Histogram widget: operands could not be broadcast together with shapes

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/afzalib/Library/CloudStorage/Box-Box/Manuscripts under
> preparation/Kidneys and C3/Figures/Some individual panels/CFB structure
> predictions/ChimeraX_human/Human_CFB_WT_alaALA_session_8-8-2023_2.cxs"

Log from Tue Aug 8 14:12:13 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/afzalib/Library/CloudStorage/Box-Box/Manuscripts under
> preparation/Kidneys and C3/Figures/Some individual panels/CFB structure
> predictions/ChimeraX_human/Human_CFB_WT_alaALA_session_8-8-2023.cxs"

Log from Tue Aug 8 12:53:06 2023You can double click a model's Name or ID in
the model panel to edit those fields  
UCSF ChimeraX version: 1.6rc202304070153 (2023-04-07)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Volumes/data/alphafold2/c3/c3_preprotein/ranked_0.pdb format pdb

No such file/path: /Volumes/data/alphafold2/c3/c3_preprotein/ranked_0.pdb  

> open /Volumes/data/alphafold2/c3/c3shortseq_withMet/ranked_0.pdb format pdb

No such file/path: /Volumes/data/alphafold2/c3/c3shortseq_withMet/ranked_0.pdb  

> open /Users/chaussdc/Desktop/ranked_0.pdb

Chain information for ranked_0.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select all

12635 atoms, 12768 bonds, 839 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select add #1

12635 atoms, 12768 bonds, 839 residues, 1 model selected  

> show sel atoms

> select subtract #1

Nothing selected  

> close session

> open "/Users/chaussdc/Desktop/untitled
> folder/Renamed/alaMUT.CFB.human.4_unrelaxed_rank_1_model_4.pdb"
> "/Users/chaussdc/Desktop/untitled
> folder/Renamed/WT.CFB.human.0_unrelaxed_rank_1_model_4.pdb"

Chain information for alaMUT.CFB.human.4_unrelaxed_rank_1_model_4.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for WT.CFB.human.0_unrelaxed_rank_1_model_4.pdb #2  
---  
Chain | Description  
A | No description available  
  

> ui mousemode right "translate selected models"

> select add #1

5982 atoms, 6117 bonds, 764 residues, 1 model selected  

> view matrix models #1,1,0,0,-81.496,0,1,0,17.628,0,0,1,39.832

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.75323,0.2106,-0.62313,-73.481,0.24221,-0.96959,-0.034908,-9.7148,-0.61153,-0.12464,-0.78134,52.55

> select subtract #1

Nothing selected  

> select add #2

6009 atoms, 6147 bonds, 764 residues, 1 model selected  

> view matrix models
> #2,-0.41539,-0.33137,0.84714,5.107,0.90158,-0.27368,0.33503,-15.765,0.12083,0.90294,0.41244,6.9349

> view matrix models
> #2,-0.43452,-0.17738,0.88302,6.0986,0.8982,-0.1577,0.41032,-15.267,0.066474,0.97143,0.22785,8.4089

> select 2:503,507,510,512,526,696,697,699,701,719,720

Expected an objects specifier or a keyword  

> select #2:503,507,510,512,526,696,697,699,701,719,720

82 atoms, 76 bonds, 11 residues, 1 model selected  

> select #2:503,507,510,512,526,696,697,699,701,719,720

82 atoms, 76 bonds, 11 residues, 1 model selected  

> select #2:503,507,510,512,526,696,697,699,701,719,720

82 atoms, 76 bonds, 11 residues, 1 model selected  

> color #2:503,507,510,512,526,696,697,699,701,719,720 red

> save "/Users/chaussdc/Desktop/untitled
> folder/Renamed/human_cfb_allala_withWT_session.cxs"

> save
> /Users/chaussdc/Desktop/PDBfiles_chimeraSession/Human_CFB_WT_alaALA_session_8-8-2023.cxs

——— End of log from Tue Aug 8 12:53:06 2023 ———

opened ChimeraX session  

> set bgColor white

> show sel surfaces

> hide sel surfaces

> show sel atoms

> ui mousemode right select

Drag select of 1528 residues, 45 atoms, 41 bonds  

> color sel bypolymer

[Repeated 1 time(s)]

> color sel bychain

[Repeated 1 time(s)]

> style sel sphere

Changed 11991 atom styles  

> style sel ball

Changed 11991 atom styles  

> style sel sphere

Changed 11991 atom styles  

> style sel ball

Changed 11991 atom styles  

> style sel stick

Changed 11991 atom styles  

> color sel bychain

> color sel byhetero

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
[Repeated 1 time(s)]Coulombic values for
alaMUT.CFB.human.4_unrelaxed_rank_1_model_4.pdb_A SES surface #1.1: minimum,
-22.77, mean -1.88, maximum 14.57  
Coulombic values for WT.CFB.human.0_unrelaxed_rank_1_model_4.pdb_A SES surface
#2.1: minimum, -26.03, mean -1.64, maximum 16.16  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp sel

