume erase #4 center 145.82,185.88,159.37 radius 11.403
> volume erase #4 center 144.46,198.06,130.44 radius 11.403
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231128-2.cxs"
> hide #!1 models
> volume erase #4 center 191.82,176.91,153.78 radius 11.403
> volume erase #4 center 190.81,174.39,156.86 radius 11.403
> volume erase #4 center 198.16,186.35,145.64 radius 11.403
> surface dust #4 size 20
> surface dust #4 size 10
> volume #4 level 0.2766
> surface dust #4 size 15
> volume #4 level 0.3901
> volume #4 level 0.3156
> volume erase #4 center 188.57,192.41,144.74 radius 11.403
> volume erase #4 center 200.95,187.67,156.72 radius 11.403
> volume erase #4 center 197.59,184.43,159.31 radius 11.403
> show #!1 models
> hide #!1 models
> surface dust #4 size 10
> surface dust #4 size 20
> volume #4 level 0.2376
> volume #4 level 0.3546
> volume #4 level 0.3192
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231128-3.cxs" includeMaps
> true
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!4 models
> lighting soft
> hide #!1 models
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting flat
> lighting full
[Repeated 1 time(s)]
> volume #4 level 0.2483
> volume #4 level 0.3475
> graphics silhouettes false
> lighting full
> lighting soft
> lighting flat
[Repeated 3 time(s)]
> lighting soft
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> hide #!4 models
> show #!1 models
> color (#!1 & sel) light gray
> select clear
> lighting soft
> show #!4 models
> color zone #4 near all distance 7
> hide #!1 models
> volume #4 level 0.2199
> volume #4 level 0.2447
> show #!1 models
> hide #!4 models
> select /B
2824 atoms, 2885 bonds, 357 residues, 1 model selected
> ui tool show "Color Actions"
> color sel salmon
> select clear
> show #!4 models
> color zone #4 near all distance 7
> ui tool show "Color Actions"
> hide #!1 models
> volume #4 level 0.2483
> lighting soft
> lighting simple
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> surface dust #4 size 10
> surface dust #4 size 15
> surface dust #4 size 20
> show #!1 models
> volume #4 level 0.5425
> volume #4 level 0.2589
> hide #!1 models
> hide #!4 models
> show #!4 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231128-4.cxs" includeMaps
> true
> open "D:/PTH1R-Arrestin
> paper/map/cryosparc_P119_J938_003_volume_map_sharp.mrc"
Opened cryosparc_P119_J938_003_volume_map_sharp.mrc as #5, grid size
360,360,360, pixel 0.73, shown at level 0.145, step 2, values float32
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> volume #5 step 1
> volume #5 level 0.1203
> volume #5 level 0.08103
> hide #!2 models
> show #!4 models
> volume #4 level 0.3688
> volume #4 level 0.25
> volume #4 level 0.24
> volume #4 level 0.25
> volume #4 level 0.26
> lighting soft
> lighting simple
> lighting full
> lighting simple
> open "D:/PTH1R-Arrestin paper/map/1.py"
Traceback (most recent call last):
File "D:/PTH1R-Arrestin paper/map/1.py", line 3, in <module>
import cPickle, base64
ModuleNotFoundError: No module named 'cPickle'
Error opening python file D:/PTH1R-Arrestin paper/map/1.py
> volume #4 level 0.248
> volume #4 level 0.28
> volume #4 level 0.26
> volume #4 level 0.27
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #4 level 0.2558
> volume #4 level 0.27
> volume #4 level 0.2062
> volume #4 level 0.27
> show #!2 models
> volume #2 level 0.1632
> volume #2 level 0.1207
> ui mousemode right "translate selected models"
> select add #5
2 models selected
> view matrix models #5,1,0,0,29.621,0,1,0,-43.492,0,0,1,38.162
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.96769,-0.21204,0.13641,301.45,-0.18559,0.96527,0.18386,-37.578,-0.17065,0.15261,-0.97344,290.74
> view matrix models
> #5,-0.91355,-0.27283,0.30165,281.43,-0.37346,0.85643,-0.35644,70.42,-0.1611,-0.43828,-0.88428,357.17
> view matrix models
> #5,-0.77999,-0.58395,-0.22499,372.14,-0.41348,0.75077,-0.51515,109.98,0.46974,-0.30878,-0.82704,248.98
> view matrix models
> #5,-0.99342,-0.085037,-0.076743,314.92,-0.059169,0.95463,-0.29187,7.445,0.098081,-0.28541,-0.95337,311.14
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.99342,-0.085037,-0.076743,297.55,-0.059169,0.95463,-0.29187,69.486,0.098081,-0.28541,-0.95337,311.34
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.99878,0.032245,-0.037509,277.61,0.041809,0.95556,-0.29181,55.97,0.026433,-0.29302,-0.95574,322.15
> view matrix models
> #5,-0.89917,0.3754,-0.2249,242.3,0.42058,0.8833,-0.20713,4.6907,0.12089,-0.28083,-0.95211,307.54
> view matrix models
> #5,-0.89313,0.388,-0.22755,240.15,0.41195,0.90871,-0.067444,-15.286,0.18061,-0.15397,-0.97143,285.12
> view matrix models
> #5,-0.94212,0.30959,-0.12869,244.59,0.32004,0.94481,-0.070043,-7.6016,0.099907,-0.10718,-0.98921,291.81
> ui mousemode right zoom
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.94212,0.30959,-0.12869,244.51,0.32004,0.94481,-0.070043,2.1786,0.099907,-0.10718,-0.98921,291.54
> ui tool show "Fit in Map"
> fitmap #5 inMap #2
Fit map cryosparc_P119_J938_003_volume_map_sharp.mrc in map
J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc using 1059748 points
correlation = 0.6472, correlation about mean = 0.3077, overlap = 2.431e+04
steps = 236, shift = 16, angle = 21 degrees
Position of cryosparc_P119_J938_003_volume_map_sharp.mrc (#5) relative to
J1221_011_volume_map_DeepEMhancer_wideTarget20231127.mrc (#2) coordinates:
Matrix rotation and translation
-0.99918383 -0.02198311 -0.03388831 299.43553129
-0.02210267 0.99975072 0.00315753 31.41065309
0.03381044 0.00390397 -0.99942064 284.09309169
Axis 0.01102529 -0.99993766 -0.00176598
Axis point 147.48627757 0.00000000 144.55644787
Rotation angle (degrees) 178.06008214
Shift along axis -28.60903496
> select subtract #5
Nothing selected
> hide #!2 models
> hide #!4 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!4 models
> volume #4 level 0.28
> volume #4 level 0.27
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> save "D:/PTH1R-Arrestin paper/figs20231123/20231128-1.png" width 2000 height
> 1510 supersample 3 transparentBackground true
> hide #!4 models
> show #!1 models
> lighting full
[Repeated 1 time(s)]
> lighting simple
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231128-5.cxs"
> save "D:/PTH1R-Arrestin paper/figs20231123/20231128-2.png" width 2000 height
> 1510 supersample 3 transparentBackground true
> hide #!1 models
> show #!5 models
> volume #5 level 0.1
> volume #5 color #fdeeff
> volume #5 color #7c8283
> volume #5 color #ecf7f9
> hide #!4 models
> volume #5 level 0.2
> volume #5 level 0.12
> volume #5 level 0.1
> volume #5 level 0.2
> volume #5 level 0.1
> color #5 light gray
> color #5 dark gray
> color #5 light gray
> transparency #5 50
> save "D:/PTH1R-Arrestin paper/figs20231123/20231128-3.png" width 2000 height
> 1510 supersample 3 transparentBackground true
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231128-6.cxs"
> help help:user
> hide #!5 models
> show #!1 models
> save "D:/PTH1R-Arrestin paper/figs20231123/20231128-4.png" width 2000 height
> 1510 supersample 3 transparentBackground true
> help help:user
> show #!4 models
> hide #!4 models
> select /C
1694 atoms, 1738 bonds, 226 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium sea green
> color sel sea green
> color sel medium turquoise
> color sel light slate gray
> color sel slate gray
> color sel dark gray
> color sel gray
> color sel light steel blue
> color sel gray
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231128-7.cxs"
——— End of log from Tue Nov 28 18:00:22 2023 ———
opened ChimeraX session
> delete atoms sel
> delete bonds sel
> select /E
1617 atoms, 1652 bonds, 2 pseudobonds, 218 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231128-8.cxs"
> open "D:/PTH1R-Arrestin paper/6nbfZLHLAPTH.pdb"
6nbfZLHLAPTH.pdb title:
Cryo-em structure of parathyroid hormone receptor type 1 In complex with A
long-acting parathyroid hormone analog and G protein [more info...]
