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Opened 5 hours ago
#19850 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-10-10.0.26200
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM1.cxs
Opened 9ZLK.mrc as #1, grid size 384,384,384, pixel 0.93, shown at level
0.111, step 1, values float32
Log from Tue Feb 10 15:38:26 2026 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> "C:/Users/mbash/OneDrive/Desktop/MgtA_paper/images_for_paper/deposited_pdb_maps/Deposited_pdbs
> Map_and coordinates_with_code/9ZLK.mrc"
> "C:/Users/mbash/OneDrive/Desktop/MgtA_paper/images_for_paper/deposited_pdb_maps/Deposited_pdbs
> Map_and coordinates_with_code/9ZLK.pdb"
Opened 9ZLK.mrc as #1, grid size 384,384,384, pixel 0.93, shown at level
0.0178, step 2, values float32
Chain information for 9ZLK.pdb #2
---
Chain | Description
A | No description available
> ui tool show "Hide Dust"
> surface dust #1 size 21.17
[Repeated 1 time(s)]
> ui tool show Toolbar
> volume #1 step 1
> volume #1 level 0.1052
> backgound colour white
Unknown command: backgound colour white
> set bgColor white
> volume #1 style mesh
> hide cartoons
> hide atoms
[Repeated 1 time(s)]
> show atoms
> select 72-105
Expected an objects specifier or a keyword
> select 73-106
Expected an objects specifier or a keyword
> select :73-106
269 atoms, 274 bonds, 34 residues, 1 model selected
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> select up
394 atoms, 401 bonds, 51 residues, 1 model selected
> select up
7167 atoms, 7288 bonds, 897 residues, 1 model selected
> set bgColor white
> select :73-106
269 atoms, 274 bonds, 34 residues, 1 model selected
> select :107-910
6414 atoms, 6524 bonds, 804 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select :22-910
7110 atoms, 7225 bonds, 894 residues, 1 model selected
> hide sel atoms
> select :73-106
269 atoms, 274 bonds, 34 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 5.58
> volume #1 level 0.1475
> ui tool show "Surface Zone"
> surface zone #1 nearAtoms #2 distance 5.58
> surface zone #1 nearAtoms #2 distance 3.52
> volume zone #1 nearAtoms sel & #2 range 5.58
> surface zone #1 nearAtoms #2 distance 1.95
> volume zone #1 nearAtoms sel & #2 range 5.58
> volume #1 level 0.1869
> volume #1 near Atoms sel  range
Expected a keyword
> volume zone #1 nearAtoms sel & #2 range 4
> volume zone #1 nearAtoms sel & #2 range 3
> volume #1 level 0.1362
> volume zone #1 nearAtoms sel & #2 range 2.5
> volume #1 level 0.08825
> transparency 50
> transparency 0
> transparency 50
> volume style image
> volume style mesh
> volume style image
> volume style mesh
> select ::name="HOH"
26 atoms, 26 residues, 1 model selected
> hide sel atoms
> select ::name="K"
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select ::name="MG"
4 atoms, 4 residues, 1 model selected
> hide sel atoms
> select ::name="ACP"
48 atoms, 50 bonds, 1 residue, 1 model selected
> hide sel atoms
> graphics silhouettes true
> lighting shadows true
> lighting flat
> lighting full
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting full
> lighting flat
> graphics silhouettes false
> lighting simple
> save
> C:/Users/mbash/OneDrive/Desktop/MgtA_paper/images_for_paper/TM1_Map_simple.png
> width 1981 height 1285 supersample 3
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM1_Map_simple.png
> width 1981 height 1285 supersample 3 transparentBackground true
> lighting full
[Repeated 1 time(s)]
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
> lighting soft
> lighting simple
> lighting soft
> volume #1 change image level -0.005576,0 level 0.01764,0.8 level 0.9387,1
> volume #1 level 0.1108
> lighting flat
> lighting full
[Repeated 1 time(s)]
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM1_Map_full.png
> width 1981 height 1285 supersample 3 transparentBackground true