Map values for surface "alaMUT.CFB.human.4_unrelaxed_rank_1_model_4.pdb_A SES
surface": minimum -27.96, mean -5.501, maximum 26.59  
Map values for surface "WT.CFB.human.0_unrelaxed_rank_1_model_4.pdb_A SES
surface": minimum -28.43, mean -5.695, maximum 25.25  
To also show corresponding color key, enter the above mlp command and add key
true  

> select add #1

11991 atoms, 6158 bonds, 1528 residues, 4 models selected  

> select clear

> select add #1

5982 atoms, 6117 bonds, 764 residues, 1 model selected  

> select add #2

11991 atoms, 12264 bonds, 1528 residues, 3 models selected  

> coulombic sel

Coulombic values for alaMUT.CFB.human.4_unrelaxed_rank_1_model_4.pdb_A SES
surface #1.1: minimum, -22.77, mean -1.88, maximum 14.57  
Coulombic values for WT.CFB.human.0_unrelaxed_rank_1_model_4.pdb_A SES surface
#2.1: minimum, -26.03, mean -1.64, maximum 16.16  
To also show corresponding color key, enter the above coulombic command and
add key true  
Drag select of WT.CFB.human.0_unrelaxed_rank_1_model_4.pdb_A SES surface, 961
of 719278 triangles, 1 residues  
Alignment identifier is 2/A  

> select #2/A:484

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/A:484-490

61 atoms, 62 bonds, 7 residues, 1 model selected  

> select clear

> select #2/A:503

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/A:503

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/A:503,507

15 atoms, 13 bonds, 2 residues, 1 model selected  

> select #2/A:503,507,510

21 atoms, 18 bonds, 3 residues, 1 model selected  

> select #2/A:503,507,510,512

29 atoms, 25 bonds, 4 residues, 1 model selected  

> select #2/A:503,507,510,512,526

39 atoms, 35 bonds, 5 residues, 1 model selected  

> select #2/A:503,507,510,512,526,696

50 atoms, 45 bonds, 6 residues, 1 model selected  

> select #2/A:503,507,510,512,526,696-697

54 atoms, 49 bonds, 7 residues, 1 model selected  

> select #2/A:503,507,510,512,526,696-697,699

60 atoms, 54 bonds, 8 residues, 1 model selected  

> select #2/A:503,507,510,512,526,696-697,699,701

64 atoms, 57 bonds, 9 residues, 1 model selected  

> select #2/A:503,507,510,512,526,696-697,699,701,719

78 atoms, 72 bonds, 10 residues, 1 model selected  

> select #2/A:503,507,510,512,526,696-697,699,701,719-720

82 atoms, 76 bonds, 11 residues, 1 model selected  

> color (#!2 & sel) red

> color (#!2 & sel) white

> undo

[Repeated 1 time(s)]

> select clear

Drag select of WT.CFB.human.0_unrelaxed_rank_1_model_4.pdb_A SES surface, 62
of 719278 triangles  

> select #2/A:503,507,510,512,526,696-697,699,701,719-720

82 atoms, 76 bonds, 11 residues, 1 model selected  

> select #1/A:503,507,510,512,526,696-697,699,701,719-720

55 atoms, 46 bonds, 11 residues, 1 model selected  

> mlp sel

Map values for surface "alaMUT.CFB.human.4_unrelaxed_rank_1_model_4.pdb_A SES
surface": minimum -27.96, mean -5.501, maximum 26.59  
To also show corresponding color key, enter the above mlp command and add key
true  

> undo

[Repeated 3 time(s)]Drag select of
alaMUT.CFB.human.4_unrelaxed_rank_1_model_4.pdb_A SES surface, 7915 of 719624
triangles, 764 residues  

> color sel bypolymer

> color sel bychain

[Repeated 1 time(s)]

> mlp sel

Map values for surface "alaMUT.CFB.human.4_unrelaxed_rank_1_model_4.pdb_A SES
surface": minimum -27.96, mean -5.501, maximum 26.59  
To also show corresponding color key, enter the above mlp command and add key
true  
Drag select of alaMUT.CFB.human.4_unrelaxed_rank_1_model_4.pdb_A SES surface,
223 of 719624 triangles, WT.CFB.human.0_unrelaxed_rank_1_model_4.pdb_A SES
surface, 45 atoms, 764 residues, 41 bonds  