Chain information for 6nbfZLHLAPTH.pdb #3
---
Chain | Description | UniProt
A | GS protein α subunit |
B | transducin β chain 1 | GBB1_RAT 2-340
G | G γ-I | GBG2_BOVIN 1-71
N | nanobody-35 |
P | long-acting parathyroid hormone analog |
R | parathyroid hormone/parathyroid hormone-related peptide receptor |
PTH1R_HUMAN 27-502
Non-standard residues in 6nbfZLHLAPTH.pdb #3
---
CLR — cholesterol
PLM — palmitic acid
> hide atoms
> show cartoons
> matchmaker #3/R to #1/A
No 'to' model specified
> matchmaker #3/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker R-Arr-fab-coot-refine20231127.pdb, chain R (#1) with
6nbfZLHLAPTH.pdb, chain R (#3), sequence alignment score = 1604.3
RMSD between 272 pruned atom pairs is 0.973 angstroms; (across all 345 pairs:
5.217)
> hide #!1 models
> hide #3.1 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231128-8.cxs"
> select #3/R
3265 atoms, 3373 bonds, 3 pseudobonds, 378 residues, 2 models selected
> color (#!3 & sel) purple
> show #!1 models
> ui tool show "Color Actions"
> color sel medium orchid
> color sel orchid
> select #3/N
961 atoms, 983 bonds, 126 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> graphics silhouettes true
> lighting full
> lighting soft
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231128-9.cxs"
> cartoon style width 1.5 thickness 0.3
> select #3/R
3265 atoms, 3373 bonds, 3 pseudobonds, 378 residues, 2 models selected
> ui tool show "Color Actions"
> color sel medium orchid
> color sel medium violet red
> color sel orchid
> color sel dark violet
> color sel medium purple
> color sel steel blue
> color sel cadet blue
> color sel royal blue
> color sel dark orchid
> color sel light sea green
> color sel green
> color sel lime green
> color sel olive drab
> color sel sea green
> color sel pale violet red
> color sel medium turquoise
> color sel dark orchid
> color sel purple
> color sel orchid
> select clear
> graphics silhouettes false
> graphics silhouettes true
> 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 soft
> select #3/B
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium aquamarine
> color sel dark cyan
> color sel teal
> color sel cadet blue
> color sel steel blue
[Repeated 1 time(s)]
> color sel dark cyan
> select clear
> cartoon style width 2 thickness 0.5
> select #3/B
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> color sel teal
> color sel cadet blue
> select clear
> transparency 10 cartoons
> transparency 90 cartoons
> transparency 0 cartoons
> transparency 5 cartoons
> transparency 0 cartoons
> lighting full
> transparency 10 cartoons
> transparency 50 cartoons
> transparency 10 cartoons
> lighting soft
> lighting simple
> transparency 10 cartoons
> select #3/B
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> color sel dark cyan
> select clear
> select #3/B
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> color sel light sea green
> select clear
> select #3/G
436 atoms, 442 bonds, 57 residues, 1 model selected
> ui tool show "Color Actions"
> color sel maroon
> color sel dark red
> color sel fire brick
> color sel olive
> color sel green
> color sel lime green
> color sel cornflower blue
> color sel indigo
> color sel dark blue
> color sel navy
> color sel royal blue
> graphics silhouettes false
> graphics silhouettes true
> color sel orange
> color sel green yellow
> color sel pale violet red
> color sel slate gray
> color sel cadet blue
> color sel steel blue
> color sel olive drab
> color sel sea green
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231128-10.cxs"
> select #3/P
271 atoms, 276 bonds, 32 residues, 1 model selected
> color sel light gray
> color sel powder blue
> color sel hot pink
> color sel dark violet
> color sel pale green
> color sel light coral
> color sel powder blue
> color sel light steel blue
> color sel light blue
> select clear
> select #3/A
1890 atoms, 1924 bonds, 3 pseudobonds, 227 residues, 2 models selected
> color sel dark gray
> color sel gray
> color sel dim gray
> color sel gray
> color sel slate gray
> color sel blue violet
> color sel purple
> color sel cornflower blue
> color sel light sea green
> color sel turquoise
> color sel dodger blue
> select clear
> hide #!1 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231128-11.cxs"
——— End of log from Wed Nov 29 00:17:11 2023 ———
opened ChimeraX session
> show #!1 models
> hide #!1 models
> select #3/P
271 atoms, 276 bonds, 32 residues, 1 model selected
> ui tool show "Color Actions"
> color sel olive
> show #!1 models
> color sel red
> color sel crimson
> ui tool show "Color Actions"
> color sel lime
> color sel green
> color sel forest green
> color sel sea green
> color sel green
> select clear
> select #3/G
436 atoms, 442 bonds, 57 residues, 1 model selected
> ui tool show "Color Actions"
> color sel sienna
> color sel chocolate
> color sel cadet blue
> color sel teal
> color sel steel blue
> select clear
> select #3/A
1890 atoms, 1924 bonds, 3 pseudobonds, 227 residues, 2 models selected
> color sel chocolate
> color sel slate gray
> color sel light slate gray
> color sel silver
> select clear
> hide #!1 models
> show #!1 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231129-1.cxs"
——— End of log from Wed Nov 29 12:06:41 2023 ———
opened ChimeraX session
> cartoon style #!1,3 modeHelix tube sides 20
> save "D:/PTH1R-Arrestin paper/figs20231123/20231129-3.png" width 2000 height
> 1218 supersample 3 transparentBackground true
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231129-2.cxs"
——— End of log from Wed Nov 29 13:39:51 2023 ———
opened ChimeraX session
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231202-1.cxs"
> open "D:/PTH1R-Arrestin paper/map/R-Arr-fab-coot-1220231201-2.pdb"
Summary of feedback from opening D:/PTH1R-Arrestin paper/map/R-Arr-fab-
coot-1220231201-2.pdb
---
warning | End residue of secondary structure not found: SHEET 3 K 3 VAL C 218
VAL C 222 -1 N VAL C 222 O TYR C 205
Chain information for R-Arr-fab-coot-1220231201-2.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 #!3 models
> hide #!6 models
> close #2
> select #6/B
2733 atoms, 2789 bonds, 2 pseudobonds, 345 residues, 2 models selected
> ui tool show "Color Actions"
> color sel deep sky blue
[Repeated 1 time(s)]
> show #!6 models
> hide #!1 models
> hide sel atoms
> show sel cartoons
> hide #6.1 models
> select #6/E
1587 atoms, 1623 bonds, 1 pseudobond, 207 residues, 2 models selected
> delete atoms (#!6 & sel)
> delete bonds (#!6 & sel)
> select #6/C
1553 atoms, 1595 bonds, 1 pseudobond, 206 residues, 2 models selected
> delete atoms (#!6 & sel)
> delete bonds (#!6 & sel)
> hide #!6 atoms
> show #!6 cartoons
> select #6/R
2912 atoms, 2988 bonds, 5 pseudobonds, 355 residues, 2 models selected
> ui tool show "Color Actions"
> color sel deep sky blue
> select #6/L
292 atoms, 297 bonds, 35 residues, 1 model selected
> ui tool show "Color Actions"
> color sel goldenrod
> select #6/B
2733 atoms, 2789 bonds, 2 pseudobonds, 345 residues, 2 models selected
> ui tool show "Color Actions"
> color sel salmon
> select clear
> show #!1 models
> hide #!1 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231202-1.cxs"
> cartoon style #!6 modeHelix tube sides 20
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!6 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!6 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!6 models
> show #!1 models
> show #!3 models
> cartoon style width 2 thickness 0.5
> cartoon style width 1.5 thickness 0.3
> cartoon style width 2 thickness 0.5
> hide #!1 models
> show #!6 models
> hide #!3 models
> cartoon style #!6 xsection oval modeHelix default
> cartoon style #!6 modeHelix tube sides 20
> show #!3 models
> cartoon style width 1.5 thickness 0.3
[Repeated 1 time(s)]
> hide #!3 models
> cartoon style width 1.5 thickness 0.5
[Repeated 1 time(s)]
> cartoon style width 2 thickness 0.5
[Repeated 2 time(s)]
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> hide #!6 models
> show #!1 models
> hide #!1 models
> show #!6 models
> hide #!6 models
> show #!1 models
> hide #!1 models
> show #!6 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231202-1.cxs"
——— End of log from Sat Dec 2 16:19:50 2023 ———
opened ChimeraX session
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-1.cxs"
> open "D:/PTH1R-Arrestin paper/6PWC NTSR1.pdb"
Chain information for 6PWC NTSR1.pdb #2
---
Chain | Description
A | No description available
B | No description available
R | No description available
> hide #2.1 models
> select #2/A
1935 atoms, 1963 bonds, 350 residues, 1 model selected
> matchmaker #2/B to #6/A
No 'to' model specified
> select clear
> matchmaker #2/B to #6/A
No 'to' model specified
> select #6/B
2733 atoms, 2789 bonds, 2 pseudobonds, 345 residues, 2 models selected
> select clear
> matchmaker #2/B to #6/A
No 'to' model specified
> select #2/B
27 atoms, 27 bonds, 5 residues, 1 model selected
> close #1
> matchmaker #2/B to #6/A
No 'to' model specified
> open "D:/PTH1R-Arrestin paper/6UP7NTSR1.pdb"
Chain information for 6UP7NTSR1.pdb #1
---
Chain | Description
B | No description available
C | No description available
R | No description available
V | No description available
> select #1/C
48 atoms, 49 bonds, 6 residues, 1 model selected
> select #1/V
45 atoms, 44 bonds, 9 residues, 1 model selected
> select #1/B
2063 atoms, 2098 bonds, 348 residues, 1 model selected
> select #2/R
1824 atoms, 1840 bonds, 2 pseudobonds, 323 residues, 2 models selected
> matchmaker #2/B to #6/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker R-Arr-fab-coot-1220231201-2.pdb, chain R (#6) with 6PWC NTSR1.pdb,
chain B (#2), sequence alignment score = 12.3
RMSD between 4 pruned atom pairs is 0.767 angstroms; (across all 5 pairs:
1.920)
> matchmaker #2/R to #6/A
No 'to' model specified
> matchmaker #2/R to #6/A
No 'to' model specified
> matchmaker #2/R to #6/A
No 'to' model specified
> matchmaker #2/R to #6/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker R-Arr-fab-coot-1220231201-2.pdb, chain R (#6) with 6PWC NTSR1.pdb,
chain R (#2), sequence alignment score = 327
RMSD between 39 pruned atom pairs is 1.206 angstroms; (across all 286 pairs:
11.550)
> matchmaker #1/R to #6/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker R-Arr-fab-coot-1220231201-2.pdb, chain R (#6) with 6UP7NTSR1.pdb,
chain R (#1), sequence alignment score = 318.8
RMSD between 38 pruned atom pairs is 0.882 angstroms; (across all 279 pairs:
9.812)
> hide #!6 models
> hide #1.1 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> open "D:/PTH1R-Arrestin paper/5w0prdophsin.pdb"
Chain information for 5w0prdophsin.pdb #7
---
Chain | Description
D | No description available
> matchmaker #7/D to #6/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker R-Arr-fab-coot-1220231201-2.pdb, chain R (#6) with
5w0prdophsin.pdb, chain D (#7), sequence alignment score = 371