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM1.cxs includeMaps
> true
——— End of log from Tue Feb 10 15:38:26 2026 ———
opened ChimeraX session
> select :73-106
269 atoms, 274 bonds, 34 residues, 1 model selected
> volume #1 color #00000080
> ui tool show Toolbar
> graphics silhouettes false
> view sel
> volume zone #1 nearAtoms sel & #2 range 2.0
> view sel
[Repeated 1 time(s)]
> select add #2
7246 atoms, 7338 bonds, 929 residues, 1 model selected
> select subtract #2
Nothing selected
> save
> C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM1_Map_simple_scale.png
> width 3000 height 2694 supersample 3 transparentBackground true
> select :73-106
269 atoms, 274 bonds, 34 residues, 1 model selected
> view
> select :14-910, Mg, HOH, BEF
7197 atoms, 7288 bonds, 927 residues, 1 model selected
> hide sel atoms
> select :73-106
269 atoms, 274 bonds, 34 residues, 1 model selected
> show sel atoms
> select add #2
7246 atoms, 7338 bonds, 929 residues, 1 model selected
> select subtract #2
Nothing selected
> save
> C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM1_Map_simple_scale.png
> width 3000 height 2694 supersample 3 transparentBackground true
> color #2#1.1#!1 byelement
> select add #1
3 models selected
> color #1.1 gray
> select clear
> select add #1
3 models selected
> color #1.1 dim gray
> select clear
> select /A:108-135
218 atoms, 219 bonds, 28 residues, 1 model selected
> show sel target ab
> select clear
[Repeated 1 time(s)]
> hide #2#1.1#!1 target a
> select /A:108-135
218 atoms, 219 bonds, 28 residues, 1 model selected
> show sel atoms
> select up
243 atoms, 245 bonds, 32 residues, 1 model selected
> select up
7167 atoms, 7288 bonds, 897 residues, 1 model selected
> select clear
> select /A:108-135
218 atoms, 219 bonds, 28 residues, 1 model selected
> volume zone #1 nearAtoms sel & #2 range 2.0
> select clear
[Repeated 1 time(s)]
> hide atoms
> select /A:675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> show sel atoms
> select up
383 atoms, 390 bonds, 49 residues, 1 model selected
> select up
7167 atoms, 7288 bonds, 897 residues, 1 model selected
> select clear
> select /A:675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> select clear
> select /A:675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> volume zone #1 nearAtoms sel & #2 range 2.0
> view name TM5
> select clear
> select ~sel & ##selected
Nothing selected
> view name TM5large
> view TM5
> select ~sel & ##selected
Nothing selected
> view TM5large
> select ~sel & ##selected
Nothing selected
> view TM5
> select ~sel & ##selected
Nothing selected
> view TM5large
> view list
Named views: TM5, TM5large
> view TM5
> view TM5large
> view TM5
> view TM5large
> view TM5
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/new_view.cxs
> includeMaps true
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM5_best.png width
> 3000 height 1960 supersample 3 transparentBackground true
> select /A:675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> select /A:675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> select /A:73-106
269 atoms, 274 bonds, 34 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select /A:675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> hide sel atoms
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM1_best.png width
> 3000 height 1960 supersample 3 transparentBackground true
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM1_best.cxs
> includeMaps true
> select /A:675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> select /A:73-106
269 atoms, 274 bonds, 34 residues, 1 model selected
> hide sel atoms
> select /A:108-135
218 atoms, 219 bonds, 28 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 1 model selected
> select subtract #2