> mlp sel

Map values for surface "WT.CFB.human.0_unrelaxed_rank_1_model_4.pdb_A SES
surface": minimum -28.43, mean -5.695, maximum 25.25  
To also show corresponding color key, enter the above mlp command and add key
true  

> select #1/A:503,507,510,512,526,696-697,699,701,719-720

55 atoms, 46 bonds, 11 residues, 1 model selected  

> select #1/A:503,507,510,512,526,696-697,699,701,719-720
> #2/A:503,507,510,512,526,696-697,699,701,719-720

137 atoms, 122 bonds, 22 residues, 2 models selected  
Drag select of WT.CFB.human.0_unrelaxed_rank_1_model_4.pdb_A SES surface, 53
of 719278 triangles  

> select #1/A:503,507,510,512,526,696-697,699,701,719-720
> #2/A:503,507,510,512,526,696-697,699,701,719-720

137 atoms, 122 bonds, 22 residues, 2 models selected  

> select clear

Drag select of alaMUT.CFB.human.4_unrelaxed_rank_1_model_4.pdb_A SES surface,
106 of 719624 triangles, WT.CFB.human.0_unrelaxed_rank_1_model_4.pdb_A SES
surface, 45 atoms, 764 residues, 41 bonds  

> ui mousemode right "move picked models"

> view matrix models
> #2,-0.43452,-0.17738,0.88302,-81.536,0.8982,-0.1577,0.41032,4.8016,0.066474,0.97143,0.22785,44.287

> view matrix models
> #2,-0.43452,-0.17738,0.88302,-79.13,0.8982,-0.1577,0.41032,-10.496,0.066474,0.97143,0.22785,46.767

> view matrix models
> #2,-0.43452,-0.17738,0.88302,-84.058,0.8982,-0.1577,0.41032,-15.443,0.066474,0.97143,0.22785,47.809

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.3746,-0.15969,0.91333,-84.541,0.91551,-0.21951,0.33711,-15.173,0.14666,0.96245,0.22842,47.355,#1.1,0.99998,-0.0014491,-0.0059418,0.047316,0.00083737,0.99482,-0.1017,0.78672,0.0060584,0.10169,0.9948,0.34108

> view matrix models
> #2,-0.40254,-0.29955,0.86501,-84.515,0.9146,-0.091919,0.39378,-15.15,-0.038446,0.94964,0.31096,47.633,#1.1,0.99144,-0.07274,0.10844,-1.0737,0.067059,0.99622,0.05515,-0.48971,-0.11204,-0.047406,0.99257,-0.047821

> view matrix models
> #2,0.81941,-0.44166,0.36538,-97.04,-0.15507,-0.78446,-0.60048,4.7466,0.55183,0.43538,-0.71128,48.617,#1.1,0.92085,-0.36643,0.1333,-5.8566,-0.040433,-0.42976,-0.90204,-7.6032,0.38782,0.82525,-0.41056,20.828

> view matrix models
> #2,0.76844,-0.52103,0.3715,-96.672,-0.22027,-0.76044,-0.61091,5.8633,0.60081,0.38762,-0.69913,47.876,#1.1,0.94912,-0.28334,0.13742,-5.0423,-0.015151,-0.47697,-0.87879,-8.412,0.31454,0.832,-0.457,21.127

> undo

[Repeated 8 time(s)]

> ui mousemode right select

Drag select of WT.CFB.human.0_unrelaxed_rank_1_model_4.pdb_A SES surface,
653044 of 719278 triangles, 45 atoms, 731 residues, 41 bonds  

> ui mousemode right "move picked models"

> view matrix models
> #2,-0.43452,-0.17738,0.88302,-69.096,0.8982,-0.1577,0.41032,10.283,0.066474,0.97143,0.22785,39.357

> view matrix models
> #2,-0.43452,-0.17738,0.88302,-28.197,0.8982,-0.1577,0.41032,-41.911,0.066474,0.97143,0.22785,-18.423

> view matrix models
> #2,-0.43452,-0.17738,0.88302,-73.564,0.8982,-0.1577,0.41032,30.725,0.066474,0.97143,0.22785,70.023

> view matrix models
> #2,-0.43452,-0.17738,0.88302,-82.797,0.8982,-0.1577,0.41032,49.445,0.066474,0.97143,0.22785,95.663

> ui mousemode right select

Drag select of alaMUT.CFB.human.4_unrelaxed_rank_1_model_4.pdb_A SES surface,
718989 of 719624 triangles, WT.CFB.human.0_unrelaxed_rank_1_model_4.pdb_A SES
surface, 1528 residues, 45 atoms, 41 bonds  

> select clear

Drag select of alaMUT.CFB.human.4_unrelaxed_rank_1_model_4.pdb_A SES surface,
396 of 719624 triangles, 1 residues  