RMSD between 31 pruned atom pairs is 0.864 angstroms; (across all 332 pairs:
14.356)
> hide #!1 models
> hide #!2 models
> open "D:/PTH1R-Arrestin paper/6TKO B1AR.pdb"
Chain information for 6TKO B1AR.pdb #8
---
Chain | Description
A | No description available
B | No description available
> matchmaker #8/A to #6/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker R-Arr-fab-coot-1220231201-2.pdb, chain R (#6) with 6TKO B1AR.pdb,
chain A (#8), sequence alignment score = 295.2
RMSD between 58 pruned atom pairs is 1.112 angstroms; (across all 261 pairs:
9.740)
> open "D:/PTH1R-Arrestin paper/6U1N M2R.pdb"
Chain information for 6U1N M2R.pdb #9
---
Chain | Description
C | No description available
R | No description available
> matchmaker #9/R to #6/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker R-Arr-fab-coot-1220231201-2.pdb, chain R (#6) with 6U1N M2R.pdb,
chain R (#9), sequence alignment score = 293.2
RMSD between 59 pruned atom pairs is 1.216 angstroms; (across all 260 pairs:
8.325)
> hide #9.1 models
> hide #8.1 models
> hide #7.1 models
> open "D:/PTH1R-Arrestin paper/7R0C V2R.pdb"
Chain information for 7R0C V2R.pdb #10
---
Chain | Description
A | No description available
B | No description available
C | No description available
> matchmaker #10/A to #6/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker R-Arr-fab-coot-1220231201-2.pdb, chain R (#6) with 7R0C V2R.pdb,
chain A (#10), sequence alignment score = 302
RMSD between 74 pruned atom pairs is 1.260 angstroms; (across all 267 pairs:
8.694)
> hide #!8 models
> hide #!7 models
> hide #!9 models
> hide #10.1 models
> hide #!6 models
> hide #!10 models
> show #!10 models
> show #!6 models
> open "D:/PTH1R-Arrestin paper/7SRSH2B.pdb"
Chain information for 7SRSH2B.pdb #11
---
Chain | Description
C | No description available
P | No description available
Q | No description available
R | No description available
> matchmaker #11/R to #6/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker R-Arr-fab-coot-1220231201-2.pdb, chain R (#6) with 7SRSH2B.pdb,
chain R (#11), sequence alignment score = 308.6
RMSD between 65 pruned atom pairs is 1.166 angstroms; (across all 264 pairs:
8.009)
> hide #11.1 models
> hide #!11 models
> cartoon style #!6,10 modeHelix tube sides 20
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-1.cxs"
> hide #!10 models
> show #!7 models
> hide #!6-7 atoms
> cartoon style #!6-7 modeHelix tube sides 20
> select #7/D
6108 atoms, 6259 bonds, 2 pseudobonds, 774 residues, 2 models selected
> select clear
> hide #!6 models
> select #7/D:324
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #7/D:321
12 atoms, 10 bonds, 2 residues, 1 model selected
> select up
163 atoms, 162 bonds, 22 residues, 1 model selected
> select clear
> select #7/D：-85 to 324
Expected an objects specifier or a keyword
> select #7/D:-85 to 324
Expected a keyword
> select sequence #7:D
Nothing selected
>
Unknown command: sequence #7/D
>
Unknown command: sequence #7/chian D
> chian D
Unknown command: sequence chian D
> chian /D
Unknown command: sequence chian /D
> chian/D
Unknown command: sequence chian/D
> sequence chain /D
Alignment identifier is 7/D
> select #7/D:-85--84
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #7/D:-85-336
3315 atoms, 3410 bonds, 1 pseudobond, 417 residues, 2 models selected
> select clear
> select #7/D:-84--83
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #7/D:-84--82
20 atoms, 19 bonds, 3 residues, 1 model selected
> select #7/D:-85--15
569 atoms, 578 bonds, 71 residues, 1 model selected
> select #7/D:-85-341
3357 atoms, 3452 bonds, 1 pseudobond, 422 residues, 2 models selected
> select #7/D:343
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/D:343-2012
13 atoms, 11 bonds, 1 pseudobond, 2 residues, 2 models selected
> select clear
> select #7/D:343
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/D:-85-343
3370 atoms, 3465 bonds, 1 pseudobond, 424 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light sea green
> show #!2 models
> hide #!2 models
> show #!6 models
> select #7/D:2012-2013
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #7/D:2012-2361
2738 atoms, 2794 bonds, 350 residues, 1 model selected
> color sel dark gray
> select clear
> hide #!7 models
> show #!8 models
> select #8/A
2266 atoms, 2320 bonds, 2 pseudobonds, 294 residues, 2 models selected
> ui tool show "Color Actions"
> color sel yellow
> color sel olive
> color sel dark violet
> select #8/B
2677 atoms, 2733 bonds, 2 pseudobonds, 343 residues, 2 models selected
> color sel steel blue
> cartoon style (#!8 & sel) modeHelix tube sides 20
> color sel cadet blue
> show #!7 models
> color sel teal
> color sel steel blue
> color sel royal blue
> color sel dark sea green
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-1.cxs"
> show #!9 models
> cartoon style (#!8 & sel) modeHelix tube sides 20
> select clear
> select #9/R
1689 atoms, 1724 bonds, 2 pseudobonds, 279 residues, 2 models selected
> color sel chocolate
> color sel tomato
[Repeated 2 time(s)]
> select #9/C
2547 atoms, 2605 bonds, 359 residues, 1 model selected
> color sel sienna
> color sel hot pink
> cartoon style width 1.5 thickness 0.3
> select clear
> cartoon style width 1.5 thickness 0.3
> cartoon style #!6-9 xsection oval modeHelix default
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-1.cxs"
> select #9/R
1689 atoms, 1724 bonds, 2 pseudobonds, 279 residues, 2 models selected
> ui tool show "Color Actions"
> color sel coral
> color sel rosy brown
> show #!10 models
> select #10/A
2181 atoms, 2235 bonds, 4 pseudobonds, 284 residues, 2 models selected
> color sel peru
> color sel cornflower blue
[Repeated 1 time(s)]
> color sel light green
[Repeated 1 time(s)]
> color sel pale green
[Repeated 1 time(s)]
> color sel aquamarine
[Repeated 1 time(s)]
> color sel sky blue
[Repeated 1 time(s)]
> color sel yellow green
> cartoon style (#!10 & sel) xsection oval modeHelix default
> color sel lime green
> select #10/C
2810 atoms, 2872 bonds, 1 pseudobond, 353 residues, 2 models selected
> color sel orange red
> color sel crimson
> color sel fire brick
> color sel indian red
> color sel orange red
> show #!11 models
> select clear
> select #11/R
2272 atoms, 2329 bonds, 2 pseudobonds, 291 residues, 2 models selected
> color sel light salmon
> color sel dark khaki
> show #!1 models
> show #!2 models
> select clear
> cartoon style #!1-2,6-11 modeHelix tube sides 20
> hide #!1-2,6-11 atoms
> cartoon style width 1.2 thickness 0.3
[Repeated 1 time(s)]
> cartoon style width 1 thickness 0.3
> cartoon style width 1 thickness 0.2
> cartoon style width 1.5 thickness 0.5
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-1.cxs"
> cartoon style width 1.5 thickness 0.3
> select #11/R
2272 atoms, 2329 bonds, 2 pseudobonds, 291 residues, 2 models selected
> select #11/C
2673 atoms, 2735 bonds, 1 pseudobond, 354 residues, 2 models selected
> ui tool show "Color Actions"
> color sel blue
> color sel navy
> color sel spring green
> color sel magenta
> color sel deep pink
> color sel medium violet red
> color sel cadet blue
> color sel dark goldenrod
> color sel dark khaki
> ui tool show "Color Actions"
> select #11/R
2272 atoms, 2329 bonds, 2 pseudobonds, 291 residues, 2 models selected
> color sel peru
> color sel crimson
> color sel magenta
> select #1/R
2010 atoms, 2055 bonds, 1 pseudobond, 323 residues, 2 models selected
> ui tool show "Color Actions"
> color sel burly wood
> color sel tan
> color sel light coral
> color sel light steel blue
> color sel powder blue
> color sel red
[Repeated 1 time(s)]
> color sel crimson
> color sel dark red
> color sel maroon
> color sel fire brick
> color sel tomato
> color sel lime
[Repeated 1 time(s)]
> color sel forest green
> color sel cyan
> color sel deep sky blue
> color sel cadet blue
> color sel medium blue
> color sel blue
> color sel royal blue
> color sel dark slate gray
> ui tool show "Color Actions"
> color sel green
> color sel chartreuse
> color sel spring green
> color sel lime green
> color sel turquoise
> color sel steel blue
> color sel medium blue
> color sel dark blue
> color sel indigo
> color sel dark olive green
> select #1/B
2063 atoms, 2098 bonds, 348 residues, 1 model selected
> color sel cadet blue
> color sel steel blue
> color sel sea green
> color sel powder blue
> color sel light steel blue
> color sel ghost white
> color sel black
> color sel yellow
> select #2/R
1824 atoms, 1840 bonds, 2 pseudobonds, 323 residues, 2 models selected
> color sel light steel blue
> select #2/A
1935 atoms, 1963 bonds, 350 residues, 1 model selected
> color sel light sky blue
> color sel sky blue
[Repeated 1 time(s)]
> color sel powder blue
> color sel light sky blue
> color sel dark turquoise
> color sel dodger blue
> color sel blue violet
> color sel blue
> color sel royal blue
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-1.cxs"
> select #2/A
1935 atoms, 1963 bonds, 350 residues, 1 model selected
> select clear
> hide #!1 models
> hide #!2 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!11 models
> hide #!10 models
> show #!1 models
> select clear
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!7 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-2.cxs"
> select #7/D:-85--83
23 atoms, 22 bonds, 3 residues, 1 model selected
> select #7/D:-85--7
640 atoms, 650 bonds, 79 residues, 1 model selected
> select clear
> select #7/D:-1-0
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #7/D:-85-0
697 atoms, 710 bonds, 86 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-3.cxs"
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!11 models
> select #11/Q
959 atoms, 985 bonds, 127 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #11/P
768 atoms, 787 bonds, 107 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-3.cxs"
> show #!6 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-3.cxs"
> hide #!11 models
> select #6/B
2733 atoms, 2789 bonds, 2 pseudobonds, 345 residues, 2 models selected
> surface (#!6 & sel)
> select clear
[Repeated 1 time(s)]
> lighting simple
> lighting full
[Repeated 1 time(s)]
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting flat
[Repeated 2 time(s)]
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting full
> lighting shadows false
> graphics silhouettes true
> lighting simple
> lighting full
> lighting shadows false
> show #!3 models
> hide #!3 models
> cartoon style width 2 thickness 0.5
> show #!8 models
> select #8/B
2677 atoms, 2733 bonds, 2 pseudobonds, 343 residues, 2 models selected
> surface (#!8 & sel)
> select clear
> show #!1 models
> select #1/B
2063 atoms, 2098 bonds, 348 residues, 1 model selected
> surface sel
> select clear
> hide #!1 models
> show #!1 models
> hide #!8 models
> hide #8.2 models
> hide #1.2 models
> hide #!1 models
> surface hidePatches #6.2#!6
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-1.png" width 2000
