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Opened 2 weeks ago
Closed 11 days ago
#19402 closed defect (limitation)
ArrayMemoryError saving large image
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: 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
Change History (2)
comment:1 by , 11 days ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ArrayMemoryError saving large image |
comment:2 by , 11 days ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
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Out of memory trying to save an absurdly large image 6000 by 5414. Error is allocating only 124 Mbytes. Machine has 16 GB. As usual the error is on Windows where out of memory errors seem very common. They don't appear to have opened large data. I wonder if memory use by other applications causes these ChimeraX out of memory errors.