> ui mousemode right select

Drag select of alaMUT.CFB.human.4_unrelaxed_rank_1_model_4.pdb_A SES surface,
717226 of 719624 triangles, 764 residues  
Drag select of alaMUT.CFB.human.4_unrelaxed_rank_1_model_4.pdb_A SES surface,
190 of 719624 triangles, 7 residues  
Drag select of alaMUT.CFB.human.4_unrelaxed_rank_1_model_4.pdb_A SES surface,
718825 of 719624 triangles, 764 residues  

> ui mousemode right "move picked models"

> view matrix models
> #1,0.75323,0.2106,-0.62313,-72.736,0.24221,-0.96959,-0.034908,-30.693,-0.61153,-0.12464,-0.78134,35.826

> view matrix models
> #1,0.75323,0.2106,-0.62313,-72.967,0.24221,-0.96959,-0.034908,-31.8,-0.61153,-0.12464,-0.78134,36.853

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.77427,0.18864,-0.60409,-73.466,0.22431,-0.97437,-0.016761,-31.956,-0.59177,-0.12253,-0.79674,36.947

> view matrix models
> #1,0.77285,0.16012,-0.61405,-73.756,0.10356,-0.9865,-0.12689,-30.89,-0.62607,0.034476,-0.779,38.959

> color sel bychain

> view matrix models
> #1,0.57772,0.3951,-0.71424,-69.322,0.52502,0.49013,0.69579,-19.333,0.62498,-0.77696,0.07572,17.933

> undo

> ui mousemode right select

Drag select of WT.CFB.human.0_unrelaxed_rank_1_model_4.pdb_A SES surface, 45
atoms, 764 residues, 41 bonds  

> transparency sel 50

> color sel bychain

> color #1 #0096ffff

> color #1 #00fdffff

> color #1 #0096ffff

> color #1 darkgrey

> select #1/A:503,507,510,512,526,696-697,699,701,719-720
> #2/A:503,507,510,512,526,696-697,699,701,719-720

137 atoms, 122 bonds, 22 residues, 2 models selected  

> color (#!1-2 & sel) red

> select clear

Drag select of alaMUT.CFB.human.4_unrelaxed_rank_1_model_4.pdb_A SES surface,
719415 of 719624 triangles, 764 residues  

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.77285,0.16012,-0.61405,-72.502,0.10356,-0.9865,-0.12689,-33.785,-0.62607,0.034476,-0.779,47.598

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.77293,0.15828,-0.61444,-72.523,0.11049,-0.98717,-0.1153,-33.906,-0.6248,0.021231,-0.7805,47.433

> view matrix models
> #1,0.77275,0.16395,-0.61317,-72.459,0.089068,-0.98451,-0.151,-33.525,-0.62843,0.06207,-0.77538,47.937

> view matrix models
> #1,0.79625,0.1605,-0.58329,-72.81,0.083271,-0.98406,-0.15711,-33.453,-0.59921,0.076526,-0.79693,48.215

> view matrix models
> #1,0.81293,0.29912,-0.49967,-71.71,0.41742,-0.89758,0.14179,-35.663,-0.40608,-0.32384,-0.85453,42.881

> view matrix models
> #1,0.82466,0.24885,-0.50795,-72.336,0.34486,-0.93301,0.10279,-35.608,-0.44834,-0.25994,-0.85523,43.844

> ui mousemode right "next docked"

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.82466,0.24885,-0.50795,-80.684,0.34486,-0.93301,0.10279,44.387,-0.44834,-0.25994,-0.85523,89.738

> view matrix models
> #1,0.82466,0.24885,-0.50795,-80.416,0.34486,-0.93301,0.10279,43.492,-0.44834,-0.25994,-0.85523,88.93

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.84211,0.11732,-0.52639,-82.041,0.29539,-0.91696,0.2682,42.522,-0.45121,-0.38134,-0.80684,86.962

> view matrix models
> #1,0.87152,0.055794,-0.48717,-83.244,0.25763,-0.89744,0.3581,42.167,-0.41723,-0.4376,-0.79651,86.046

> view matrix models
> #1,0.85502,0.45619,-0.24665,-79.875,0.4816,-0.87489,0.051336,44.273,-0.19237,-0.16268,-0.96774,90.371

> view matrix models
> #1,0.68235,-0.0032124,-0.73101,-81.528,-0.29754,-0.91463,-0.27372,48.575,-0.66773,0.40428,-0.62506,96.415

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.68235,-0.0032124,-0.73101,-85.401,-0.29754,-0.91463,-0.27372,67.333,-0.66773,0.40428,-0.62506,120.19

