![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 hours ago
#19402 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_interface/gpr161_tubby_interface_2.cxs
Opened cryosparc_P4_J1321_003_volume_map_sharp_cut.mrc as #2, grid size
256,256,256, pixel 1.11, shown at level 0.3, step 1, values float32
Log from Thu Nov 20 13:41:58 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/GPR161_TUBBY_Align_to_GPR161_Gprotein/gpr161_tubby_Compare_Gprotein_TM_side_view.cxs
Opened cryosparc_P4_J1321_003_volume_map_sharp_cut.mrc as #2, grid size
256,256,256, pixel 1.11, shown at level 0.3, step 1, values float32
Log from Sun Nov 16 19:39:18 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_Compare_Gprotein.cxs
Opened cryosparc_P4_J1321_003_volume_map_sharp_cut.mrc as #2, grid size
256,256,256, pixel 1.11, shown at level 0.3, step 1, values float32
Log from Thu Nov 13 17:41:04 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_map_model_7.cxs
Opened cryosparc_P4_J1321_003_volume_map_sharp_cut.mrc as #2, grid size
256,256,256, pixel 1.11, shown at level 0.3, step 1, values float32
Log from Thu Nov 13 12:33:36 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_map_model_7.cxs
Opened cryosparc_P4_J1321_003_volume_map_sharp_cut.mrc as #2, grid size
256,256,256, pixel 1.11, shown at level 0.3, step 1, values float32
Log from Thu Nov 13 11:07:25 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_map_model_7_1.cxs
Opened cryosparc_P4_J1321_003_volume_map_sharp_cut.mrc as #2, grid size
256,256,256, pixel 1.11, shown at level 0.3, step 1, values float32
Log from Thu Nov 13 10:36:32 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> C:\MJ_Research\IFTA\Gpr161_tubby\mj127_113_structure\J1109_pdb_map\model_analysis\raw_fig_cargo\gpr161_tubby_map_model_7_1.cxs
> format session
Opened cryosparc_P4_J1321_003_volume_map_sharp_cut.mrc as #2, grid size
256,256,256, pixel 1.11, shown at level 0.3, step 1, values float32
Log from Thu Nov 13 10:35:30 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> C:\MJ_Research\IFTA\Gpr161_tubby\mj127_113_structure\J1109_pdb_map\model_analysis\raw_fig_cargo\gpr161_tubby_map_model_7.cxs
> format session
Opened cryosparc_P4_J1321_003_volume_map_sharp (1).mrc as #2, grid size
256,256,256, pixel 1.11, shown at level 0.3, step 1, values float32
Log from Thu Nov 13 09:30:15 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> C:\MJ_Research\IFTA\Gpr161_tubby\mj127_113_structure\J1109_pdb_map\model_analysis\raw_fig_cargo\gpr161_tubby_map_model_6.cxs
> format session
Opened cryosparc_P4_J1321_003_volume_map_sharp (1).mrc as #2, grid size
256,256,256, pixel 1.11, shown at level 0.3, step 1, values float32
Log from Wed Nov 12 13:37:28 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_map_model_20251109_2.cxs
Opened cryosparc_P4_J1321_003_volume_map_sharp (1).mrc as #2, grid size
256,256,256, pixel 1.11, shown at level 0.3, step 1, values float32
Log from Tue Nov 11 17:30:49 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Sun Nov 9 17:06:16 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_J1321/gpr161_tubby_2PIP2_fit1321_refined_052.cif-
> coot-4.pdb
Summary of feedback from opening
C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_J1321/gpr161_tubby_2PIP2_fit1321_refined_052.cif-
coot-4.pdb
---
warning | Start residue of secondary structure not found: SHEET 1 A 1 0 0 0
Chain information for gpr161_tubby_2PIP2_fit1321_refined_052.cif-coot-4.pdb #1
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> set bgColor white
> open
> "C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/data_processing_cryosparc/cryosparc_P4_J1321_003_volume_map_sharp
> (1).mrc"
Opened cryosparc_P4_J1321_003_volume_map_sharp (1).mrc as #2, grid size
256,256,256, pixel 1.11, shown at level 0.117, step 1, values float32
> surface dust #2 size 11.1
> volume #2 level 0.3457
> volume #2 level 0.3
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> volume zone #2 nearAtoms #1 range 6.63
> surface dust #2 size 11.1
> transparency 50
> color #2 #b2b2b2c8 models
> transparency 0
> color #2 #b2b2b20a models
> color #2 #b2b2b2be models
> color #2 #b2b2b214 models
> color #2 #b2b2b2c8 models
> hide #!2 models
Drag select of 1 atoms
> delete sel
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif
> relModel #1
Not saving entity_poly_seq for non-authoritative sequences
> close #1
> open
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif
Summary of feedback from opening
C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif
---
warnings | Unknown polymer entity '1' on line 124
Unknown polymer entity '2' on line 2265
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1
---
Chain | Description
A | No description available
B | No description available
> show #!2 models
> surface zone #2 nearAtoms #1
> volume #2 style mesh
> volume #2 style image
> volume #2 style surface
> surface zone #2 nearAtoms #1 5
Expected a keyword
> surface zone #2 nearAtoms #1 @<5
> surface zone #2 nearAtoms #1 @<20
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume style surface
[Repeated 1 time(s)]
> volume show
[Repeated 1 time(s)]
> volume style mesh
[Repeated 1 time(s)]
> volume style image
> volume style surface
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume zone #2 nearAtoms #1 range 6.63
[Repeated 1 time(s)]
> volume style surface
> surface dust #2 size 11.1
> volume #2 color #b2b2b2dc
> volume zone #2 nearAtoms #1 range 6.63
> surface dust #2 size 11.1
> volume zone #2 nearAtoms #1 range 5 newMap false
> volume #2 level 0.4187
> volume #2 level 0.3
> surface dust #2 size 2
> surface dust #2 size 5
> surface dust #2 size 10
> surface dust #2 size8
Expected a keyword
> surface dust #2 size 8
> surface dust #2 size 10
> volume zone #2 nearAtoms #1 range 5 newMap false
> volume #2 style surface
> volume zone #2 nearAtoms #1 range 5 newMap false
> surface dust #2 size 10
> hide #2.1 models
> hide #!2 models
> show #!2 models
> show #2.1 models
> hide #2.1 models
> cartoon style radius 1
> cartoon style width 1.5 thickness 0.2
> select /a
2141 atoms, 2209 bonds, 2 pseudobonds, 280 residues, 2 models selected
> ui tool show "Color Actions"
> color sel cyan
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel medium slate blue
> color sel orchid
> color sel cadet blue
> color sel dark sea green
> color sel dark gray
> color sel violet
> color sel wheat
> color sel moccasin
> color sel navajo white
> color sel peach puff
> color sel pink
> color sel dark green
> color sel dark sea green
> color sel yellow green
> color sel green
> color sel lime
> color sel forest green
> color sel medium sea green
> color sel sea green
> color sel olive drab
> color sel dark red
> color sel maroon
> color sel fire brick
> color sel tomato
> color sel brown
> color sel chocolate
> color sel saddle brown
> color sel coral
> color sel lime
> select add #2
2094 atoms, 2137 bonds, 263 residues, 4 models selected
> select add #2
2094 atoms, 2137 bonds, 263 residues, 4 models selected
> select clear
> show #2.1 models
> color zone #2 near #1 distance 6.63
> hide #!2 models
> color bychain
> undo
> color byhetero
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_map_model_20251109.cxs
——— End of log from Sun Nov 9 17:06:16 2025 ———
> view name session-start
opened ChimeraX session
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting flat
[Repeated 2 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> lighting full
> lighting simple
> lighting soft
> ui tool show "Side View"
> lighting simple
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "The operation
completed successfully."