> height 1150 supersample 3 transparentBackground true
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-4.cxs"
> show #!7 models
> show #!6-7 atoms
> hide #!6-7 atoms
> open "D:/PTH1R-Arrestin paper/8JRV GCGR.pdb"
Chain information for 8JRV GCGR.pdb #12
---
Chain | Description
A | No description available
G | No description available
R | No description available
> hide #12.1 models
> select #12/R
2338 atoms, 2389 bonds, 4 pseudobonds, 319 residues, 2 models selected
> matchmaker #12/R to #6/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker R-Arr-fab-coot-1220231201-2.pdb, chain R (#6) with 8JRV GCGR.pdb,
chain R (#12), sequence alignment score = 661.6
RMSD between 125 pruned atom pairs is 1.226 angstroms; (across all 295 pairs:
11.525)
> show #!1 models
> show #!2 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-5.cxs"
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> ui tool show "Color Actions"
> color sel silver
> color sel light gray
> color sel ghost white
> color sel light slate gray
> color sel lavender
> matchmaker #12/R to #12/A
Must use different reference and match structures
> select #12/A
2672 atoms, 2733 bonds, 1 pseudobond, 356 residues, 2 models selected
> color sel teal
> color sel dark cyan
> color sel medium aquamarine
> color sel light sea green
> color sel cadet blue
> color sel sky blue
> color sel pale turquoise
> color sel blue
> color sel indigo
> color sel sky blue
> color sel light sky blue
> color sel medium aquamarine
> color sel cornflower blue
> color sel teal
> color sel cadet blue
> color sel steel blue
> color sel sky blue
> color sel light blue
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-5.cxs"
> select clear
> hide #!1-2,6-12 atoms
> cartoon style #6.2#!1-2,6-12 modeHelix tube sides 20
> hide #!12 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> show #!6 models
> hide #!2 models
> hide #!1 models
> show #!7 models
> help help:user
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-5.cxs"
> cartoon style helix width 1.5 thickness 0.3
[Repeated 1 time(s)]
> cartoon style helix width 1 thickness 0.3
[Repeated 1 time(s)]
> cartoon style helix width 1 thickness 0.2
> select clear
> cartoon style helix width 1 thickness 0.2
> lighting simple
[Repeated 1 time(s)]
> lighting full
> lighting shadows false
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-2rho.png" width 2000
> height 1150 supersample 3 transparentBackground true
> hide #!7 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!8 models
> hide #!6 models
> select ::name="H98"
25 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> color sel byhetero
> select clear
> show #!6 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-2B1AR.png" width
> 2000 height 1150 supersample 3 transparentBackground true
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!9 models
> select ::name="2CU"
29 atoms, 32 bonds, 1 residue, 1 model selected
> color sel purple
> show sel atoms
> color sel byhetero
> size sel stickRadius 0.3
Changed 32 bond radii
> color sel lime
> color sel byhetero
> select clear
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-3M2R.png" width 2000
> height 1150 supersample 3 transparentBackground true
> hide #!9 models
> show #!8 models
> select ::name="H98"
25 atoms, 26 bonds, 1 residue, 1 model selected
> size sel stickRadius 0.3
Changed 26 bond radii
> select clear
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-2rho.png" width 2000
> height 1150 supersample 3 transparentBackground true
> hide #!8 models
> show #!10 models
> hide #!6 models
> show #!6 models
> select #10/B
75 atoms, 77 bonds, 10 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark slate blue
> color sel blue
> color sel medium blue
> color sel purple
> color sel dark magenta
> cartoon style helix width 2 thickness 0.5
> select clear
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-3V2R.png" width 2000
> height 1150 supersample 3 transparentBackground true
> hide #!10 models
> show #!11 models
> hide #!6 models
> select ::name="7LD"
24 atoms, 27 bonds, 1 residue, 1 model selected
> show sel atoms
> size sel stickRadius 0.3
Changed 27 bond radii
> color sel forest green
> color sel byhetero
> select clear
> show #!6 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-3H2BR.png" width
> 2000 height 1150 supersample 3 transparentBackground true
> hide #!11 models
> show #!12 models
> select #12/G
168 atoms, 171 bonds, 25 residues, 1 model selected
> color sel orange
> color sel light sea green
> ui tool show "Color Actions"
> color sel steel blue
> color sel rebecca purple
> color sel dark slate blue
> color sel medium slate blue
> color sel rebecca purple
> color sel violet
> ui tool show "Color Actions"
> select clear
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-3GCGR.png" width
> 2000 height 1150 supersample 3 transparentBackground true
> hide #!12 models
> show #!1 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-3NTSR16UP7.png"
> width 2000 height 1150 supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> show #!2 models
> show #!8 models
> show #8.2 models
> show #!7 models
> show #!9 models
> show #!10 models
> show #!12 models
> show #!11 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #8.2 models
> hide #!8 models
> hide #!7 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #1.1 models
> select #1/B
2063 atoms, 2098 bonds, 348 residues, 1 model selected
> show sel cartoons
> cartoon style helix width 2 thickness 0.5
> ui tool show "Color Actions"
> color sel dark magenta
> undo
[Repeated 3 time(s)]
> cartoon style helix width 1.5 thickness 0.3
[Repeated 1 time(s)]
> select #1/A
Nothing selected
> show #!1,6 cartoons
> hide #!1,6 cartoons
> show #!1,6 cartoons
> select #1/A
Nothing selected
> show #!1,6 atoms
> hide #!1,6 atoms
> hide #!6 models
> select #1/C
48 atoms, 49 bonds, 6 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light coral
> color sel sienna
> color sel saddle brown
> color sel brown
> cartoon style helix width 1.5 thickness 0.3
[Repeated 3 time(s)]
> cartoon style helix width 2 thickness 0.5
> select clear
> cartoon style helix width 2 thickness 0.5
> ui tool show "Color Actions"
> show #!6 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-3NTSR16UP7.png"
> width 2000 height 1150 supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> cartoon style helix width 2 thickness 0.5
> select #2/b
27 atoms, 27 bonds, 5 residues, 1 model selected
> hide #!6 models
> show sel cartoons
> ui tool show "Color Actions"
> color sel coral
> color sel peru
> select clear
> show #!6 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-3NTSR16pwc.png"
> width 2000 height 1150 supersample 3 transparentBackground true
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-6.cxs"
——— End of log from Mon Dec 4 15:32:57 2023 ———
opened ChimeraX session
> hide #!2 models
> show #!7 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-2rho.png" width 2000
> height 1150 supersample 3 transparentBackground true
> hide #!7 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!8 models
> hide #!8 models
> show #!9 models
> show #!10 models
> hide #!9 models
> show #!11 models
> show #!12 models
> show #!8 models
> show #!9 models
> show #!7 models
> show #!1 models
> show #!2 models
> hide #!12 models
> hide #!1 models
> hide #!2 models
> hide #!6 models
> hide #!7 models
> hide #!11 models
> show #!12 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> show #!6 models
> ui tool show "Side View"
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-7.cxs"
> cartoon style helix width 1.5 thickness 0.3
[Repeated 1 time(s)]
> cartoon style width 1.5 thickness 0.3
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-3GCGR-1.png" width
> 2000 height 1150 supersample 3 transparentBackground true
> cartoon style width 2 thickness 0.5
[Repeated 1 time(s)]
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-3GCGR-1.png" width
> 2000 height 1150 supersample 3 transparentBackground true
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-3GCGR-2.png" width
> 2000 height 1150 supersample 3 transparentBackground true
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-3GCGR-3.png" width
> 2000 height 1150 supersample 3 transparentBackground true
> lighting shadows true
> lighting simple
> lighting soft
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes true
> lighting simple
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-3GCGR-4.png" width
> 2000 height 1150 supersample 3 transparentBackground true
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-3GCGR-5.png" width
> 2000 height 1150 supersample 3 transparentBackground true
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-8.cxs"
> hide #!12 models
> show #!1 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-3NTSR16UP7-1.png"
> width 2000 height 1150 supersample 3 transparentBackground true
> hide #!1 models
> show #!8 models
> select #8/A
2266 atoms, 2320 bonds, 2 pseudobonds, 294 residues, 2 models selected
> select #8/B
2677 atoms, 2733 bonds, 2 pseudobonds, 343 residues, 2 models selected
> surface (#!8 & sel)
> undo
[Repeated 3 time(s)]
> show #!11 models
> show #!10 models
> show #!7 models
> show #!8 models
> show #!9 models
> surface hidePatches #6.2#8.2#!1,6-11
> transparency 10 cartoons
> transparency 0 cartoons
> show #!2 models
> transparency 500 cartoons
> transparency 50 cartoons
> transparency 20 cartoons
> transparency 0 cartoons
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!2 models
> hide #!1 models
> select #6/B
2733 atoms, 2789 bonds, 2 pseudobonds, 345 residues, 2 models selected
> surface (#!6 & sel)
> transparency (#!6 & sel) 90
> select clear
> show #!2 models
> hide #!2 models
> transparency #6.2#!6 90
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1/B
2063 atoms, 2098 bonds, 348 residues, 1 model selected
> surface (#!1 & sel)
> transparency (#!1 & sel) 90
> select clear
> transparency #1.2#6.2#!1,6 40
> transparency #1.2#6.2#!1,6 60
> transparency #1.2#6.2#!1,6 80
> show #!2 models
> select #2/A
1935 atoms, 1963 bonds, 350 residues, 1 model selected
> surface sel
> select clear
> transparency #1.2#2.2#6.2#!1-2,6 70
> select clear
> transparency #1.2#2.2#6.2#!1-2,6 90
> graphics silhouettes false
> graphics silhouettes true
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-4.png" width 2000
> height 1150 supersample 3 transparentBackground true
> hide #!1 models
> hide #!2 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> show #!12 models
> hide #!12 models
> hide #!10 models
> hide #!11 models
> select #7/D
5411 atoms, 5548 bonds, 2 pseudobonds, 688 residues, 2 models selected
> surface (#!7 & sel)
> undo
[Repeated 2 time(s)]
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!11 models
> show #!7 models
> surface hidePatches #7.2#!7