> view matrix models
> #1,0.68235,-0.0032124,-0.73101,-80.664,-0.29754,-0.91463,-0.27372,45.793,-0.66773,0.40428,-0.62506,101.08

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.68591,-0.087033,-0.72246,-81.84,-0.33674,-0.91808,-0.20911,45.344,-0.64508,0.38671,-0.65903,101.05

> view matrix models
> #1,0.69266,-0.16281,-0.70264,-83.01,-0.3752,-0.91334,-0.15824,45.109,-0.61599,0.37324,-0.69372,101.07

> view matrix models
> #1,0.86216,-0.19096,-0.46927,-85.727,-0.35161,-0.8924,-0.28284,46.311,-0.36476,0.40885,-0.83653,101.96

> view matrix models
> #1,0.90782,0.41838,0.028637,-81.857,0.4185,-0.90822,0.0020975,41.628,0.026886,0.01008,-0.99959,96.923

> view matrix models
> #1,0.9458,0.23213,-0.22709,-82.361,0.22179,-0.97255,-0.070433,41.927,-0.2372,0.016252,-0.97132,97.533

> view matrix models
> #1,0.70237,0.034286,-0.71098,-80.391,0.063471,-0.99788,0.014581,41.369,-0.70897,-0.055368,-0.70306,95.8

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.70237,0.034286,-0.71098,-82.037,0.063471,-0.99788,0.014581,46.51,-0.70897,-0.055368,-0.70306,98.129

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.72992,-0.042871,-0.68219,-83.356,0.046278,-0.99264,0.1119,45.85,-0.68197,-0.11325,-0.72256,97.45

> view matrix models
> #1,0.72851,-0.077554,-0.68063,-83.819,0.034302,-0.98819,0.14931,45.644,-0.68418,-0.13212,-0.71725,97.166

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.72851,-0.077554,-0.68063,-63.363,0.034302,-0.98819,0.14931,-2.3037,-0.68418,-0.13212,-0.71725,43.034

> view matrix models
> #1,0.72851,-0.077554,-0.68063,-62.379,0.034302,-0.98819,0.14931,-5.5619,-0.68418,-0.13212,-0.71725,39.17

> view matrix models
> #1,0.72851,-0.077554,-0.68063,-62.423,0.034302,-0.98819,0.14931,-5.5655,-0.68418,-0.13212,-0.71725,39.074

> view matrix models
> #1,0.72851,-0.077554,-0.68063,-63.71,0.034302,-0.98819,0.14931,-9.4905,-0.68418,-0.13212,-0.71725,41.469

> view matrix models
> #1,0.72851,-0.077554,-0.68063,-77.616,0.034302,-0.98819,0.14931,-7.267,-0.68418,-0.13212,-0.71725,40.052

> view matrix models
> #1,0.72851,-0.077554,-0.68063,-76.615,0.034302,-0.98819,0.14931,-8.3675,-0.68418,-0.13212,-0.71725,41.187

> view matrix models
> #1,0.72851,-0.077554,-0.68063,-76.925,0.034302,-0.98819,0.14931,-8.0831,-0.68418,-0.13212,-0.71725,41.361

> ui mousemode right tug

Missing atoms or parameterization needed by force field.  
All heavy atoms and hydrogens with standard names are required.  
  
Error with ignoreExternalBonds=False was  
No template found for residue 1 (MET). The set of atoms is similar to MET, but
it is missing 9 hydrogen atoms. For more information, see
https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template  
Error with ignoreExternalBonds=True was  
No template found for residue 1 (MET). The set of atoms is similar to MET, but
it is missing 9 hydrogen atoms. For more information, see
https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template  

[Repeated 1 time(s)]

> ui mousemode right minimize

> ui mousemode right "next docked"

> Matchmaker

Unknown command: Matchmaker  

> matchmaker

Missing or invalid "matchAtoms" argument: empty atom specifier  

> select add #2

11991 atoms, 6147 bonds, 1528 residues, 3 models selected  

> select add #1

11991 atoms, 12264 bonds, 1528 residues, 4 models selected  

> matchmaker

Missing or invalid "matchAtoms" argument: empty atom specifier  

> matchmaker

Missing or invalid "matchAtoms" argument: empty atom specifier  

> matchmaker #1 #2

Missing required "to" argument  

> matchmaker #1 #2

Missing required "to" argument  

> matchmaker #1 to #2

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 WT.CFB.human.0_unrelaxed_rank_1_model_4.pdb, chain A (#2) with
alaMUT.CFB.human.4_unrelaxed_rank_1_model_4.pdb, chain A (#1), sequence
alignment score = 3907.7  
RMSD between 702 pruned atom pairs is 0.581 angstroms; (across all 764 pairs:
2.835)  
  