Nothing selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM2_best.png width
> 3000 height 1960 supersample 3 transparentBackground true
> select /A:108-135
218 atoms, 219 bonds, 28 residues, 1 model selected
> hide sel atoms
> select /A:268-299
263 atoms, 270 bonds, 32 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 1 model selected
> select subtract #2
Nothing selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM3_best.png width
> 3000 height 1960 supersample 3 transparentBackground true
> select /A:302-340
280 atoms, 284 bonds, 39 residues, 1 model selected
> show sel atoms
> select /A:268-299
263 atoms, 270 bonds, 32 residues, 1 model selected
> hide sel atoms
> select /A:302-340
280 atoms, 284 bonds, 39 residues, 1 model selected
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 1 model selected
> select subtract #2
Nothing selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM4_best.png width
> 3000 height 1960 supersample 3 transparentBackground true
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM4_best_1.png
> width 3000 height 1960 supersample 3 transparentBackground true
> select /A:302-340
280 atoms, 284 bonds, 39 residues, 1 model selected
> hide sel atoms
> select /A:675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 1 model selected
> select subtract #2
Nothing selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM5_best_1.png
> width 3000 height 1960 supersample 3 transparentBackground true
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM5_best_2.png
> width 3000 height 1960 supersample 3 transparentBackground true
> select /A:675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> hide sel atoms
> select /A:675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> show sel atoms
> select /A:675-716, Mg
326 atoms, 330 bonds, 42 residues, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> show sel cartoons
> hide sel cartoons
> show sel cartoons
[Repeated 1 time(s)]
> hide sel cartoons
> show sel surfaces
> hide sel surfaces
> select /A:675-716, Mg
326 atoms, 330 bonds, 42 residues, 1 model selected
> show sel atoms
> select :675-716, Mg
330 atoms, 330 bonds, 46 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM5_best_Mg.png
> width 3000 height 1960 supersample 3 transparentBackground true
> select :675-716, Mg
330 atoms, 330 bonds, 46 residues, 1 model selected
> hide sel atoms
> select :718-742
199 atoms, 205 bonds, 25 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM6_best.png width
> 3000 height 1960 supersample 3 transparentBackground true
> select :718-742
199 atoms, 205 bonds, 25 residues, 1 model selected
> hide sel atoms
> select :758-794
287 atoms, 296 bonds, 37 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :758-794, Mg
291 atoms, 296 bonds, 41 residues, 1 model selected
> select :758-794, Mg
291 atoms, 296 bonds, 41 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM7_best.png width
> 3000 height 1960 supersample 3 transparentBackground true
> select :799-833, Mg
286 atoms, 292 bonds, 39 residues, 1 model selected
> select :758-794, Mg
291 atoms, 296 bonds, 41 residues, 1 model selected
> hide sel atoms
> select :799-833, Mg
286 atoms, 292 bonds, 39 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM8_best.png width
> 3000 height 1960 supersample 3 transparentBackground true
> select :799-833, Mg
286 atoms, 292 bonds, 39 residues, 1 model selected
> hide sel atoms
> select :845-868
176 atoms, 180 bonds, 24 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM9_best.png width
> 3000 height 1960 supersample 3 transparentBackground true
> select :845-868
176 atoms, 180 bonds, 24 residues, 1 model selected
> hide sel atoms
> select :877-908
274 atoms, 284 bonds, 32 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM10_best.png width
> 3000 height 1960 supersample 3 transparentBackground true