> show #!6 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> show #!7 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!7 models
> sequence chain /D
Destroying pre-existing alignment with identifier 7/D
Alignment identifier is 7/D
> select #7/D:2012
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #7/D:2012-2361
2738 atoms, 2794 bonds, 350 residues, 1 model selected
> surface (#!7 & sel)
> transparency (#!7 & sel) 70
> color (#!7 & sel) dark gray
> select clear
> hide #!7 models
> show #!8 models
> select #8/B
2677 atoms, 2733 bonds, 2 pseudobonds, 343 residues, 2 models selected
> surface (#!8 & sel)
> transparency (#!8 & sel) 70
> select clear
> show #!1 models
> show #!2 models
> show #!5 models
> hide #!5 models
> show #!7 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-9.cxs"
> hide #!7 models
> hide #!2 models
> hide #!1 models
> hide #!8 models
> show #!9 models
> select #9/C
2547 atoms, 2605 bonds, 359 residues, 1 model selected
> surface sel
> transparency (#!9 & sel) 70
> select clear
> hide #!9 models
> show #!10 models
> select #10/C
2810 atoms, 2872 bonds, 1 pseudobond, 353 residues, 2 models selected
> surface (#!10 & sel)
> transparency (#!10 & sel) 70
> select clear
> hide #!10 models
> show #!11 models
> select #11/C
2673 atoms, 2735 bonds, 1 pseudobond, 354 residues, 2 models selected
> surface (#!11 & sel)
> transparency (#!11 & sel) 70
> select clear
> show #!10 models
> show #!9 models
> show #!8 models
> show #!7 models
> show #!2 models
> show #!1 models
> show #!6 models
> transparency #1.2#2.2#6.2#7.2#8.2#9.2#10.2#11.2#!1-2,6-11 80
> transparency #1.2#2.2#6.2#7.2#8.2#9.2#10.2#11.2#!1-2,6-11 90
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-10.cxs"
——— End of log from Mon Dec 4 17:18:04 2023 ———
opened ChimeraX session
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!2 models
> hide #!1 models
> hide #!11 models
> hide #!10 models
> show #!6 models
> show #!1 models
> hide #!6 models
> hide #!1 models
> show #!6 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-11.png" width 2000
> height 1150 supersample 3 transparentBackground true
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-13.cxs"
——— End of log from Mon Dec 4 20:46:50 2023 ———
opened ChimeraX session
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!11 models
> show #!12 models
> show #!7 models
> show #!8 models
> hide #!12 models
> show #!2 models
> show #!9 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> select #1/V:413
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
45 atoms, 44 bonds, 9 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark olive green
> select clear
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-13.cxs"
> show #!6 models
> hide #!2 models
> hide #!1 models
> show #!7 models
> show #!1 models
> hide #!1 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!10 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> hide #!10 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!1 models
> cartoon style #1.2#6.2#!1,6 xsection oval modeHelix default
> cartoon style width 1.0 thickness 0.3
> cartoon style #1.2#6.2#!1,6 modeHelix tube sides 20
> cartoon style #1.2#6.2#!1,6 xsection oval modeHelix default
> lighting soft
> cartoon style #1.2#6.2#!1,6 xsection rectangle modeHelix default
> cartoon style (#1.2#6.2#!1,6 & coil) xsection oval
> cartoon style #1.2#6.2#!1,6 xsection barbell modeHelix default
> cartoon style #1.2#6.2#!1,6 modeHelix tube sides 20
> cartoon style width 1.5 thickness 0.3
> show #!2 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> cartoon style width 2 thickness 0.5
> cartoon style #1.2#2.2#6.2#7.2#8.2#9.2#10.2#11.2#!1-2,6-11 modeHelix tube
> sides 20
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> hide #!9 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> hide #!8 models
> hide #!7 models
> hide #!10 models
> hide #!2 models
> hide #!1 models
> lighting simple
[Repeated 2 time(s)]
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> show #!1 models
> show #!7 models
> hide #!7 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!1 models
> hide #!1 models
> show #!7 models
> hide #!7 models
> show #!1 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-17.png" width 2000
> height 1150 supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-18.png" width 2000
> height 1150 supersample 3 transparentBackground true
> hide #!2 models
> show #!7 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-19.png" width 2000
> height 1150 supersample 3 transparentBackground true
> hide #!7 models
> show #!8 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-20.png" width 2000
> height 1150 supersample 3 transparentBackground true
> hide #!8 models
> show #!9 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-21.png" width 2000
> height 1150 supersample 3 transparentBackground true
> hide #!9 models
> show #!10 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-22.png" width 2000
> height 1150 supersample 3 transparentBackground true
> hide #!10 models
> show #!11 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-23.png" width 2000
> height 1150 supersample 3 transparentBackground true
> hide #!11 models
> show #!12 models
> select #12/A
2672 atoms, 2733 bonds, 1 pseudobond, 356 residues, 2 models selected
> surface (#!12 & sel)
> transparency (#!12 & sel) 50
> transparency (#!12 & sel) 90
> select clear
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-24.png" width 2000
> height 1150 supersample 3 transparentBackground true
> hide #!12 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!8 models
> show #!7 models
> hide #!8 models
> hide #!7 models
> show #!9 models
> show #!7 models
> hide #!9 models
> show #!9 models
> show #!11 models
> hide #!9 models
> hide #!7 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20231204-16.cxs"
——— End of log from Mon Dec 4 22:44:42 2023 ———
opened ChimeraX session
> show #!5 models
> hide #!5 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20240106-5.cxs"
> open "D:/PTH1R-Arrestin paper/map/20240104-2/R-Arr-fab-
> coot-14_real_space_refined_032 Arrestin.pdb"
Chain information for R-Arr-fab-coot-14_real_space_refined_032 Arrestin.pdb
#13
---
Chain | Description
B | No description available
C | No description available
E | No description available
L | No description available
R | No description available
> hide #!6,11,13 atoms
> show #!6,11,13 cartoons
> select #13/E
1587 atoms, 1621 bonds, 1 pseudobond, 207 residues, 2 models selected
> hide sel cartoons
> select #13/C
1551 atoms, 1591 bonds, 1 pseudobond, 205 residues, 2 models selected
> hide sel cartoons
> select #13/B
2659 atoms, 2713 bonds, 2 pseudobonds, 334 residues, 2 models selected
> ui tool show "Color Actions"
> color sel salmon
> hide #!6 models
> select clear
> hide #13.1 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20240106-5.cxs"
> select #11/R
2272 atoms, 2329 bonds, 2 pseudobonds, 291 residues, 2 models selected
> hide sel cartoons
> surface (#!11 & sel)
> undo
[Repeated 1 time(s)]
> surface hidePatches #11.2-3#!11,13
> select #11/R
2272 atoms, 2329 bonds, 2 pseudobonds, 291 residues, 2 models selected
> hide sel cartoons
> select #13/R
2807 atoms, 2881 bonds, 5 pseudobonds, 341 residues, 2 models selected
> hide sel cartoons
> select #13/B
2659 atoms, 2713 bonds, 2 pseudobonds, 334 residues, 2 models selected
> surface (#!13 & sel)
> transparency (#!13 & sel) 70
> select #11/C
2673 atoms, 2735 bonds, 1 pseudobond, 354 residues, 2 models selected
> surface (#!11 & sel)
> transparency (#!11 & sel) 70
> undo
> select #11/C
2673 atoms, 2735 bonds, 1 pseudobond, 354 residues, 2 models selected
> transparency (#!11 & sel) 90
> select #13/C
1551 atoms, 1591 bonds, 1 pseudobond, 205 residues, 2 models selected
> select #13/C
1551 atoms, 1591 bonds, 1 pseudobond, 205 residues, 2 models selected
> transparency (#!13 & sel) 90
> select clear
Drag select of 33 residues
> hide sel cartoons
> show #!10 models
> select #10/A
2181 atoms, 2235 bonds, 4 pseudobonds, 284 residues, 2 models selected
> hide sel cartoons
Drag select of 8 residues
Drag select of 9 residues
> hide sel cartoons
> hide #!10 models
> hide #!11 models
> hide #!13 models
> show #!13 models
> hide #13.2 models
> show #13.2 models
> show #!2 models
> select #2/R
1824 atoms, 1840 bonds, 2 pseudobonds, 323 residues, 2 models selected
> hide sel cartoons
Drag select of 5 residues
> hide sel cartoons
> show #!7 models
> select #7/D
5411 atoms, 5548 bonds, 2 pseudobonds, 688 residues, 2 models selected
> hide sel cartoons
> hide #!2 models
> select #7/D
5411 atoms, 5548 bonds, 2 pseudobonds, 688 residues, 2 models selected
> show sel cartoons
> select clear
> hide #!13 models
> hide #13.2 models
Drag select of 5w0prdophsin.pdb_D SES surface, 29 of 632392 triangles, 220
residues
> hide sel cartoons
Drag select of 40 residues
> select down
1920 atoms, 242 residues, 2 models selected
> hide sel cartoons
Drag select of 2 residues
> hide sel cartoons
> select add #7/D:60
1943 atoms, 12 bonds, 245 residues, 2 models selected
> select up
2284 atoms, 2358 bonds, 289 residues, 2 models selected
> hide sel cartoons
> select add #7/D:319
2291 atoms, 2364 bonds, 290 residues, 2 models selected
> select up
2376 atoms, 2450 bonds, 300 residues, 2 models selected
> hide sel cartoons
> select add #7/D:66
2385 atoms, 2458 bonds, 301 residues, 2 models selected
> select up
2402 atoms, 2475 bonds, 303 residues, 2 models selected
> hide sel cartoons
> select add #7/D:147
2413 atoms, 2485 bonds, 304 residues, 2 models selected
> select up
2453 atoms, 2527 bonds, 309 residues, 2 models selected
> hide sel cartoons
> select add #7/D:310
2461 atoms, 2534 bonds, 310 residues, 2 models selected
> select up
2469 atoms, 2544 bonds, 311 residues, 2 models selected
> hide sel cartoons
> select add #7/D:323
2475 atoms, 2549 bonds, 312 residues, 2 models selected
> select up
2540 atoms, 2614 bonds, 322 residues, 2 models selected
> hide sel cartoons
> select add #7/D:70
2547 atoms, 2620 bonds, 323 residues, 2 models selected
> select up
2558 atoms, 2633 bonds, 324 residues, 2 models selected
> hide sel cartoons
> select add #7/D:65
2568 atoms, 2643 bonds, 325 residues, 2 models selected
> hide sel cartoons
> select add #7/D:148
2579 atoms, 2654 bonds, 326 residues, 2 models selected
> select up
2583 atoms, 2662 bonds, 327 residues, 2 models selected
> hide sel cartoons
> select add #7/D:141
2592 atoms, 2670 bonds, 328 residues, 2 models selected
> hide sel cartoons
> select add #7/D:340
2599 atoms, 2676 bonds, 329 residues, 2 models selected
> select up
2627 atoms, 2707 bonds, 332 residues, 2 models selected
> hide sel cartoons
> select add #7/D:2013@CG1
2628 atoms, 2707 bonds, 333 residues, 2 models selected
> select clear
> select add #7/D:342
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
20 atoms, 18 bonds, 3 residues, 2 models selected
> select clear
> select #7/D:342