> select #1/A:503,507,510,512,526,696-697,699,701,719-720

55 atoms, 46 bonds, 11 residues, 1 model selected  

> color (#!1 & sel) black

> ui mousemode right select

> select clear

> select add #1

5982 atoms, 6117 bonds, 764 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.76178,-0.1554,-0.62893,-86.701,0.031667,-0.96071,0.27574,-17.785,-0.64707,-0.22997,-0.72692,47.388

> ui mousemode right select

Drag select of alaMUT.CFB.human.4_unrelaxed_rank_1_model_4.pdb_A SES surface,
WT.CFB.human.0_unrelaxed_rank_1_model_4.pdb_A SES surface, 1528 residues, 45
atoms, 41 bonds  

> hide sel surfaces

> select add #1

11991 atoms, 6158 bonds, 1528 residues, 4 models selected  

> select add #2

11991 atoms, 12264 bonds, 1528 residues, 4 models selected  

> select subtract #2

5982 atoms, 6117 bonds, 764 residues, 3 models selected  
Drag select of 8 residues  

> select add #1

5982 atoms, 6117 bonds, 764 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.76178,-0.1554,-0.62893,-86.03,0.031667,-0.96071,0.27574,-7.7369,-0.64707,-0.22997,-0.72692,54.566

> select #1/A:503,507,510,512,526,696-697,699,701,719-720

55 atoms, 46 bonds, 11 residues, 1 model selected  

> show sel atoms

> ui mousemode right select

> select clear

> select #1/A:503,507,510,512,526,696-697,699,701,719-720

55 atoms, 46 bonds, 11 residues, 1 model selected  

> color (#!1 & sel) red

> select clear

[Repeated 1 time(s)]

> select add #1

5982 atoms, 6117 bonds, 764 residues, 1 model selected  

> color (#!1 & sel) byhetero

> color (#!1 & sel) blue

> color (#!1 & sel) #c0c0c0ff

> color (#!1 & sel) #0096ffff

> select clear

> select add #1

5982 atoms, 6117 bonds, 764 residues, 1 model selected  

> color (#!1 & sel) #76d6ffff

> color (#!1 & sel) #0096ffff

> color (#!1 & sel) #0433ffff

> color (#!1 & sel) #9437ffff

> color (#!1 & sel) #0096ffff

> select #1/A:503,507,510,512,526,696-697,699,701,719-720

55 atoms, 46 bonds, 11 residues, 1 model selected  

> color (#!1 & sel) orange

> select clear

> lighting shadows true

> lighting full

> view

> ui tool show "Side View"

> select clear

> select add #1

5982 atoms, 6117 bonds, 764 residues, 1 model selected  

> select add #2

11991 atoms, 12264 bonds, 1528 residues, 3 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.76178,-0.1554,-0.62893,-80.351,0.031667,-0.96071,0.27574,2.8413,-0.64707,-0.22997,-0.72692,47.68,#2,-0.43452,-0.17738,0.88302,-77.118,0.8982,-0.1577,0.41032,60.023,0.066474,0.97143,0.22785,88.777

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.4152,-0.2462,-0.87578,-86.448,-0.76861,-0.60993,-0.19293,14.397,-0.48666,0.75324,-0.44248,93.549,#2,-0.35781,0.25057,0.89955,-65.603,0.66889,0.74096,0.059667,74.243,-0.65158,0.62304,-0.43273,62.676

> view matrix models
> #1,0.38586,-0.4871,-0.78348,-96.733,-0.84917,-0.51946,-0.095247,16.608,-0.3606,0.70206,-0.61407,93.743,#2,-0.10876,0.22491,0.96829,-61.091,0.66955,0.73655,-0.095878,70.805,-0.73476,0.63789,-0.2307,66.146

> view matrix models
> #1,0.77592,-0.34891,-0.52556,-89.602,-0.0019027,-0.83441,0.55114,8.8837,-0.63083,-0.42664,-0.64809,49.818,#2,-0.23368,-0.24563,0.94078,-75.795,0.93758,-0.31323,0.15111,54.174,0.25756,0.91736,0.30349,102.04

> view matrix models
> #1,0.72725,-0.40811,-0.55187,-91.926,-0.15078,-0.87938,0.45161,6.83,-0.66961,-0.24522,-0.70106,56.457,#2,-0.18131,-0.18881,0.96513,-72.767,0.97845,-0.13328,0.15773,59.968,0.098852,0.97293,0.2089,98.629

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.72725,-0.40811,-0.55187,-87.007,-0.15078,-0.87938,0.45161,10.518,-0.66961,-0.24522,-0.70106,41.303,#2,-0.18131,-0.18881,0.96513,-67.849,0.97845,-0.13328,0.15773,63.656,0.098852,0.97293,0.2089,83.475