[Repeated 1 time(s)]
> show #!2 models
> lighting soft
> lighting full
> hide #!2 models
> show #!2 models
> hide #!2 models
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> ui tool show "Color Actions"
> color sel sienna
> color sel coral
> color sel saddle brown
> color sel chocolate
> color sel brown
> color sel chocolate
> color sel fire brick
> color sel maroon
> color sel crimson
> color sel orange red
> color sel red
> color sel yellow
> color sel indian red
> color sel orange
> color sel dark orange
> color sel goldenrod
> color sel green yellow
> color sel goldenrod
> color sel green yellow
> color sel dark orange
> color sel sandy brown
> show #!2 models
> color zone #2 near sel & #1 distance 6.63
> select clear
> color zone #2 near #1 distance 6.63
[Repeated 2 time(s)]
> select clear
> hide #!2 models
> show #!2 models
> color zone #2 near #1 distance 6.63
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel sandy brown
> hide #!2 models
> color sel goldenrod
> color sel sandy brown
> show #!2 models
> color zone #2 near sel & #1 distance 6.63
> select add #1
4235 atoms, 4346 bonds, 2 pseudobonds, 543 residues, 2 models selected
> select subtract #1
Nothing selected
> color zone #2 near #1 distance 6.63
> hide #!2 models
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel green yellow
> select clear
> show #!2 models
> color zone #2 near #1 distance 6.63
> hide atoms
> color zone #2 near #1 distance 6.63
[Repeated 1 time(s)]
> color #2 #aaaaffdc models
> color zone #2 near #1 distance 6.63
> hide #!2 models
> show atoms
> color byhetero
[Repeated 1 time(s)]
> hide atoms
> show #!2 models
> color zone #2 near #1 distance 6.63
[Repeated 1 time(s)]
> hide #!2 models
> show atoms
Unknown or unsupported skia image format
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> select add #1
4235 atoms, 4346 bonds, 2 pseudobonds, 543 residues, 2 models selected
> select clear
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel yellow green
> select clear
> show #!2 models
> color zone #2 near #1 distance 6.63
> select /a
2141 atoms, 2209 bonds, 2 pseudobonds, 280 residues, 2 models selected
> color sel cyan
> color zone #2 near sel & #1 distance 6.63
> select clear
> color zone #2 near #1 distance 6.63
> hide #!2 models
> show #!2 models
> select /a
2141 atoms, 2209 bonds, 2 pseudobonds, 280 residues, 2 models selected
> color sel medium slate blue
> color zone #2 near sel & #1 distance 6.63
> select clear
> color zone #2 near #1 distance 6.63
> hide #!2 models
> select /a
2141 atoms, 2209 bonds, 2 pseudobonds, 280 residues, 2 models selected
> color sel medium spring green
> color sel cyan
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel green yellow
> color sel lawn green
> color sel spring green
> color sel lawn green
> color sel chartreuse
[Repeated 1 time(s)]
> color sel green
> color sel lime
> color sel lawn green
> color sel spring green
[Repeated 1 time(s)]
> color sel lawn green
> select clear
> show #!2 models
> color zone #2 near #1 distance 6.63
> hide #!1 models
> show #!1 models
> hide #!2 models
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel lime green
> color sel green yellow
> select clear
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel lime
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> color zone #2 near #1 distance 6.63
> hide #!2 models
> color byhetero
> hide atoms
> cartoon style width 1.2 thickness 0.2
> cartoon style width 1.2 thickness 0.5
> cartoon style width 1.2 thickness 0.3
> cartoon style width 1.4 thickness 0.3
> cartoon style width 1.4 thickness 0.4
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> select #2/B:501,502
Nothing selected
> show atoms
> hide atoms
> select #2/B:501,502
Nothing selected
> show atoms
> hide atoms
> show atoms
> select #1/B:501,502
51 atoms, 51 bonds, 2 residues, 1 model selected
> show sel atoms
> select clear
> hide atoms
> select #1/B:501,502
51 atoms, 51 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel black
> color sel byhetero
> style sel ball
Changed 51 atom styles
> color sel byhetero
> select clear
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_map_model_20251109.cxs
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_map_model_20251109.cxs
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_map_model_20251109.cxs
> includeMaps true
> turn x 90
> turn x -90
> cartoon style width 1.5 thickness 0.4
> cartoon style width 1.6 thickness 0.4
> cartoon style width 1.5 thickness 0.4
> cartoon style width 1.5 thickness 0.3
> cartoon style width 1.5 thickness 0.4
> select #1/a:401
28 atoms, 31 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> style sel ball
Changed 28 atom styles
> style sel stick
Changed 28 atom styles
> select clear
> turn x 90
> turn x -90
> turn y 180
[Repeated 1 time(s)]
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_map_model_20251109.cxs
> includeMaps true
> turn y 180
[Repeated 1 time(s)]
> lighting simple
> lighting full
> lighting soft
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> lighting soft
[Repeated 5 time(s)]
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> turn y 180
[Repeated 1 time(s)]
> turn x 180
[Repeated 1 time(s)]
> turn x 90
[Repeated 7 time(s)]
> turn y 90
[Repeated 3 time(s)]
> turn z 90
[Repeated 3 time(s)]
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_mode_1.tif
> width 6000 height 6917 supersample 3 transparentBackground true
> turn y 180
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_mode_y180_1.tif
> width 6000 height 6917 supersample 3 transparentBackground true
> turn x 90
[Repeated 3 time(s)]
> turn y 180
> turn x 90
> turn x -90
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_map_model_20251109_1.cxs
> turn x -90
> turn x 90
[Repeated 1 time(s)]
> turn x -90
> lighting simple
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_map_model_20251109_2.cxs
> includeMaps true
——— End of log from Tue Nov 11 17:30:49 2025 ———
> view name session-start
opened ChimeraX session
> turn y 180
[Repeated 1 time(s)]
> show #!2 models
> hide #!2 models
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_mode_3.tif
> width 6000 height 6917 supersample 3 transparentBackground true
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark orchid
> color sel dark blue
> color sel goldenrod
> color sel indigo
> color sel dark slate gray
> color sel powder blue
> color sel light steel blue
> color sel thistle
> color sel light sky blue
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "The operation
completed successfully."