> select :877-908
274 atoms, 284 bonds, 32 residues, 1 model selected
> hide sel atoms
> select :73-106
269 atoms, 274 bonds, 34 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> select :73
6 atoms, 5 bonds, 1 residue, 1 model selected
> select :73-106
269 atoms, 274 bonds, 34 residues, 1 model selected
> hide sel atoms
> select :108-135
218 atoms, 219 bonds, 28 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :108
4 atoms, 3 bonds, 1 residue, 1 model selected
> select :108-109
13 atoms, 12 bonds, 2 residues, 1 model selected
> select :108-135
218 atoms, 219 bonds, 28 residues, 1 model selected
> hide sel atoms
> select :268-299
263 atoms, 270 bonds, 32 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :268
7 atoms, 6 bonds, 1 residue, 1 model selected
> select :26270
Nothing selected
> select :26-270
1884 atoms, 1906 bonds, 246 residues, 1 model selected
> select :268-270
27 atoms, 27 bonds, 3 residues, 1 model selected
> select :268-299
263 atoms, 270 bonds, 32 residues, 1 model selected
> hide sel atoms
> select :302-340
280 atoms, 284 bonds, 39 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :302-305
36 atoms, 37 bonds, 4 residues, 1 model selected
> select :302-340
280 atoms, 284 bonds, 39 residues, 1 model selected
> hide sel atoms
> select :675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :675-680
49 atoms, 48 bonds, 6 residues, 1 model selected
> select :675-699
203 atoms, 204 bonds, 25 residues, 1 model selected
> select :675-750
608 atoms, 622 bonds, 76 residues, 1 model selected
> hide sel atoms
> select :718-742
199 atoms, 205 bonds, 25 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :718-720
26 atoms, 27 bonds, 3 residues, 1 model selected
> select :718-800
670 atoms, 694 bonds, 83 residues, 1 model selected
> hide sel atoms
> select :758-794
287 atoms, 296 bonds, 37 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :758-765
58 atoms, 58 bonds, 8 residues, 1 model selected
> select :758-800
333 atoms, 344 bonds, 43 residues, 1 model selected
> hide sel atoms
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :799-805
42 atoms, 42 bonds, 7 residues, 1 model selected
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> select :799-805
42 atoms, 42 bonds, 7 residues, 1 model selected
> select :1-910
7198 atoms, 7288 bonds, 928 residues, 1 model selected
> hide sel atoms
> select :799-833
282 atoms, 292 bonds, 35 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :799-805
42 atoms, 42 bonds, 7 residues, 1 model selected
> select :799-900
810 atoms, 837 bonds, 102 residues, 1 model selected
> hide sel atoms
> select :845-865
155 atoms, 158 bonds, 21 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select :845-850
41 atoms, 41 bonds, 6 residues, 1 model selected
> select :1-910
7198 atoms, 7288 bonds, 928 residues, 1 model selected
> hide sel atoms
> select :acp
48 atoms, 50 bonds, 1 residue, 1 model selected
> show sel atoms
> select :ACP
48 atoms, 50 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="ACP"
48 atoms, 50 bonds, 1 residue, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> volume #1 level 0.1108
> select sel @< 5
260 atoms, 228 bonds, 30 residues, 1 model selected
> select sel @< 5
7222 atoms, 630 bonds, 905 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :ACP
48 atoms, 50 bonds, 1 residue, 1 model selected
> select :1-910
7198 atoms, 7288 bonds, 928 residues, 1 model selected
> hide sel atoms
> select :ACP
48 atoms, 50 bonds, 1 residue, 1 model selected
> select sel @< 5
260 atoms, 228 bonds, 30 residues, 1 model selected
> select sel @< 5
7222 atoms, 630 bonds, 905 residues, 1 model selected
> show sel atoms
> select sel :< 5
7245 atoms, 7338 bonds, 928 residues, 1 model selected
> select sel :< 5
7246 atoms, 7338 bonds, 929 residues, 1 model selected
> select :ACP