> ui mousemode right select

> select clear

> select add #1

5982 atoms, 6117 bonds, 764 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.72725,-0.40811,-0.55187,-83.604,-0.15078,-0.87938,0.45161,25.1,-0.66961,-0.24522,-0.70106,51.017

> select add #2

11991 atoms, 12264 bonds, 1528 residues, 3 models selected  

> view matrix models
> #1,0.72725,-0.40811,-0.55187,-85.878,-0.15078,-0.87938,0.45161,16.211,-0.66961,-0.24522,-0.70106,45.96,#2,-0.18131,-0.18881,0.96513,-70.123,0.97845,-0.13328,0.15773,54.767,0.098852,0.97293,0.2089,78.418

> ui mousemode right select

> select clear

> select #2/A:503,507,510,512,526,696-697,699,701,719-720

82 atoms, 76 bonds, 11 residues, 1 model selected  

> select add #1

6064 atoms, 6193 bonds, 775 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.68226,-0.44723,-0.57837,-86.645,-0.27235,-0.88961,0.36663,16.62,-0.67849,-0.092618,-0.72875,49.978,#2,-0.14657,-0.13558,0.97986,-67.906,0.98858,0.014847,0.14993,58.819,-0.034876,0.99065,0.13186,75.597

> select add #2

11991 atoms, 12264 bonds, 1528 residues, 4 models selected  

> select subtract #2

5982 atoms, 6117 bonds, 764 residues, 3 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.68226,-0.44723,-0.57837,-85.188,-0.27235,-0.88961,0.36663,17.755,-0.67849,-0.092618,-0.72875,45.559

> view matrix models
> #1,0.68226,-0.44723,-0.57837,-85.187,-0.27235,-0.88961,0.36663,17.768,-0.67849,-0.092618,-0.72875,45.576

> ui mousemode right select

> select clear

> select add #2

6009 atoms, 6147 bonds, 764 residues, 1 model selected  

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> ~label (#!2 & sel) residues

> select #2/A:503,507,510,512,526,696-697,699,701,719-720

82 atoms, 76 bonds, 11 residues, 1 model selected  

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> ui mousemode right label

> label #2/A:631

> ~label (#!2 & sel) residues

> ui mousemode right label

> ui mousemode right select

> select add #2

6009 atoms, 6147 bonds, 764 residues, 3 models selected  

> ~label (#!2 & sel) residues

> select #2/A:503,507,510,512,526,696-697,699,701,719-720

82 atoms, 76 bonds, 11 residues, 1 model selected  

> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> label height 3

> select #2/A:503,507,510,512,526,696-697,699,701,719-720 lebel height 2

Expected a keyword  

> select #2/A:503,507,510,512,526,696-697,699,701,719-720 label height 2

Expected a keyword  

> select #2/A:503,507,510,512,526,696-697,699,701,719-720

82 atoms, 76 bonds, 11 residues, 1 model selected  

> label height 2

> label height 1

> save "/Users/afzalib/Library/CloudStorage/Box-Box/Manuscripts under
> preparation/Kidneys and C3/Figures/Some individual panels/CFB structure
> predictions/ChimeraX_human/DNA binding sites WT and Mut.tif" width 1248
> height 849 supersample 3 transparentBackground true

> ~label (#!2 & sel) residues

> select clear

> save "/Users/afzalib/Library/CloudStorage/Box-Box/Manuscripts under
> preparation/Kidneys and C3/Figures/Some individual panels/CFB structure
> predictions/ChimeraX_human/DNA binding sites WT and Mut_no labels.tif" width
> 1248 height 849 supersample 3 transparentBackground true

> select add #1

5982 atoms, 6117 bonds, 764 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.68226,-0.44723,-0.57837,-87.981,-0.27235,-0.88961,0.36663,5.5711,-0.67849,-0.092618,-0.72875,37.223

> show sel surfaces

> select add #2

11991 atoms, 12264 bonds, 1528 residues, 3 models selected  

> select subtract #1

6009 atoms, 6147 bonds, 764 residues, 3 models selected  

> show sel surfaces

> view matrix models
> #2,-0.14657,-0.13558,0.97986,-65.726,0.98858,0.014847,0.14993,68.22,-0.034876,0.99065,0.13186,81.922

> ui mousemode right select

> select clear

> select add #1

5982 atoms, 6117 bonds, 764 residues, 2 models selected  

> select add #2

11991 atoms, 12264 bonds, 1528 residues, 5 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.68226,-0.44723,-0.57837,-91.674,-0.27235,-0.88961,0.36663,2.1922,-0.67849,-0.092618,-0.72875,43.909,#2,-0.14657,-0.13558,0.97986,-69.418,0.98858,0.014847,0.14993,64.841,-0.034876,0.99065,0.13186,88.608