[Repeated 8 time(s)]
> cartoon style width 1.8 thickness 0.4
> cartoon style width 1.8 thickness 0.3
> select add #1
4235 atoms, 4346 bonds, 2 pseudobonds, 543 residues, 2 models selected
> select subtract #1
Nothing selected
> cartoon style width 1.7 thickness 0.4
> color lime
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel light steel blue
> color sel pale turquoise
> color sel light steel blue
> color sel pale turquoise
> color sel light blue
> color sel light sky blue
> color sel sky blue
> color sel aquamarine
> color sel light steel blue
> color sel pale turquoise
> select clear
> select /a
2141 atoms, 2209 bonds, 2 pseudobonds, 280 residues, 2 models selected
> color sel slate blue
> color sel medium slate blue
> select clear
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel cadet blue
> color sel steel blue
> color sel cadet blue
> color sel aquamarine
> color sel gold
> color sel medium blue
> color sel olive drab
> color sel sea green
> color sel medium sea green
> color sel goldenrod
> color sel light sky blue
> color sel aquamarine
> color sel light steel blue
> color sel powder blue
> color sel dark gray
> color sel pale green
> color sel powder blue
> select clear
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel pale green
> color sel light green
> color sel lime
> color sel lime green
> color sel green yellow
> color sel yellow green
> color sel green yellow
> color sel yellow green
> color sel light cyan
> color sel alice blue
> color sel honeydew
> color sel wheat
> select clear
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel chartreuse
> color sel lawn green
> color sel yellow green
> color sel dark sea green
> color sel yellow green
> color sel lime
> color sel yellow green
> color sel light green
> color sel dark sea green
> color sel yellow green
> select clear
> select /a
2141 atoms, 2209 bonds, 2 pseudobonds, 280 residues, 2 models selected
> color sel dodger blue
> color sel dark turquoise
> color sel light sky blue
> color sel sky blue
> color sel light sky blue
> color sel light blue
> color sel light sky blue
> color sel sky blue
> color sel light sky blue
> color sel sky blue
> color sel light sky blue
> select clear
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel pink
> color sel peach puff
> color sel tan
> color sel wheat
> select clear
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel peach puff
> color sel navajo white
> color sel peach puff
> color sel pink
> color sel peach puff
> color sel bisque
> color sel misty rose
> color sel peach puff
> color sel linen
> color sel antique white
> color sel wheat
[Repeated 1 time(s)]
> color sel peach puff
> color sel wheat
[Repeated 1 time(s)]
> select clear
> save C:\Users\mjiang64/Desktop\image1.png supersample 3
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel peach puff
> select clear
> save C:\Users\mjiang64/Desktop\image2.png supersample 3
> show #!2 models
> color zone #2 near #1 distance 6.63
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel wheat
> save C:\Users\mjiang64/Desktop\image3.png supersample 3
> color zone #2 near sel & #1 distance 6.63
> select clear
> color zone #2 near #1 distance 6.63
> save C:\Users\mjiang64/Desktop\image4.png supersample 3
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel light sky blue
> color sel sky blue
> color sel light sky blue
> select /a
2141 atoms, 2209 bonds, 2 pseudobonds, 280 residues, 2 models selected
> color sel wheat
> hide #!2 models
> select clear
> show #!2 models
> color zone #2 near #1 distance 6.63
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel pale green
> color sel light green
> color sel turquoise
> color sel lawn green
> color sel medium slate blue
> color sel pale green
> color sel violet
> color sel light cyan
> color sel coral
> color sel chocolate
> color sel dark red
> color sel green yellow
> color sel yellow green
> select clear
> show #!2 models
> color zone #2 near #1 distance 6.63
> hide #!2 models
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel dodger blue
> color sel medium spring green
> color sel dark turquoise
> color sel light salmon
> color sel dark goldenrod
> color sel yellow green
> color sel olive
> color sel lime
> color sel green
> color sel chartreuse
> color sel lawn green
> color sel spring green
> color sel forest green
> color sel lime green
> color sel olive drab
> color sel deep sky blue
> color sel dark turquoise
> color sel medium spring green
> color sel dodger blue
> color sel turquoise
> select add #1
4235 atoms, 4346 bonds, 2 pseudobonds, 543 residues, 2 models selected
> select subtract #1
Nothing selected
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel medium turquoise
> color sel light sea green
> color sel cornflower blue
> color sel dark cyan
> color sel medium aquamarine
> color sel teal
> color sel steel blue
> color sel cadet blue
> color sel light slate gray
> color sel slate gray
> color sel blue
> color sel medium blue
> color sel blue
> color sel medium blue
> color sel dark blue
> color sel navy
> color sel indigo
> color sel royal blue
> color sel medium slate blue
> color sel slate blue
> color sel dark slate blue
> color sel rebecca purple
> color sel magenta
> color sel deep pink
> color sel dark violet
> color sel hot pink
> color sel blue violet
> color sel orchid
> color sel medium orchid
> color sel dark orchid
> color sel dark magenta
> color sel purple
> color sel medium purple
> color sel pale violet red
> color sel midnight blue
> color sel dark slate gray
> color sel midnight blue
> select clear
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> show #!2 models
> color zone #2 near #1 distance 6.63
> hide #!2 models
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel medium blue
> color sel blue
> color sel medium blue
> color sel blue
> select add #1
4235 atoms, 4346 bonds, 2 pseudobonds, 543 residues, 2 models selected
> select subtract #1
Nothing selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> show #!2 models
> color zone #2 near #1 distance 6.63
> hide #!2 models
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel dark slate gray
> color sel dark olive green
> color sel dim gray
> color sel gray
> color sel light green
[Repeated 1 time(s)]
> color sel pale green
> color sel dark gray
> color sel rosy brown
> select clear
> show #!2 models
> color zone #2 near #1 distance 6.63
> hide #!2 models
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel tan
> color sel burly wood
> color sel aquamarine
> color sel sky blue
> color sel light sky blue
> color sel sky blue
> color sel light sky blue
> color sel sky blue
> color sel light sky blue
> color sel light blue
> color sel pale turquoise
> color sel light steel blue
> color sel powder blue
> color sel silver
> color sel light gray
[Repeated 1 time(s)]
> color sel thistle
> select add #1
4235 atoms, 4346 bonds, 2 pseudobonds, 543 residues, 2 models selected
> select subtract #1
Nothing selected
> show #!2 models
> color zone #2 near #1 distance 6.63
> hide #!2 models
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel gainsboro
> color sel plum
> color sel light cyan