48 atoms, 50 bonds, 1 residue, 1 model selected
> select sel :< 5
463 atoms, 454 bonds, 30 residues, 1 model selected
> select :1-910
7198 atoms, 7288 bonds, 928 residues, 1 model selected
> hide sel atoms
> select :ACP
48 atoms, 50 bonds, 1 residue, 1 model selected
> select sel :< 5
463 atoms, 454 bonds, 30 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :ACP, Mg
52 atoms, 50 bonds, 5 residues, 1 model selected
> select sel :< 5
623 atoms, 594 bonds, 54 residues, 1 model selected
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :1-910
7198 atoms, 7288 bonds, 928 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select :ACP, Mg
52 atoms, 50 bonds, 5 residues, 1 model selected
> show sel atoms
> select subtract /B:1@MG
51 atoms, 50 bonds, 4 residues, 1 model selected
> hide sel atoms
> undo
> select add /B:1@MG
52 atoms, 50 bonds, 5 residues, 1 model selected
> select /B:1@MG
1 atom, 1 residue, 1 model selected
> select #1
3 models selected
> select :1-910
7198 atoms, 7288 bonds, 928 residues, 1 model selected
Drag select of 1 9ZLK.mrc , 1 atoms
> select clear
Drag select of 1 9ZLK.mrc , 48 atoms, 49 bonds
> select #1
3 models selected
> select clear
> volume hide
Drag select of 48 atoms, 49 bonds
Drag select of 49 atoms, 50 bonds
Drag select of 46 atoms, 48 bonds
> select clear
> select /B:1@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:2@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:3@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
Drag select of 49 atoms, 50 bonds
> volume zone #1 nearAtoms sel & #2 range 2.0
> volume show
> select sel :< 4
376 atoms, 366 bonds, 24 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> vop resample #1 spacing 0.5
Opened 9ZLK.mrc resampled as #3, grid size 714,714,714, pixel 0.5, shown at
step 1, values float32
> volume zone #1 nearAtoms sel & #2 range 2.0
[Repeated 1 time(s)]
> volume show
> volume zone #1 nearAtoms sel & #2 range 2.0
> hide #!1 models
> show #!1 models
> hide #!3 models
> volume #1 level 0.08284
> volume zone #1 nearAtoms sel & #2 range 2.5
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> select add #2
7246 atoms, 7338 bonds, 929 residues, 1 model selected
> select subtract #2
1 model selected
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting soft
> lighting simple
> graphics silhouettes true
> lighting simple
> graphics silhouettes false
> lighting simple
> volume #1 level 0.07775
> volume #1 level 0.111
> volume #1 level 0.08
> show #!3 models
> hide #!1 models
> volume zone #1 nearAtoms sel & #2 range 2.5
no atoms specified for zone
> select add #2
7246 atoms, 7338 bonds, 929 residues, 1 model selected
> volume zone #1 nearAtoms sel & #2 range 2.5
> hide #!3 models
> show #!1 models
> vop resample #1 spacing 0.5
Opened 9ZLK.mrc resampled as #4, grid size 714,714,714, pixel 0.5, shown at
step 1, values float32
> hide #!2 models
> show #!2 models
> volume zone #4 nearAtoms sel & #2 range 2.5
> hide #!4 models
> show sel atoms
> hide sel atoms
> select :ACP, Mg
52 atoms, 50 bonds, 5 residues, 1 model selected
> show sel atoms
> select /B:1@MG
1 atom, 1 residue, 1 model selected
> select /B:1@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:2@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
Drag select of 49 atoms, 50 bonds
> select sel :< 4
376 atoms, 366 bonds, 24 residues, 1 model selected
> show sel atoms
> volume zone #4 nearAtoms sel & #2 range 2.5
> show #!4 models
> color (#!2 & sel) gray
> color (#!2 & sel) byhetero
> color #4 #5d5d41ff models
> color #4 #646446ff models
> color #4 #70704eff models
> color #4 #bfbf85ff models
> color #4 #787854ff models
> color #4 #5b5b40ff models
> color #4 #53533aff models
> color #4 #616144ff models
> color #4 #6d6d4cff models
> view sel
> volume zone #4 nearAtoms sel & #2 range 2.