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #7/D:343
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide #!7 models
> show #!8 models
> select #8/A
2266 atoms, 2320 bonds, 2 pseudobonds, 294 residues, 2 models selected
> hide sel cartoons
Drag select of 6TKO B1AR.pdb_B SES surface, 231 of 315882 triangles, cap far,
99 of 14206 triangles, 25 atoms, 26 bonds
> hide sel cartoons
> select clear
Drag select of 25 atoms, 26 bonds
> hide sel cartoons
[Repeated 1 time(s)]
> hide sel atoms
> ui tool show "Side View"
> hide #!8 models
> show #!9 models
> select #9/R
1689 atoms, 1724 bonds, 2 pseudobonds, 279 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> show #!10 models
> hide #!9 models
> show #!11 models
> show #!12 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> show #!13 models
> show #13.2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #13/B
2659 atoms, 2713 bonds, 2 pseudobonds, 334 residues, 2 models selected
> surface (#!13 & sel)
> transparency (#!13 & sel) 90
> select clear
> show #!2 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> hide #!13 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!10 models
> hide #!2 models
> select #10/C
2810 atoms, 2872 bonds, 1 pseudobond, 353 residues, 2 models selected
> transparency (#!10 & sel) 90
> transparency (#!10 & sel) 80
> transparency (#!10 & sel) 90
> select clear
> cartoon style #10.2#13.2#!10,13 modeHelix tube sides 20
> show #!2 models
> matchmaker #13/R to #6/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker R-Arr-fab-coot-1220231201-2.pdb, chain R (#6) with R-Arr-fab-
coot-14_real_space_refined_032 Arrestin.pdb, chain R (#13), sequence alignment
score = 1693.4
RMSD between 338 pruned atom pairs is 0.493 angstroms; (across all 341 pairs:
0.702)
> show #!8 models
> show #!9 models
> show #!11 models
> show #!7 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!13 models
> hide #13.2 models
> show #!13 models
> show #!7 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20240106-6.cxs"
> select #7/D:238
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
33 atoms, 32 bonds, 4 residues, 2 models selected
> hide sel cartoons
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20240106-6.cxs"
——— End of log from Sat Jan 6 16:28:40 2024 ———
opened ChimeraX session
> show #!8 models
> show #!9 models
> show #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!10 models
> show #!2 models
> hide #!2 models
> select #13/B
2659 atoms, 2713 bonds, 2 pseudobonds, 334 residues, 2 models selected
> surface (#!13 & sel)
> select clear
> show #!2 models
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20240106-7.cxs"
——— End of log from Sat Jan 6 16:36:56 2024 ———
opened ChimeraX session
> close #6
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20240109-2.cxs"
> close #5
> close #4
> save "D:/PTH1R-Arrestin paper/figs20231123/cxc/20240109-2.cxs"
——— End of log from Tue Jan 9 15:58:33 2024 ———
opened ChimeraX session
> show #!1 models
> show #!3 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> show #!12 models
> close #13
> show cartoons
[Repeated 1 time(s)]
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/新建文件夹/20250117
> V2R_J6700-coot-0.pdb"
Chain information for 20250117 V2R_J6700-coot-0.pdb #4
---
Chain | Description
B | No description available
C | No description available
E | No description available
L | No description available
R | No description available
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/新建文件夹/20250117
> WT_J6702_complex2_arrestin.pdb"
Chain information for 20250117 WT_J6702_complex2_arrestin.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
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/新建文件夹/20250117 WT_J6703
> PTH1R_arrestin_.pdb"
Chain information for 20250117 WT_J6703 PTH1R_arrestin_.pdb #6
---
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
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/新建文件夹/20250117ZLH
> V2R_J6701arrestin-coot-0.pdb"
Chain information for 20250117ZLH V2R_J6701arrestin-coot-0.pdb #13
---
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
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-5 Receptor-
> Arrestin.cxs"
> hide atoms
> show cartoons
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> show #!6 models
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-5 Receptor-
> Arrestin.cxs"
——— End of log from Sat Jan 18 17:02:31 2025 ———
opened ChimeraX session
> show #!5 models
> matchmaker #5/A to #6/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250117 WT_J6703 PTH1R_arrestin_.pdb, chain A (#6) with 20250117
WT_J6702_complex2_arrestin.pdb, chain A (#5), sequence alignment score = 1495
RMSD between 290 pruned atom pairs is 0.246 angstroms; (across all 293 pairs:
0.330)
> hide #!1 models
> select #5/C
3061 atoms, 3101 bonds, 1 pseudobond, 205 residues, 2 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> select #6/C
3061 atoms, 3101 bonds, 1 pseudobond, 205 residues, 2 models selected
> delete atoms (#!6 & sel)
> delete bonds (#!6 & sel)
> select #5/E
3154 atoms, 3188 bonds, 1 pseudobond, 207 residues, 2 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> select #6/E
3154 atoms, 3188 bonds, 1 pseudobond, 207 residues, 2 models selected
> delete atoms (#!6 & sel)
> delete bonds (#!6 & sel)
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-5 Receptor-
> Arrestin.cxs"
> select #5/B
5529 atoms, 5587 bonds, 2 pseudobonds, 346 residues, 2 models selected
> ui tool show "Color Actions"
> color sel medium violet red
> select clear
> select #5/B:192
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #5/B:192@CA
1 atom, 1 residue, 1 model selected
> select add #6/B:107@CA
2 atoms, 2 residues, 2 models selected
> select add #6/B:192@CA
3 atoms, 3 residues, 2 models selected
> ui tool show Angles/Torsions
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-5 Receptor-
> Arrestin.cxs"
——— End of log from Sun Jan 19 14:20:13 2025 ———
opened ChimeraX session
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118
> WT_P119_J6703_arrestin_R-Fab-coot-2.pdb"
Chain information for 20250118 WT_P119_J6703_arrestin_R-Fab-coot-2.pdb #14
---
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 sel atoms
[Repeated 2 time(s)]
> select clear
> hide #!5-6,14 atoms
> show #!5-6,14 cartoons
> hide #!5 models
> close #6
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-5 Receptor-
> Arrestin.cxs"
> select #14/C
3061 atoms, 3101 bonds, 1 pseudobond, 205 residues, 2 models selected
> delete atoms (#!14 & sel)
> delete bonds (#!14 & sel)
> select #14/E
3154 atoms, 3188 bonds, 1 pseudobond, 207 residues, 2 models selected
> delete atoms (#!14 & sel)
> delete bonds (#!14 & sel)
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-5 Receptor-
> Arrestin.cxs"
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #14/A
4832 atoms, 4898 bonds, 4 pseudobonds, 293 residues, 2 models selected
> ui tool show "Color Actions"
> color sel deep sky blue
> select #14/B
5554 atoms, 5612 bonds, 2 pseudobonds, 346 residues, 2 models selected
> color sel salmon
> select clear
> select add #14/R:506
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
47 atoms, 45 bonds, 3 residues, 1 model selected
> select add #14/R:507
61 atoms, 58 bonds, 4 residues, 1 model selected
> select up
68 atoms, 66 bonds, 5 residues, 1 model selected
> select add #14/R:503
85 atoms, 81 bonds, 6 residues, 1 model selected
> select up
132 atoms, 129 bonds, 9 residues, 1 model selected
> color sel deep sky blue
> select clear
> select #14/L
571 atoms, 576 bonds, 33 residues, 1 model selected
> color sel goldenrod
> select clear
> hide #14.1 models
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-5 Receptor-
> Arrestin.cxs"
> show #!2 models
> cartoon style width 2 thickness 0.5
[Repeated 1 time(s)]
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-5 Receptor-
> Arrestin.cxs"
> hide #!2 models
> hide #!14 models
> show #!5 models
> hide #5.1 models
> select #5/A
4832 atoms, 4898 bonds, 4 pseudobonds, 293 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dodger blue
> select add #5/R:505
4848 atoms, 4913 bonds, 4 pseudobonds, 294 residues, 2 models selected
> select up
4879 atoms, 4944 bonds, 4 pseudobonds, 296 residues, 2 models selected
> select add #5/R:507
4893 atoms, 4956 bonds, 4 pseudobonds, 297 residues, 2 models selected
> select up
4900 atoms, 4964 bonds, 4 pseudobonds, 298 residues, 2 models selected
> select add #5/R:503
4917 atoms, 4980 bonds, 4 pseudobonds, 299 residues, 2 models selected
> select up
4964 atoms, 5029 bonds, 4 pseudobonds, 302 residues, 2 models selected
> color sel dodger blue
> select #5/L
571 atoms, 576 bonds, 33 residues, 1 model selected
> ui tool show "Color Actions"
> color sel gold
> cartoon style width 2 thickness 0.5
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-5 Receptor-
> Arrestin.cxs"
> select clear
[Repeated 1 time(s)]
> hide #!5 models
> show #!4 models
> select #4/C
3061 atoms, 3101 bonds, 1 pseudobond, 205 residues, 2 models selected
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> select #4/E
3154 atoms, 3188 bonds, 1 pseudobond, 207 residues, 2 models selected
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> select #4/L
571 atoms, 576 bonds, 33 residues, 1 model selected
> ui tool show "Color Actions"
> color sel tomato
> show #!3 models
> show #!9 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> hide #!9 models
> select #4/R
5409 atoms, 5477 bonds, 6 pseudobonds, 334 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark turquoise
> select #4/B
5386 atoms, 5440 bonds, 2 pseudobonds, 334 residues, 2 models selected
> color sel dark goldenrod
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-5 Receptor-
> Arrestin.cxs"
> hide #!4 models
> hide #4.1 models
> show #!13 models
> select #13/C
1552 atoms, 1594 bonds, 1 pseudobond, 205 residues, 2 models selected
> delete atoms (#!13 & sel)
> delete bonds (#!13 & sel)
> select #13/L
20 atoms, 18 bonds, 1 pseudobond, 3 residues, 2 models selected
> select #13/E
1588 atoms, 1624 bonds, 1 pseudobond, 207 residues, 2 models selected
> delete atoms (#!13 & sel)
> delete bonds (#!13 & sel)
> hide #13.1 models
> select #13/R
2717 atoms, 2785 bonds, 6 pseudobonds, 334 residues, 2 models selected
> color (#!13 & sel) light sea green
> select #13/A
279 atoms, 284 bonds, 33 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light salmon
> select #13/B
2660 atoms, 2714 bonds, 2 pseudobonds, 334 residues, 2 models selected
> color sel sandy brown
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-5 Receptor-
> Arrestin.cxs"
> select clear
> hide #!13 models
> show #!14 models
> show #!1 models
> matchmaker #1/R to #14/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250118 WT_P119_J6703_arrestin_R-Fab-coot-2.pdb, chain A (#14)
with 6UP7NTSR1.pdb, chain R (#1), sequence alignment score = 304.2