> color sel lavender
> color sel violet
> color sel pale goldenrod
> color sel khaki
> color sel honeydew
[Repeated 1 time(s)]
> color sel azure
> color sel wheat
> color sel beige
> color sel white smoke
> color sel mint cream
> color sel ghost white
> color sel antique white
> color sel linen
> color sel light goldenrod yellow
> color sel old lace
> color sel light pink
> color sel pink
> color sel peach puff
> color sel navajo white
> color sel bisque
> color sel navajo white
> color sel moccasin
> color sel misty rose
> color sel blanched almond
> color sel papaya whip
> color sel lavender blush
> color sel light yellow
> color sel ivory
> color sel black
> color sel dark green
> color sel light sky blue
> color sel dark blue
> color sel royal blue
> color sel light sky blue
> color sel green yellow
> color sel yellow green
> color sel green yellow
> color sel dark blue
> color sel navy
[Repeated 1 time(s)]
> color sel dark blue
> color sel medium blue
> color sel dark blue
> color sel indigo
> color sel medium slate blue
> color sel slate blue
> color sel medium slate blue
> color sel dark blue
> select clear
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> show #!2 models
> color zone #2 near #1 distance 6.63
> lighting soft
> hide #!2 models
> lighting soft
> lighting simple
> save C:\Users\mjiang64/Desktop\image5.png supersample 3
> show #!2 models
> lighting soft
> save C:\Users\mjiang64/Desktop\image6.png supersample 3
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> hide #!2 models
> color sel light sky blue
> show #!2 models
> select add #1
4235 atoms, 4346 bonds, 2 pseudobonds, 543 residues, 2 models selected
> select subtract #1
Nothing selected
> color zone #2 near #1 distance 6.63
> save C:\Users\mjiang64/Desktop\image7.png supersample 3
> hide #!2 models
> lighting simple
> save C:\Users\mjiang64/Desktop\image8.png supersample 3
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel wheat
> select /a
2141 atoms, 2209 bonds, 2 pseudobonds, 280 residues, 2 models selected
> color sel dark blue
> select clear
> show #!2 models
> color zone #2 near #1 distance 6.63
> hide #!2 models
> select /a
2141 atoms, 2209 bonds, 2 pseudobonds, 280 residues, 2 models selected
> color sel yellow green
> color sel green yellow
> color sel yellow green
> color sel green yellow
> color sel yellow green
> color sel green yellow
> select add #1
4235 atoms, 4346 bonds, 2 pseudobonds, 543 residues, 2 models selected
> select subtract #1
Nothing selected
> show #!2 models
> save C:\Users\mjiang64/Desktop\image9.png supersample 3
> color zone #2 near #1 distance 6.63
> hide #!2 models
> show #!2 models
> hide #!2 models
> save C:\Users\mjiang64/Desktop\image10.png supersample 3
> show #!2 models
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> lighting simple
> save C:\Users\mjiang64/Desktop\image11.png supersample 3
> hide #!2 models
> select /a
2141 atoms, 2209 bonds, 2 pseudobonds, 280 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark blue
> color sel navy
> color sel dark blue
> color sel medium blue
> color sel dark blue
> color sel medium blue
> select clear
> save C:\Users\mjiang64/Desktop\image12.png supersample 3
> show #!2 models
> color zone #2 near #1 distance 6.63
> lighting soft
> lighting simple
> save C:\Users\mjiang64/Desktop\image13.png supersample 3
> hide #!2 models
> color dark blue
> undo
> select /a
2141 atoms, 2209 bonds, 2 pseudobonds, 280 residues, 2 models selected
> color sel dark blue
> select clear
> save C:\Users\mjiang64/Desktop\image14.png supersample 3
> select /a
2141 atoms, 2209 bonds, 2 pseudobonds, 280 residues, 2 models selected
> color sel medium blue
> color sel blue
> color sel medium blue
> color sel blue
> color sel medium blue
> color sel blue
> color sel medium blue
> select clear
> show atoms
> color byhetero
> color slate blue
> undo
> select /a
2141 atoms, 2209 bonds, 2 pseudobonds, 280 residues, 2 models selected
> color sel pale violet red
> color sel chartreuse
> color sel medium slate blue
> color sel light coral
> color sel pink
> color sel dark slate blue
> color sel medium slate blue
> select clear
> hide atoms
> show #!2 models
> color zone #2 near #1 distance 6.63
> hide #!2 models
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel wheat
> select /a
2141 atoms, 2209 bonds, 2 pseudobonds, 280 residues, 2 models selected
> select add #1
4235 atoms, 4346 bonds, 2 pseudobonds, 543 residues, 2 models selected
> select subtract #1
Nothing selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> show #!2 models
> color zone #2 near #1 distance 6.63
> hide #!1 models
> show #!1 models
> hide #!2 models
> color #1 #360000ff
> color #1 #f1f1f1ff
> color #1 #f0f0f0ff
> color #1 #c5c5c5ff
> color #1 #f7f7f7ff
> color #1 #fafafaff
> color #1 #f0f0f0ff
> color #1 #f1f1f1ff
> color #1 #a3ccf3ff
> color #1 #787878ff
> color #1 #f2f2f2ff
> color #1 #f1f1f1ff
> color #1 #f2f2f2ff
> color #1 #f3f3f3ff
> color #1 #ff0000ff
> color #1 #f0f0f0ff
> color #1 #b9b9b9ff
> color #1 #f0f0f0ff
> color #1 #b9b9b9ff
> color #1 #ff0000ff
> color #1 #b9b9b9ff
> color #1 #f0f0f0ff
> color #1 #0055ffff
> color #1 #b9b9b9ff
> color #1 #f0f0f0ff
> color #1 #aaaaffff
> color #1 #b9b9b9ff
> color #1 #f0f0f0ff
> color #1 #b9b9b9ff
> color #1 #00aa7fff
> color #1 #f0f0f0ff
> color #1 #aa557fff
> color #1 #00557fff
> color #1 #b9b9b9ff
> color #1 #f0f0f0ff
> color #1 #005500ff
> color #1 #f0f0f0ff
> color #1 #aa007fff
> color #1 #fdfdfdff
> color #1 #fafafaff
> color #1 #f0f0f0ff
> color #1 #c5c5c5ff
> color #1 #efefefff
> color #1 #f0f0f0ff
> color #1 #f1f1f1ff
> color #1 #f6f6f6ff
> color #1 #f3f3f3ff
> color #1 #f1f1f1ff
> color #1 #f0f0f0ff
> color #1 #c5c5c5ff
> color #1 #eeeeeeff
> color #1 #efefefff
> color #1 #f7f7f7ff
> color #1 #f9f9f9ff
> color #1 #fafafaff
> color #1 #fbfbfbff
> color #1 #fcfcfcff
> color #1 #c5c5c5ff
> color #1 #9bc868ff
> color #1 #a4c862ff
> color #1 #dbdbdbff
> color #1 #d5be8aff
> color #1 #f9f2eaff
> color #1 #f9f2ebff
> color #1 #ffffffff
> color #1 #aaaaffff
> color #1 #aaffffff
> color #1 #0055ffff
> color #1 #ffaa7fff
> color #1 #ffaa00ff
> color #1 #55557fff
> color #1 #555500ff
> color #1 #5500ffff
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel wheat
> select clear
> show atoms
> color byhetero
> select /a
2141 atoms, 2209 bonds, 2 pseudobonds, 280 residues, 2 models selected
> color sel blue
> color sel medium blue
> select clear
> color byhetero
[Repeated 1 time(s)]
> hide atoms
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel khaki
> color sel pale goldenrod
> color sel antique white
> color sel linen
> color sel antique white
> color sel azure
> color sel honeydew
> color sel pale goldenrod
> select clear
> show #!2 models
> color zone #2 near #1 distance 6.63
[Repeated 1 time(s)]
> select /a
2141 atoms, 2209 bonds, 2 pseudobonds, 280 residues, 2 models selected
> color sel medium blue
> select add #1
4235 atoms, 4346 bonds, 2 pseudobonds, 543 residues, 2 models selected
> select subtract #1
Nothing selected
> color zone #2 near #1 distance 6.63
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "The operation
completed successfully."