> volume zone #4 nearAtoms sel & #2 range 2.2
> volume #4 level 0.1109
> volume #4 level 0.06453
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/AMPPCP_Mg_4.png
> width 3000 height 1960 supersample 3 transparentBackground true
> color (#!2 & sel) byelement
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/AMPPCP_Mg_5.png
> width 3000 height 1960 supersample 3 transparentBackground true
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/AMPPCP_Mg_5.png
> width 3000 height 1960 supersample 3 transparentBackground true
> select :ACP, Mg
52 atoms, 50 bonds, 5 residues, 1 model selected
> select /B:3@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select :ACP, Mg
52 atoms, 50 bonds, 5 residues, 1 model selected
> select sel :< 3
346 atoms, 332 bonds, 25 residues, 1 model selected
> select sel :< 6
7227 atoms, 1472 bonds, 910 residues, 1 model selected
> hide sel atoms
> select :ACP, Mg
52 atoms, 50 bonds, 5 residues, 1 model selected
> show sel atoms
> select /B:1@MG
1 atom, 1 residue, 1 model selected
> select /B:1@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:2@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:3@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select sel :< 4
24 atoms, 20 bonds, 4 residues, 1 model selected
> show sel atoms
> volume #!4 hide
Drag select of 49 atoms, 50 bonds
> select sel :< 4
376 atoms, 366 bonds, 24 residues, 1 model selected
> show sel atoms
> volume zone #4 nearAtoms sel & #2 range 2.2
> show #!4 models
> volume zone #4 nearAtoms sel & #2 range 2.2
> color #4 #b0b07bff models
> color #4 #86865eff models
> color #4 #6b6b4bff models
> color #4 #55553bff models
> volume #4 step 1
> volume #4 level 0.111
> volume #4 level 0.07625
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/AMPPCP_Mg_6.png
> width 3000 height 1960 supersample 3 transparentBackground true
> volume zone #4 nearAtoms sel & #2 range 2.0
no atoms specified for zone
> select add #2
7246 atoms, 7338 bonds, 929 residues, 1 model selected
> volume zone #4 nearAtoms sel & #2 range 2.0
> select :ACP, Mg
52 atoms, 50 bonds, 5 residues, 1 model selected
> select :1-910
7198 atoms, 7288 bonds, 928 residues, 1 model selected
> hide sel atoms
> select :ACP, Mg
52 atoms, 50 bonds, 5 residues, 1 model selected
> show sel atoms
> select /B:1@MG
1 atom, 1 residue, 1 model selected
> select /B:1@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:2@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:3@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
Drag select of 49 atoms, 50 bonds
> select sel :< 3
319 atoms, 311 bonds, 19 residues, 1 model selected
> show sel atoms
> volume zone #4 nearAtoms sel & #2 range 2.0
> show #!4 models
> volume #4 level 0.111
> volume #4 level 0.08
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/AMPPCP_Mg_7.png
> width 3000 height 1960 supersample 3 transparentBackground true
> sel: 1-910
Unknown command: sel: 1-910
> show atoms
> hide atoms
> sel: 675-716
Unknown command: sel: 675-716
> show atoms
> sel: 675-716
Unknown command: sel: 675-716
> hide atoms
> sel: 675-716
Unknown command: sel: 675-716
> select :675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> show sel atoms
> volume zone #4 nearAtoms sel & #2 range 2.0
> show #!1 models
> hide #!1 models
> select :675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> hide sel atoms
> select :ACP, Mg
52 atoms, 50 bonds, 5 residues, 1 model selected
> show sel atoms
> select /B:3@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:1@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:2@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select sel :< 3
9 atoms, 7 bonds, 2 residues, 1 model selected
> show sel atoms
> undo
Drag select of 49 atoms, 50 bonds
> select sel :< 3
319 atoms, 311 bonds, 19 residues, 1 model selected
> show sel atoms
> volume zone #4 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/AMPPCP_4.png width
> 3000 height 1960 supersample 3 transparentBackground true
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/AMPPCP_Mg_2.cxs
> includeMaps true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 641, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
^^^^^^^^^^^^^^^^
File "msgpack/_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
MemoryError
MemoryError
File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\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\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\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\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\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\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\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\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\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 641, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
^^^^^^^^^^^^^^^^
File "msgpack/_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
MemoryError
MemoryError
File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/AMPPCP_Mg_2.cxs
> includeMaps true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 641, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
^^^^^^^^^^^^^^^^
File "msgpack/_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack
MemoryError
MemoryError
File "msgpack/_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\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\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\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\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\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\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\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\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\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 641, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
^^^^^^^^^^^^^^^^
File "msgpack/_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack
MemoryError
MemoryError
File "msgpack/_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 581.04
OpenGL renderer: NVIDIA GeForce RTX 3060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: en_CA.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: XPS 8950
OS: Microsoft Windows 11 Home (Build 26200)
Memory: 16,890,650,624
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.3
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.7
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.2.1
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
comtypes: 1.1.14
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pywin32: 305
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
WMI: 1.5.1
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