RMSD between 53 pruned atom pairs is 0.974 angstroms; (across all 264 pairs:
8.569)
> show #!2 models
> hide #!1 models
> matchmaker #2/R to #14/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250118 WT_P119_J6703_arrestin_R-Fab-coot-2.pdb, chain A (#14)
with 6PWC NTSR1.pdb, chain R (#2), sequence alignment score = 317
RMSD between 34 pruned atom pairs is 1.100 angstroms; (across all 264 pairs:
9.228)
> hide #!2 models
> show #!3 models
> matchmaker #3/R to #14/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250118 WT_P119_J6703_arrestin_R-Fab-coot-2.pdb, chain A (#14)
with 6nbfZLHLAPTH.pdb, chain R (#3), sequence alignment score = 1437.5
RMSD between 258 pruned atom pairs is 0.788 angstroms; (across all 291 pairs:
1.325)
> ui tool show "Side View"
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/map and PDB/map and model of
> ado1771/PTH1R-Arrestin complex.pdb"
Chain information for PTH1R-Arrestin complex.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 #!3,6,14 atoms
> show #!3,6,14 cartoons
> hide #!14 models
> hide #!3 models
> select #6/C
1551 atoms, 1593 bonds, 1 pseudobond, 205 residues, 2 models selected
> delete atoms (#!6 & sel)
> delete bonds (#!6 & sel)
> select #6/E
1587 atoms, 1623 bonds, 1 pseudobond, 207 residues, 2 models selected
> delete atoms (#!6 & sel)
> delete bonds (#!6 & sel)
> matchmaker #6/R to #14/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250118 WT_P119_J6703_arrestin_R-Fab-coot-2.pdb, chain A (#14)
with PTH1R-Arrestin complex.pdb, chain R (#6), sequence alignment score =
1516.6
RMSD between 272 pruned atom pairs is 0.841 angstroms; (across all 288 pairs:
1.174)
> show #!14 models
> show #!3 models
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-5 Receptor-
> Arrestin.cxs"
——— End of log from Mon Jan 20 13:33:51 2025 ———
opened ChimeraX session
> hide #!3 models
> show #!3 models
> cartoon style #6#!3,14 xsection oval modeHelix default
> hide #!3 models
> hide #!6 models
> show #!3 models
> select #14/A:388@CA
1 atom, 1 residue, 1 model selected
> select add #3/R:388@CA
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #14/A:388@CA #3/R:388@CA
Distance between 20250118 WT_P119_J6703_arrestin_R-Fab-coot-2.pdb #14/A LYS
388 CA and 6nbfZLHLAPTH.pdb #3/R LYS 388 CA: 3.546Å
> select clear
[Repeated 1 time(s)]
> select #14/A:387@CA
1 atom, 1 residue, 1 model selected
> select add #3/R:387@CA
2 atoms, 2 residues, 2 models selected
> distance #14/A:387@CA #3/R:387@CA
Distance between 20250118 WT_P119_J6703_arrestin_R-Fab-coot-2.pdb #14/A THR
387 CA and 6nbfZLHLAPTH.pdb #3/R THR 387 CA: 3.751Å
> select clear
> select #14/A:389@CA
1 atom, 1 residue, 1 model selected
> select add #3/R:389@CA
2 atoms, 2 residues, 2 models selected
> distance #14/A:389@CA #3/R:389@CA
Distance between 20250118 WT_P119_J6703_arrestin_R-Fab-coot-2.pdb #14/A LEU
389 CA and 6nbfZLHLAPTH.pdb #3/R LEU 389 CA: 2.138Å
> show #!6 models
> hide #!6 models
> show #!13 models
> hide #!15 models
> hide #!13 models
> hide #!3 models
> show #!4 models
> matchmaker #4/R to #14/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250118 WT_P119_J6703_arrestin_R-Fab-coot-2.pdb, chain A (#14)
with 20250117 V2R_J6700-coot-0.pdb, chain R (#4), sequence alignment score =
1512.3
RMSD between 276 pruned atom pairs is 0.778 angstroms; (across all 288 pairs:
1.093)
> hide #!4 models
> show #!5 models
> matchmaker #4/A to #14/A
No molecules/chains to match specified
> matchmaker #5/A to #14/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250118 WT_P119_J6703_arrestin_R-Fab-coot-2.pdb, chain A (#14)
with 20250117 WT_J6702_complex2_arrestin.pdb, chain A (#5), sequence alignment
score = 1495
RMSD between 290 pruned atom pairs is 0.246 angstroms; (across all 293 pairs:
0.330)
> hide #!5 models
> show #!4 models
> matchmaker #4/R to #14/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250118 WT_P119_J6703_arrestin_R-Fab-coot-2.pdb, chain A (#14)
with 20250117 V2R_J6700-coot-0.pdb, chain R (#4), sequence alignment score =
1512.3
RMSD between 276 pruned atom pairs is 0.778 angstroms; (across all 288 pairs:
1.093)
> hide #!4 models
> show #!6 models
> matchmaker #6/R to #14/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250118 WT_P119_J6703_arrestin_R-Fab-coot-2.pdb, chain A (#14)
with PTH1R-Arrestin complex.pdb, chain R (#6), sequence alignment score =
1516.6
RMSD between 272 pruned atom pairs is 0.841 angstroms; (across all 288 pairs:
1.174)
> show #!7 models
> matchmaker #7/D to #14/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250118 WT_P119_J6703_arrestin_R-Fab-coot-2.pdb, chain A (#14)
with 5w0prdophsin.pdb, chain D (#7), sequence alignment score = 330.5
RMSD between 40 pruned atom pairs is 1.014 angstroms; (across all 265 pairs:
9.900)
> hide #!7 models
> show #!8 models
> matchmaker #8/A to #14/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250118 WT_P119_J6703_arrestin_R-Fab-coot-2.pdb, chain A (#14)
with 6TKO B1AR.pdb, chain A (#8), sequence alignment score = 284.4
RMSD between 57 pruned atom pairs is 1.157 angstroms; (across all 242 pairs:
8.675)
> hide #!8 models
> show #!9 models
> hide #15.1 models
> hide #!6 models
> matchmaker #9/R to #14/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250118 WT_P119_J6703_arrestin_R-Fab-coot-2.pdb, chain A (#14)
with 6U1N M2R.pdb, chain R (#9), sequence alignment score = 271.9
RMSD between 38 pruned atom pairs is 1.289 angstroms; (across all 235 pairs:
10.218)
> hide #!9 models
> show #!10 models
> matchmaker #10/A to #14/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250118 WT_P119_J6703_arrestin_R-Fab-coot-2.pdb, chain A (#14)
with 7R0C V2R.pdb, chain A (#10), sequence alignment score = 312.1
RMSD between 61 pruned atom pairs is 1.318 angstroms; (across all 241 pairs:
6.124)
> hide #!10 models
> show #!11 models
> matchmaker #11/R to #14/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250118 WT_P119_J6703_arrestin_R-Fab-coot-2.pdb, chain A (#14)
with 7SRSH2B.pdb, chain R (#11), sequence alignment score = 288.2
RMSD between 76 pruned atom pairs is 1.284 angstroms; (across all 246 pairs:
7.152)
> hide #!11 models
> show #!12 models
> matchmaker #12/R to #14/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250118 WT_P119_J6703_arrestin_R-Fab-coot-2.pdb, chain A (#14)
with 8JRV GCGR.pdb, chain R (#12), sequence alignment score = 675.8
RMSD between 129 pruned atom pairs is 1.247 angstroms; (across all 256 pairs:
5.520)
> hide #!12 models
> show #!13 models
> matchmaker #13/R to #14/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250118 WT_P119_J6703_arrestin_R-Fab-coot-2.pdb, chain A (#14)
with 20250117ZLH V2R_J6701arrestin-coot-0.pdb, chain R (#13), sequence
alignment score = 1512.3
RMSD between 276 pruned atom pairs is 0.778 angstroms; (across all 288 pairs:
1.093)
> matchmaker #13/R to #14/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250118 WT_P119_J6703_arrestin_R-Fab-coot-2.pdb, chain A (#14)
with 20250117ZLH V2R_J6701arrestin-coot-0.pdb, chain R (#13), sequence
alignment score = 1512.3
RMSD between 276 pruned atom pairs is 0.778 angstroms; (across all 288 pairs:
1.093)
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250118-5 Receptor-
> Arrestin.cxs"
——— End of log from Mon Jan 20 14:15:48 2025 ———
opened ChimeraX session
> hide #!13 models
> show #!5 models
> select clear
> cartoon style #!5,14 modeHelix tube sides 20
> hide #!5 models
> show #!5 models
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250120-1 Receptor-
> Arrestin.cxs"
> ui tool show "Side View"
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250120-1 Receptor-
> Arrestin.cxs"
——— End of log from Mon Jan 20 16:12:38 2025 ———
opened ChimeraX session
> hide #!5 models
> show #!1 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> show #!12 models
> show #!13 models
> show #!15 models
> cartoon style #1.2#7.2#8.2#9.2#10.2#11.2-3#12.2#!1,3,7-15 modeHelix tube
> sides 20
> cartoon style width 1.0 thickness 0.2
> surface hidePatches #1.2#7.2#8.2#9.2#10.2#11.2-3#12.2#!1,3,7-15
> show #!2 models
> show #!5 models
> hide #!1 models
> hide #!3 models
> hide #!5 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> show #!14 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!13 models
> hide #!13 models
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250211 receptor-
> arrestin.cxs"
> close #4
> close #5
> close #6
> close #13
> close #14
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250208 20250124-2
> WT_complex2_J6702_arrestin_R_FAB-coot-12.pdb"
Chain information for 20250208 20250124-2 WT_complex2_J6702_arrestin_R_FAB-
coot-12.pdb #4
---
Chain | Description
B | No description available
C | No description available
E | No description available
L | No description available
R | No description available
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250208
> WT_P119_J6703_arrestin_R-Fab-coot-19.pdb"
Chain information for 20250208 WT_P119_J6703_arrestin_R-Fab-coot-19.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 #!4-5 atoms
> show #!4-5 cartoons
> select #1/C#4/C#5/C#9/C#10/C#11/C
11182 atoms, 11445 bonds, 4 pseudobonds, 1482 residues, 10 models selected
> hide sel & #!4-5 cartoons
> select #4/E#5/E
3176 atoms, 3245 bonds, 2 pseudobonds, 414 residues, 4 models selected
> hide sel cartoons
> select #5/R
2470 atoms, 2536 bonds, 5 pseudobonds, 301 residues, 2 models selected
> ui tool show "Color Actions"
> color sel deep sky blue
> select #5/R
2470 atoms, 2536 bonds, 5 pseudobonds, 301 residues, 2 models selected
> color sel royal blue
> select #4/B
2745 atoms, 2803 bonds, 2 pseudobonds, 346 residues, 2 models selected
> color sel salmon
> select #5/B
2758 atoms, 2816 bonds, 2 pseudobonds, 346 residues, 2 models selected
> color sel medium violet red
> select #4/L
279 atoms, 284 bonds, 33 residues, 1 model selected
> color sel goldenrod
> select #5/R
2470 atoms, 2536 bonds, 5 pseudobonds, 301 residues, 2 models selected
> color sel deep sky blue
[Repeated 1 time(s)]
> color sel royal blue
> select #5/R
2470 atoms, 2536 bonds, 5 pseudobonds, 301 residues, 2 models selected
> color sel deep sky blue
> select #4/R
2547 atoms, 2614 bonds, 4 pseudobonds, 312 residues, 2 models selected
> color sel royal blue
> select #5/B
2758 atoms, 2816 bonds, 2 pseudobonds, 346 residues, 2 models selected
> color sel salmon
> select #4/B
2745 atoms, 2803 bonds, 2 pseudobonds, 346 residues, 2 models selected
> color sel medium violet red
> select #4/R
2547 atoms, 2614 bonds, 4 pseudobonds, 312 residues, 2 models selected
> color sel gold
> color sel royal blue
> select #4/L
279 atoms, 284 bonds, 33 residues, 1 model selected
> color sel gold
> select #5/L
279 atoms, 284 bonds, 33 residues, 1 model selected
> color sel goldenrod
> matchmaker #4/R to #5/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250208 WT_P119_J6703_arrestin_R-Fab-coot-19.pdb, chain R (#5)