[Repeated 7 time(s)]
> hide #!2 models
> select #1/B:501,502
51 atoms, 51 bonds, 2 residues, 1 model selected
> color sel black
> show sel atoms
> color sel byhetero
> style sel ball
Changed 51 atom styles
> select clear
> select #1/A:401
28 atoms, 31 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> turn y 180
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_mode_3.tif
> width 6000 height 6917 supersample 3 transparentBackground true
> turn y 180
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_mode_y180_3.tif
> width 6000 height 6917 supersample 3 transparentBackground true
> turn y 180
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_map_model_3.cxs
> save C:\Users\mjiang64/Desktop\image15.png supersample 3
> select b/b
Expected an objects specifier or a keyword
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium purple
> color sel pale violet red
> color sel plum
> color sel lavender
> color sel pink
> color sel peach puff
> select clear
> color navajo white
> undo
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel navajo white
> color sel moccasin
> color sel bisque
> color sel misty rose
> color sel blanched almond
[Repeated 1 time(s)]
> color sel papaya whip
[Repeated 1 time(s)]
> color sel lavender blush
[Repeated 1 time(s)]
> color sel seashell
> color sel cornsilk
> color sel lemon chiffon
> color sel light yellow
> color sel lemon chiffon
> select clear
> color burly wood
> undo
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel burly wood
> color sel rosy brown
> color sel burly wood
> select clear
> save C:\Users\mjiang64/Desktop\image16.png supersample 3
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel goldenrod
> select clear
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel sandy brown
> color sel goldenrod
> select clear
> select /b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color sel burly wood
> select clear
> show #!2 models
> color zone #2 near #1 distance 6.63
> select clear
> hide #!2 models
> select #1/B:501,502
51 atoms, 51 bonds, 2 residues, 1 model selected
> color sel black
> color sel byhetero
> hide #!2 models
> select clear
> lighting simple
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_map_model_4.cxs
> includeMaps true
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_mode_4.tif
> width 6000 height 6917 supersample 3 transparentBackground true
> turn y 180
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_mode_y180_4.tif
> width 6000 height 6917 supersample 3 transparentBackground true
> turn y 180
> turn x 90
> turn x -90
> turn y 180
> turn x 90
[Repeated 3 time(s)]
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_map_model_5.cxs
> includeMaps true
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_mode_5.tif
> width 6000 height 6917 supersample 3 transparentBackground true
> turn x 90
> turn x -90
> turny 180
Unknown command: turny 180
> turn y 180
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_mode_y180_5.tif
> width 6000 height 6917 supersample 3 transparentBackground true
> turn x 90
> turn x -90
> turn y 180
> turn x 90
> turn x -90
> turn x 90
> turn x -90
[Repeated 4 time(s)]
> turn y 180
[Repeated 1 time(s)]
> turn x 45
[Repeated 1 time(s)]
> turn x -90
> turn x 90
[Repeated 3 time(s)]
> turn y 180
[Repeated 1 time(s)]
> show #!2 models
> turn y 180
[Repeated 1 time(s)]
> hide #!2 models
> turn y 180
[Repeated 1 time(s)]
> turn x 90
[Repeated 3 time(s)]
> show #!2 models
> hide #!2 models
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_map_model_6.cxs
> includeMaps true
——— End of log from Wed Nov 12 13:37:28 2025 ———
> view name session-start
opened ChimeraX session
> cartoon style width 1.7 thickness 0.6
> style ball 0.4 stick 0.3
Expected a keyword
> size ligand atomRadius +.5
Changed 79 atom radii
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_model_7.tif
> width 6000 height 5334 supersample 3 transparentBackground true
> turn y 180
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_model_y180_7.tif
> width 6000 height 5334 supersample 3 transparentBackground true
> turn y 180
> turn x 90
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_model_x90_7.tif
> width 6000 height 5334 supersample 3 transparentBackground true
> turn x -90
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_map_model_7.cxs
> includeMaps true
——— End of log from Thu Nov 13 09:30:15 2025 ———
> view name session-start
opened ChimeraX session
> open
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/cryosparc_P4_J1321_003_volume_map_sharp_cut.mrc
Opened cryosparc_P4_J1321_003_volume_map_sharp_cut.mrc as #3, grid size
256,256,256, pixel 1.11, shown at level 0.11, step 1, values float32
> surface dust #3 size 11.1
> close #3
> close #2
> open
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/cryosparc_P4_J1321_003_volume_map_sharp_cut.mrc
Opened cryosparc_P4_J1321_003_volume_map_sharp_cut.mrc as #2, grid size
256,256,256, pixel 1.11, shown at level 0.11, step 1, values float32
> volume #2 level 0.3
> surface dust #2 size 11.1
> hide #!2 models
> show #!2 models
> color #2 #b2b2b2cd models
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_map_model_7_1.cxs
——— End of log from Thu Nov 13 10:35:30 2025 ———
> view name session-start
opened ChimeraX session
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_map_model_7_1.cxs
> includeMaps true
——— End of log from Thu Nov 13 10:36:32 2025 ———
> view name session-start
opened ChimeraX session
> hide #!2 models
> show #!2 models
> hide #!2 models
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_map_model_7.cxs
——— End of log from Thu Nov 13 11:07:25 2025 ———
> view name session-start
opened ChimeraX session
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> turn x 90
> turn x -90
> view
> ui tool show "Side View"
> turn x 90
> turn x -90
> turn x 90
> turn x -90
> turn x 90
> turn x -90
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_map_model_7.cxs
> includeMaps true
——— End of log from Thu Nov 13 12:33:36 2025 ———
> view name session-start
opened ChimeraX session
> open
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/8SMV_gpr161_Gs_NSMB.cif
8SMV_gpr161_Gs_NSMB.cif title:
GPR161 Gs heterotrimer [more info...]
Chain information for 8SMV_gpr161_Gs_NSMB.cif #3
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAS2_HUMAN 5-64 204-394
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
N | Nanobody 35 |
R | G-protein coupled receptor 161 | GP161_HUMAN 1-529
Non-standard residues in 8SMV_gpr161_Gs_NSMB.cif #3
---
CLR — cholesterol
> hide atoms
> show cartoons
> mmaker #3 to #1/a
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif, chain A (#1)
with 8SMV_gpr161_Gs_NSMB.cif, chain R (#3), sequence alignment score = 1344.3
RMSD between 238 pruned atom pairs is 0.877 angstroms; (across all 266 pairs:
1.416)
> show ligand
> select #3
8169 atoms, 8354 bonds, 2 pseudobonds, 1035 residues, 2 models selected
> color (#!3 & sel) light gray
> select clear
> style stick
Changed 12404 atom styles
> ui mousemode right "tape measure"
> marker segment #4 position 141.5,154.6,149.1 toPosition 144,156.7,143 color
> yellow radius 0.1 label 6.87 labelHeight 0.687 labelColor yellow
> marker delete #4
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_Compare_Gprotein.cxs
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_Compare_Gprotein.tif
> width 6000 height 5247 supersample 3 transparentBackground true
> select #3
8169 atoms, 8354 bonds, 2 pseudobonds, 1035 residues, 2 models selected
> color (#!3 & sel) dark gray
> select clear
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_Compare_Gprotein_1.tif
> width 6000 height 5247 supersample 3 transparentBackground true
> select #3
8169 atoms, 8354 bonds, 2 pseudobonds, 1035 residues, 2 models selected
> color (#!3 & sel) gray
> select clear
> undo
[Repeated 2 time(s)]
> select clear
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_Compare_Gprotein.cxs
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_Compare_Gprotein.cxs
> includeMaps true
——— End of log from Thu Nov 13 17:41:04 2025 ———
> view name session-start
opened ChimeraX session
> select #1/a:186-226 #3/R:186-226
633 atoms, 658 bonds, 76 residues, 2 models selected
> select ~sel
11771 atoms, 12040 bonds, 1 pseudobond, 1502 residues, 5 models selected
> hide sel cartoons
> hide sel atoms
> ui mousemode right distance
> ui mousemode right label
[Repeated 1 time(s)]
> ui mousemode right "tape measure"
> marker segment #4 position 145.6,158.3,149.7 toPosition 150.3,158.6,146.5
> color yellow radius 0.1 label 5.713 labelHeight 0.5713 labelColor yellow
> select #1/a:186-226 #3/R:186-226
633 atoms, 658 bonds, 76 residues, 2 models selected
> select #1/a:226 #3/R:226
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/a:220 #3/R:220
22 atoms, 20 bonds, 2 residues, 2 models selected
> show sel atoms
> close #4
> ui mousemode right distance
> distance #1/A:220@CD #3/R:220@CG
Distance between gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A ARG
220 CD and 8SMV_gpr161_Gs_NSMB.cif #3/R ARG 220 CG: 4.749Å
> close #4
> style sel sphere
Changed 22 atom styles
> style sel ball
Changed 22 atom styles
> distance #1/A:220@CA #3/R:220@CA
Distance between gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A ARG
220 CA and 8SMV_gpr161_Gs_NSMB.cif #3/R ARG 220 CA: 5.713Å
> distance #1/A:220@CA #3/R:220@CA
Distance already exists; modify distance properties with 'distance style'
> close #4.1
> close #4
> distance #1/A:220@CA #3/R:220@CA
Distance between gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A ARG
220 CA and 8SMV_gpr161_Gs_NSMB.cif #3/R ARG 220 CA: 5.713Å
> hide sel atoms
> hide #4.1 models
> hide #!4 models
> select clear
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_Compare_Gprotein_TM5_compare.cxs
> includeMaps true
[Repeated 1 time(s)]
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_Compare_Gprotein_TM5_compare.tif
> width 6000 height 5140 supersample 3 transparentBackground true
> show cartoons
> select #1/a #3/R
4321 atoms, 4461 bonds, 4 pseudobonds, 549 residues, 5 models selected
> select ~sel
8083 atoms, 8239 bonds, 1 pseudobond, 1029 residues, 6 models selected
> hide sel cartoons
> volume #2 level 0.3
> hide #!3 models
> show #!3 models
> hide #!2 models
> ui tool show "Side View"
> hide pseudobonds
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_Compare_Gprotein_TM_top_view.tif
> width 6000 height 5140 supersample 3 transparentBackground true
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_Compare_Gprotein_TM_top_view.cxs
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_Compare_Gprotein_TM_side_view.cxs
> includeMaps true
——— End of log from Sun Nov 16 19:39:18 2025 ———
> view name session-start
opened ChimeraX session
> open C:/Users/mjiang64/Downloads/8KH4.cif/8kh4.cif
8kh4.cif title:
Cryo-EM structure of the GPR161-Gs complex [more info...]
Chain information for 8kh4.cif #5
---
Chain | Description | UniProt
A | G-protein coupled receptor 161 | GP161_HUMAN 2-348
B | Guanine nucleotide-binding protein G(olf) subunit alpha,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAL_HUMAN 5-195, GNAS2_HUMAN 204-394
C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
E | Nanobody 35 |
Non-standard residues in 8kh4.cif #5
---
CLR — cholesterol
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> select clear
> select add #5
7511 atoms, 7684 bonds, 2 pseudobonds, 1002 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> mmaker #5 to #3
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 8SMV_gpr161_Gs_NSMB.cif, chain B (#3) with 8kh4.cif, chain C (#5),
sequence alignment score = 1779.7
RMSD between 334 pruned atom pairs is 0.979 angstroms; (across all 336 pairs:
1.002)
> select subtract #5
Nothing selected
> mmaker #5 to #1
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 gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif, chain A (#1)
with 8kh4.cif, chain A (#5), sequence alignment score = 1379.7
RMSD between 224 pruned atom pairs is 1.152 angstroms; (across all 266 pairs:
1.708)
> select #5 /a
2076 atoms, 2142 bonds, 1 pseudobond, 267 residues, 2 models selected
> select ~sel & ##selected
5435 atoms, 5542 bonds, 1 pseudobond, 735 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/GPR161_TUBBY_Align_to_GPR161_Gprotein/gpr161_tubby_Compare_Gprotein_TM_side_view_3pdb.tif
> width 6000 height 8393 supersample 3 transparentBackground true
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/GPR161_TUBBY_Align_to_GPR161_Gprotein/gpr161_tubby_Compare_Gprotein_TM_side_view_3pdb.cxs
> includeMaps true
> rotate x 90
Unknown command: rotate x 90
> turn x 90
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/GPR161_TUBBY_Align_to_GPR161_Gprotein/gpr161_tubby_Compare_Gprotein_TM_side_view_3pdb_turnX90.cxs
> includeMaps true
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/GPR161_TUBBY_Align_to_GPR161_Gprotein/gpr161_tubby_Compare_Gprotein_TM_side_view_3pdb_turnX90.tif
> width 6000 height 8393 supersample 3 transparentBackground true
> turn x -90
> show #!2 models
> select add #1
9670 atoms, 9888 bonds, 3 pseudobonds, 1278 residues, 4 models selected
> select add #5
11746 atoms, 12030 bonds, 4 pseudobonds, 1545 residues, 4 models selected
> select subtract #5
4235 atoms, 4346 bonds, 2 pseudobonds, 543 residues, 2 models selected
> hide #!5 models
> select subtract #1
Nothing selected
> show #!1,3 atoms
> hide #!3 models
> show #!3 models
> hide #!3 models
> color #!1 byhetero
> ui mousemode right "tape measure"
> marker segment #6 position 139.4,155.9,140.3 toPosition 146.3,162.8,139.3
> color yellow radius 0.2763 label 9.857 labelHeight 0.9857 labelColor yellow
> marker segment #6 position 144.4,159.4,134.9 toPosition 146.3,162.8,139.3
> color yellow radius 0.2763 label 5.882 labelHeight 0.5882 labelColor yellow
> hide #!2 models
> marker segment #6 position 150.7,157.6,137.2 toPosition 146.3,162.8,139.3
> color yellow radius 0.2763 label 7.193 labelHeight 0.7193 labelColor yellow
> marker delete #6
> hide #!1 atoms
> show #!1 cartoons
> open
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/tubby_pip2_Xcry.pdb
Chain information for tubby_pip2_Xcry.pdb #6
---
Chain | Description
B | No description available
Computing secondary structure
> hide #6 models
> mmaker #6 to #1/b:424-435
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 gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif, chain B (#1)
with tubby_pip2_Xcry.pdb, chain B (#6), sequence alignment score = 57.9
RMSD between 12 pruned atom pairs is 0.492 angstroms; (across all 12 pairs:
0.492)
> show #6 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/GPR161_TUBBY_Align_to_GPR161_Gprotein/gpr161_tubby_Compare_Xcry_Tubby.cxs
> includeMaps true
> show ligand
> show #!2 models
> hide #6 models
> hide #!1 models
> open
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif
Summary of feedback from opening
C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif
---
warnings | Unknown polymer entity '1' on line 124
Unknown polymer entity '2' on line 2265
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #7
---
Chain | Description
A | No description available
B | No description available
> show #6 models
> hide #!7 models
> close #7
> open C:/Users/mjiang64/Downloads/1I7E.cif/1i7e.cif
Summary of feedback from opening C:/Users/mjiang64/Downloads/1I7E.cif/1i7e.cif
---
note | Fetching CCD IBS from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/IBS/IBS.cif
1i7e.cif title:
C-Terminal Domain Of Mouse Brain Tubby Protein bound to Phosphatidylinositol
4,5-bis-phosphate [more info...]