with 20250208 20250124-2 WT_complex2_J6702_arrestin_R_FAB-coot-12.pdb, chain R
(#4), sequence alignment score = 1510.9
RMSD between 277 pruned atom pairs is 0.665 angstroms; (across all 301 pairs:
1.867)
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250211 receptor-
> arrestin.cxs"
> select clear
[Repeated 1 time(s)]
> show #!1 models
> show #!2 models
> show #!3 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> cartoon style width 1.0 thickness 0.2
> cartoon style #4-5#1.2#2.2#7.2#8.2#9.2#10.2#!1-3,7-10 modeHelix tube sides
> 20
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> show #!5 models
> matchmaker #1/R to #5/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250208 WT_P119_J6703_arrestin_R-Fab-coot-19.pdb, chain R (#5)
with 6UP7NTSR1.pdb, chain R (#1), sequence alignment score = 299.9
RMSD between 56 pruned atom pairs is 1.064 angstroms; (across all 255 pairs:
10.378)
> hide #4.1 models
> hide #5.1 models
> hide #!1 models
> show #!2 models
> matchmaker #2/R to #5/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250208 WT_P119_J6703_arrestin_R-Fab-coot-19.pdb, chain R (#5)
with 6PWC NTSR1.pdb, chain R (#2), sequence alignment score = 308.6
RMSD between 43 pruned atom pairs is 1.304 angstroms; (across all 275 pairs:
9.851)
> hide #!2 models
> matchmaker #3/R to #5/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250208 WT_P119_J6703_arrestin_R-Fab-coot-19.pdb, chain R (#5)
with 6nbfZLHLAPTH.pdb, chain R (#3), sequence alignment score = 1258.7
RMSD between 249 pruned atom pairs is 0.772 angstroms; (across all 276 pairs:
1.254)
> show #!3 models
> matchmaker #3/R to #5/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250208 WT_P119_J6703_arrestin_R-Fab-coot-19.pdb, chain R (#5)
with 6nbfZLHLAPTH.pdb, chain R (#3), sequence alignment score = 1258.7
RMSD between 249 pruned atom pairs is 0.772 angstroms; (across all 276 pairs:
1.254)
> hide #!3 models
> show #!7 models
> matchmaker #7/D to #5/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250208 WT_P119_J6703_arrestin_R-Fab-coot-19.pdb, chain R (#5)
with 5w0prdophsin.pdb, chain D (#7), sequence alignment score = 331.8
RMSD between 39 pruned atom pairs is 1.272 angstroms; (across all 278 pairs:
9.435)
> hide #!7 models
> show #!8 models
> matchmaker #8/A to #5/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250208 WT_P119_J6703_arrestin_R-Fab-coot-19.pdb, chain R (#5)
with 6TKO B1AR.pdb, chain A (#8), sequence alignment score = 282.2
RMSD between 80 pruned atom pairs is 1.232 angstroms; (across all 254 pairs:
6.738)
> matchmaker #8/A to #5/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250208 WT_P119_J6703_arrestin_R-Fab-coot-19.pdb, chain R (#5)
with 6TKO B1AR.pdb, chain A (#8), sequence alignment score = 282.2
RMSD between 80 pruned atom pairs is 1.232 angstroms; (across all 254 pairs:
6.738)
> hide #!8 models
> show #!9 models
> matchmaker #9/R to #5/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250208 WT_P119_J6703_arrestin_R-Fab-coot-19.pdb, chain R (#5)
with 6U1N M2R.pdb, chain R (#9), sequence alignment score = 306.2
RMSD between 63 pruned atom pairs is 1.139 angstroms; (across all 255 pairs:
7.084)
> hide #!9 models
> show #!10 models
> matchmaker #10/A to #5/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250208 WT_P119_J6703_arrestin_R-Fab-coot-19.pdb, chain R (#5)
with 7R0C V2R.pdb, chain A (#10), sequence alignment score = 306.8
RMSD between 60 pruned atom pairs is 1.251 angstroms; (across all 251 pairs:
7.474)
> hide #!10 models
> show #!11 models
> matchmaker #11/R to #5/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250208 WT_P119_J6703_arrestin_R-Fab-coot-19.pdb, chain R (#5)
with 7SRSH2B.pdb, chain R (#11), sequence alignment score = 280.9
RMSD between 71 pruned atom pairs is 1.220 angstroms; (across all 251 pairs:
7.961)
> show #!12 models
> matchmaker #12/R to #5/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250208 WT_P119_J6703_arrestin_R-Fab-coot-19.pdb, chain R (#5)
with 8JRV GCGR.pdb, chain R (#12), sequence alignment score = 651.8
RMSD between 135 pruned atom pairs is 1.254 angstroms; (across all 276 pairs:
11.936)
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> surface hidePatches #2.2#7.2#8.2#9.2#10.2#11.2-3#12.2#!2-5,7-12
> hide #!3 models
> hide #!2 models
> hide #!8 models
> hide #!7 models
> hide #!10 models
> hide #!9 models
> hide #!11 models
> hide #!12 models
> show #!9 models
> show #!2 models
> show #!7 models
> show #!8 models
> show #!10 models
> show #!11 models
> show #!12 models
> cartoon style width 1.0 thickness 0.2
> cartoon style width 0.5 thickness 0.1
> cartoon style width 0.5 thickness 0.2
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250211 receptor-
> arrestin.cxs"
> transparency 5 ribbons
> transparency 0 ribbons
> transparency 95 ribbons
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250211-1.png" width
> 2000 height 1245 supersample 3 transparentBackground true
> transparency 0 ribbons
> select #1/B#2/B#4/B#5/B#8/B#10/B
10345 atoms, 10554 bonds, 6 pseudobonds, 1398 residues, 9 models selected
> hide sel & #!2,4-5,8,10 cartoons
> select #1/C#4/C#5/C#9/C#10/C#11/C
11182 atoms, 11445 bonds, 4 pseudobonds, 1482 residues, 10 models selected
> hide sel & #!4-5,9-11 cartoons
> select #2/A#8/A#10/A#12/A
9054 atoms, 9251 bonds, 7 pseudobonds, 1284 residues, 7 models selected
> select clear
Drag select of 701 residues
> select up
6301 atoms, 6318 bonds, 885 residues, 13 models selected
> hide sel cartoons
Drag select of 97 residues
> select up
7251 atoms, 7288 bonds, 1028 residues, 13 models selected
> hide sel cartoons
Drag select of 65 residues
> select clear
Drag select of 80 residues
> hide sel cartoons
Drag select of 7 residues
> select up
813 atoms, 812 bonds, 123 residues, 7 models selected
> hide sel cartoons
> select #10/A:238
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
76 atoms, 76 bonds, 10 residues, 1 model selected
> hide sel cartoons
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250211-2.png" width
> 2000 height 1245 supersample 3 transparentBackground true
> save "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250211 receptor-
> arrestin-2.cxs"
> hide #!2 models
> hide #!7 models
> hide #!8 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!4 models
> hide #!9 models
> show #!12 models
> select #1/B#2/B#4/B#5/B#8/B#10/B
10345 atoms, 10554 bonds, 6 pseudobonds, 1398 residues, 9 models selected
> show sel & #!5 cartoons
> select #12/A
2672 atoms, 2733 bonds, 1 pseudobond, 356 residues, 2 models selected
> show sel cartoons
> select clear
> show #!4 models
> hide #!4 models
> select clear
[Repeated 1 time(s)]
> select add #5/B:76
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
[Repeated 2 time(s)]
> select subtract #15
Nothing selected
> select clear
> select #5/B:75
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/B:75
11 atoms, 11 bonds, 1 residue, 1 model selected
> select subtract #5/B:75
Nothing selected
> show #!5,12 atoms
> hide #!5,12 atoms
> select #5/B:75
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/B:75
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> matchmaker #12/A to #5/B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250208 WT_P119_J6703_arrestin_R-Fab-coot-19.pdb, chain B (#5)
with 8JRV GCGR.pdb, chain A (#12), sequence alignment score = 1484
RMSD between 307 pruned atom pairs is 0.854 angstroms; (across all 337 pairs:
1.428)
> hide #!5 models
> show #!4 models
> hide #!12 models
> show #!12 models
> matchmaker #12/A to #4/B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20250208 20250124-2 WT_complex2_J6702_arrestin_R_FAB-coot-12.pdb,
chain B (#4) with 8JRV GCGR.pdb, chain A (#12), sequence alignment score =
1506.2
RMSD between 296 pruned atom pairs is 0.813 angstroms; (across all 337 pairs:
1.466)
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250201-J6703
> interaction fingerloopWidth1.2 thick 0.3 trans 5.cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 734, in restore
obj = sm.restore_snapshot(self, data)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\session.py", line 219, in restore_snapshot
grids = grid_data_from_state(data, gdcache, session, rfp)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\session.py", line 383, in grid_data_from_state
a = a.copy()
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 325. MiB for an
array with shape (85184000,) and data type float32
opened ChimeraX session
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250201-J6703
> interaction fingerloopWidth1.2 thick 0.3 trans 5.cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 734, in restore
obj = sm.restore_snapshot(self, data)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\session.py", line 219, in restore_snapshot
grids = grid_data_from_state(data, gdcache, session, rfp)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\session.py", line 383, in grid_data_from_state
a = a.copy()
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 325. MiB for an
array with shape (85184000,) and data type float32
opened ChimeraX session
> open "D:/PTH1R-Arrestin paper/2024年1月16日投稿/2025New/20250201-J6703
> interaction fingerloop trans 5.cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 734, in restore
obj = sm.restore_snapshot(self, data)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\session.py", line 219, in restore_snapshot
grids = grid_data_from_state(data, gdcache, session, rfp)
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\session.py", line 383, in grid_data_from_state
a = a.copy()
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 325. MiB for an
array with shape (85184000,) and data type float32
opened ChimeraX session
> open "D:\PTH1R-Arrestin
> paper\2024年1月16日投稿\2025New\cryosparc_P119_J6696_class_01_00142_volume.mrc"
> format mrc
Opened cryosparc_P119_J6696_class_01_00142_volume.mrc as #1, grid size
128,128,128, pixel 2.51, shown at level 0.384, step 1, values float32
OpenGL version: 3.3.0 NVIDIA 538.78
OpenGL renderer: NVIDIA GeForce MX150/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows
Manufacturer: LENOVO
Model: 20L6A09YCD
OS: Microsoft Windows 10 家庭中文版 (Build 19045)
Memory: 17,027,555,328
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz
OSLanguage: zh-CN
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
comtypes: 1.1.14
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pywin32: 305
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
WMI: 1.5.1
zipp: 3.15.0
Change History (2)
comment:1 by , 8 months ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Restore session: MemoryError in grid_data_from_state |
comment:2 by , 8 months ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
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As the traceback says, error trying to allocate 325 Mbytes. Machine has 16 Gbytes. Perhaps the session contains other very large data sets.