Chain information for 1i7e.cif #7
---
Chain | Description | UniProt
A | TUBBY PROTEIN | TUB_MOUSE 243-505
Non-standard residues in 1i7e.cif #7
---
IBS — L-α-glycerophospho-D-myo-inositol-4,5-bis-phosphate
> open C:/Users/mjiang64/Downloads/3C5N.cif/3c5n.cif
Summary of feedback from opening C:/Users/mjiang64/Downloads/3C5N.cif/3c5n.cif
---
note | Fetching CCD I3P from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/I3P/I3P.cif
3c5n.cif title:
Structure of human TULP1 in complex with IP3 [more info...]
Chain information for 3c5n.cif #8
---
Chain | Description | UniProt
A B | Tubby-related protein 1 | TULP1_HUMAN 238-483
Non-standard residues in 3c5n.cif #8
---
I3P — D-myo-inositol-1,4,5-triphosphate
3c5n.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
55 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> mmaker #7-8 to #1/b:424-435
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 gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif, chain B (#1)
with 1i7e.cif, chain A (#7), sequence alignment score = 51
RMSD between 12 pruned atom pairs is 0.415 angstroms; (across all 12 pairs:
0.415)
Matchmaker gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif, chain B (#1)
with 3c5n.cif, chain A (#8), sequence alignment score = 47.4
RMSD between 12 pruned atom pairs is 0.447 angstroms; (across all 12 pairs:
0.447)
> hide #!2 models
> hide #!8 models
> close #6
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!8 models
> hide #!7 models
> hide #!1 models
> show #!7 models
> hide #!8 models
> mmaker #8/b to #1/b:424-435
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 gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif, chain B (#1)
with 3c5n.cif, chain B (#8), sequence alignment score = 47.4
RMSD between 12 pruned atom pairs is 0.475 angstroms; (across all 12 pairs:
0.475)
> show #!8 models
> show #!1 models
> hide #!7 models
> hide #!8 models
> show #!8 models
> hide #!1 models
> show #!2 models
> volume #2 level 0.244
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!8 models
> show #!8 models
> hide #!1 models
> hide #!2 models
> delete #8/a
> show #!1 models
> show #!2 models
> hide #!8 models
> show #!8 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!8 models
> show #!8 models
> hide #!2 models
> hide #!1 models
> show #!7 models
> hide #!7-8 cartoons
> hide #!7-8 atoms
> show ligand
> hide #!8 models
> show #!8 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> hide #!7 models
> show #!1 models
> coulombic #!1
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A ILE 28
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A PHE 31
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A ILE 32
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A ILE 35
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A CYS 42
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A LEU 43
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A LEU 46
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A LYS 54
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A ASN 63
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A ARG 90
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A ARG 91
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A GLU 92
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A PHE 95
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A PHE 102
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A MET 133
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A MET 137
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A LYS 138
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A ARG 143
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A LEU 160
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A TRP 166
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A GLU 173
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A TYR 261
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A ASN 264
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A GLU 293
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A SER 299
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A SER 304
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A LYS 329
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A LYS 333
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A GLU 334
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/A LEU 335
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/B ARG 205
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/B ASP 214
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/B ARG 215
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/B LEU 217
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/B PHE 218
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/B GLU 228
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/B LYS 242
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/B ARG 260
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/B LYS 268
gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif #1/B ARG 270
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif_A SES
surface #1.2: minimum, -20.73, mean 0.69, maximum 16.52
Coulombic values for gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif_B SES
surface #1.3: minimum, -20.95, mean 0.19, maximum 14.16
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp #!1
Map values for surface "gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif_A
SES surface": minimum -27.64, mean 1.062, maximum 24.26
Map values for surface "gpr161_tubby_2pip2_fit1321_refined_052_coot-4_1.cif_B
SES surface": minimum -27.85, mean -4.295, maximum 23.78
To also show corresponding color key, enter the above mlp command and add key
true
> hide #1.1 models
> hide #1.3 models
> show #1.3 models
> show #1.1 models
> hide #1.2 models
> hide #1.3 models
> hide #1.1 models
> show #!1 atoms
> ui mousemode right "tape measure"
[Repeated 1 time(s)]
> marker segment #6 position 144.4,159.4,134.9 toPosition 146.1,162.1,140.1
> color yellow radius 0.2763 label 6.042 labelHeight 0.6042 labelColor yellow
> marker segment #6 position 141.3,157.7,139.3 toPosition 145.3,162.3,140
> color yellow radius 0.2763 label 6.09 labelHeight 0.609 labelColor yellow
> hide #!6 models
> hide #!1 atoms
> show ligand
> interfaces #!1 & ~solvent
1 buried areas: A B 890
> show sel atoms
> select clear
> style #!1 stick
Changed 4235 atom styles
> ui mousemode right "tape measure"
> marker segment #6 position 144.3,160.2,143.7 toPosition 145.3,162.3,140
> color yellow radius 0.2763 label 4.362 labelHeight 0.5525 labelColor yellow
> marker segment #6 position 142.5,161.6,143.9 toPosition 142.5,163.1,142.4
> color yellow radius 0.2763 label 2.103 labelHeight 0.5525 labelColor yellow
> marker segment #6 position 142.5,161.6,143.9 toPosition 142.8,163.8,142.6
> color yellow radius 0.2763 label 2.532 labelHeight 0.5525 labelColor yellow
> marker segment #6 position 147.3,156.4,140.7 toPosition 147.2,159.7,144
> color yellow radius 0.2763 label 4.687 labelHeight 0.5525 labelColor yellow
> ui mousemode right "tape measure"
> marker segment #6 position 147.3,156.4,140.7 toPosition 149.4,161.5,142.9
> color yellow radius 0.2763 label 5.907 labelHeight 0.5907 labelColor yellow
> marker delete #6
> marker segment #6 position 147.3,156.4,140.7 toPosition 147,159.5,143.8
> color yellow radius 0.2763 label 4.36 labelHeight 0.5525 labelColor yellow
> marker segment #6 position 147.3,156.4,140.7 toPosition 147,155.2,148 color
> yellow radius 0.2763 label 7.316 labelHeight 0.7316 labelColor yellow
> marker delete #6
> marker segment #6 position 144,157.1,139.9 toPosition 145.5,161.5,141.1
> color yellow radius 0.2763 label 4.833 labelHeight 0.5525 labelColor yellow
> marker delete #6
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #2 level 0.3
> hide #!2 models
> marker segment #6 position 142.5,161.6,143.9 toPosition 143.2,163,141.7
> color yellow radius 0.2763 label 2.697 labelHeight 0.5525 labelColor yellow
> marker segment #6 position 142.1,159.4,143.6 toPosition 145.5,161.5,141.1
> color yellow radius 0.2763 label 4.741 labelHeight 0.5525 labelColor yellow
> marker delete #6
> show #!2 models
> volume #2 level 0.2
> hide #!2 models
> cartoon style helix width 1.5 thickness 0.3
> cartoon style width 1.5 thickness 0.3
> cartoon style width 1.2 thickness 0.3
> cartoon style strand xsection rectangle width 1
> select /a:186-226, 260-295
1817 atoms, 1862 bonds, 4 pseudobonds, 230 residues, 7 models selected
> select ~sel & ##selected
20365 atoms, 20441 bonds, 7 pseudobonds, 2971 residues, 8 models selected
> undo
> select ~sel & #1/a selected
Expected a keyword
> select ~sel & #1/a: selected
Nothing selected
> select /a:186-226, 260-295, /b
Expected an objects specifier or a keyword
> select /a:186-226, 260-295 /b
12122 atoms, 12185 bonds, 8 pseudobonds, 1431 residues, 9 models selected
> select ~sel & ##selected
13870 atoms, 13819 bonds, 6 pseudobonds, 2140 residues, 7 models selected
> hide sel & #!1 cartoons
> hide sel & #!1 atoms
> show #!2 models
> volume #2 level 0.3
> hide #!2 models
> select #1/b: 404-434
238 atoms, 243 bonds, 31 residues, 1 model selected
> select #1/b: 404-434, 178-248
785 atoms, 798 bonds, 102 residues, 1 model selected
> color (#!1 & sel) dark gray
> color (#!1 & sel) light gray
> select clear
> select #1/b: 404-438, 178-271
985 atoms, 1002 bonds, 129 residues, 1 model selected
> color (#!1 & sel) light gray
> select clear
> select #1/b: 404-438, 178-271
985 atoms, 1002 bonds, 129 residues, 1 model selected
> color (#!1 & sel) white
> select clear
> select #1/b: 502
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_interface/gpr161_tubby_interface.cxs
> includeMaps true
> style sel ball
Changed 20 atom styles
> style sel ball
Changed 20 atom styles
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_interface/gpr161_tubby_interface.tif
> width 6000 height 5190 supersample 3 transparentBackground true
> select #1/b: 404-438, 178-271
985 atoms, 1002 bonds, 129 residues, 1 model selected
> color sel burly wood
> select clear
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_interface/gpr161_tubby_interface_1.tif
> width 6000 height 5190 supersample 3 transparentBackground true
> cartoon style width 1 thickness 0.3
> cartoon style strand xsection rectangle width 0.8
> marker segment #6 position 140.3,166.4,171.8 toPosition 140.3,166.4,171.8
> color yellow radius 0.2763 label 0 labelHeight 0.5525 labelColor yellow
> marker delete #6
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_interface/gpr161_tubby_interface_2.tif
> width 6000 height 5414 supersample 3 transparentBackground true
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_interface/gpr161_tubby_interface_2.cxs
> includeMaps true
——— End of log from Thu Nov 20 13:41:58 2025 ———
> view name session-start
opened ChimeraX session
> lighting soft
> select #1/b: 178-302
949 atoms, 964 bonds, 125 residues, 1 model selected
> hide sel cartoons
> select #1/b: 395-438
349 atoms, 358 bonds, 44 residues, 1 model selected
> hide sel cartoons
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_interface/gpr161_tubby_interface_3.cxs
> includeMaps true
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_interface/gpr161_tubby_interface_3.tif
> width 6000 height 5414 supersample 3 transparentBackground true
> lighting simple
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_interface/gpr161_tubby_interface_4.tif
> width 6000 height 5414 supersample 3 transparentBackground true
> select #1/b:
Expected an objects specifier or a keyword
> select #1/b
2094 atoms, 2137 bonds, 263 residues, 1 model selected
> color (#!1 & sel) light gray
> undo
> color (#!1 & sel) cartoons light gray
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select clear
> cartoon style width 0.6 thickness 0.3
> cartoon style width 0.8 thickness 0.3
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_interface/gpr161_tubby_interface_5.tif
> width 6000 height 5414 supersample 3 transparentBackground true
> cartoon style width 0.8 thickness 0.4
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_interface/gpr161_tubby_interface_6.tif
> width 6000 height 5414 supersample 3 transparentBackground true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\image_formats\\__init__.py", line 56, in save
save_image(session, path, format_name, **kw)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\image_formats\save.py", line 134, in save_image
i = view.image(width, height, supersample=supersample,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\view.py", line 452, in image
rgba = self.image_rgba(width=width, height=height, supersample=supersample,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\view.py", line 514, in image_rgba
srgba += r.frame_buffer_image(w, h)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1328, in frame_buffer_image
rgba = empty((h, w, 4), uint8)
^^^^^^^^^^^^^^^^^^^^^^^
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 124. MiB for an
array with shape (5414, 6000, 4) and data type uint8
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 124. MiB for an
array with shape (5414, 6000, 4) and data type uint8
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1328, in frame_buffer_image
rgba = empty((h, w, 4), uint8)
^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> save
> C:/MJ_Research/IFTA/Gpr161_tubby/mj127_113_structure/J1109_pdb_map/model_analysis/raw_fig_cargo/gpr161_tubby_interface/gpr161_tubby_interface_6.tif
> width 6000 height 5414 supersample 3 transparentBackground true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\image_formats\\__init__.py", line 56, in save
save_image(session, path, format_name, **kw)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\image_formats\save.py", line 134, in save_image
i = view.image(width, height, supersample=supersample,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\view.py", line 452, in image
rgba = self.image_rgba(width=width, height=height, supersample=supersample,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\view.py", line 506, in image_rgba
srgba = zeros((h, w, 4), float32)
^^^^^^^^^^^^^^^^^^^^^^^^^
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 496. MiB for an
array with shape (5414, 6000, 4) and data type float32
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 496. MiB for an
array with shape (5414, 6000, 4) and data type float32
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\view.py", line 506, in image_rgba
srgba = zeros((h, w, 4), float32)
^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 32.0.101.6881
OpenGL renderer: Intel(R) Arc(TM) Pro
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: Dell Pro Max 14 MC14250
OS: Microsoft Windows 11 Enterprise (Build 26100)
Memory: 16,597,598,208
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) Ultra 7 265H
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2025.7.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.10
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 310
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
WMI: 1.5.1
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