> view matrix models
> #1,0.68226,-0.44723,-0.57837,-93.014,-0.27235,-0.88961,0.36663,-0.10444,-0.67849,-0.092618,-0.72875,42.313,#2,-0.14657,-0.13558,0.97986,-70.758,0.98858,0.014847,0.14993,62.544,-0.034876,0.99065,0.13186,87.012

> save "/Users/afzalib/Library/CloudStorage/Box-Box/Manuscripts under
> preparation/Kidneys and C3/Figures/Some individual panels/CFB structure
> predictions/ChimeraX_human/WT and Mut_front.tif" width 1248 height 849
> supersample 3 transparentBackground true

> view matrix models
> #1,0.68226,-0.44723,-0.57837,-99.662,-0.27235,-0.88961,0.36663,2.7236,-0.67849,-0.092618,-0.72875,41.554,#2,-0.14657,-0.13558,0.97986,-77.406,0.98858,0.014847,0.14993,65.372,-0.034876,0.99065,0.13186,86.252

> save "/Users/afzalib/Library/CloudStorage/Box-Box/Manuscripts under
> preparation/Kidneys and C3/Figures/Some individual panels/CFB structure
> predictions/ChimeraX_human/WT and Mut_top.tif" width 1248 height 849
> supersample 3 transparentBackground true

> view matrix models
> #1,0.68226,-0.44723,-0.57837,-101.21,-0.27235,-0.88961,0.36663,1.5447,-0.67849,-0.092618,-0.72875,44.635,#2,-0.14657,-0.13558,0.97986,-78.956,0.98858,0.014847,0.14993,64.193,-0.034876,0.99065,0.13186,89.333

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/afzalib/Desktop/movie1.mp4

Movie saved to /Users/afzalib/Desktop/movie1.mp4  
  

> save "/Users/afzalib/Library/CloudStorage/Box-Box/Manuscripts under
> preparation/Kidneys and C3/Figures/Some individual panels/CFB structure
> predictions/ChimeraX_human/Human_CFB_WT_alaALA_session_8-8-2023_2.cxs"

——— End of log from Tue Aug 8 14:12:13 2023 ———

opened ChimeraX session  

> hide sel surfaces

> select clear

> matchmaker #1 to #2 showAlignment true

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 WT.CFB.human.0_unrelaxed_rank_1_model_4.pdb, chain A (#2) with
alaMUT.CFB.human.4_unrelaxed_rank_1_model_4.pdb, chain A (#1), sequence
alignment score = 3907.7  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1:
alaMUT.CFB.human.4_unrelaxed_rank_1_model_4.pdb #1/A,
WT.CFB.human.0_unrelaxed_rank_1_model_4.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 702 pruned atom pairs is 0.581 angstroms; (across all 764 pairs:
2.835)  
  

> select clear

> ui tool show "Render By Attribute"

> color byattribute r:seq_rmsd #!1-2 target sabc palette
> 1,#0fc7cf:3,white:5,#9e205e

11991 atoms, 1528 residues, 2 surfaces, atom seq_rmsd range 0.0362 to 16.6  

> select clear

> key cyan-white-maroon :1 :3 :5 showTool true

> ui mousemode right "color key"

> key pos 0.69000,0.08000

> key pos 0.68000,0.08000

> key pos 0.67000,0.08000

> key pos 0.66000,0.08000

> select add #1

5982 atoms, 6117 bonds, 764 residues, 2 models selected  

> select add #2

11991 atoms, 12264 bonds, 1528 residues, 5 models selected  

> ui mousemode right select

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.68226,-0.44723,-0.57837,-97.77,-0.27235,-0.88961,0.36663,23.438,-0.67849,-0.092618,-0.72875,77.446,#2,-0.14657,-0.13558,0.97986,-96.858,0.98858,0.014847,0.14993,24.208,-0.034876,0.99065,0.13186,77.037

> select subtract #2

5982 atoms, 6117 bonds, 764 residues, 4 models selected  

> ui mousemode right select

> select clear

> hide #!2 models

> show #!2 models

> hide #!2 models

> key font "Myriad Pro"

> key size 0.24000,0.05000

> key size 0.23000,0.05000

> key size 0.22000,0.05000

> key size 0.21000,0.05000

> key size 0.20000,0.05000

> key size 0.19000,0.05000

> key size 0.18000,0.05000

> key size 0.17000,0.05000

> key size 0.16000,0.05000

> key size 0.15000,0.05000

> key size 0.15000,0.04000

> key size 0.15000,0.03000

> key size 0.15000,0.02000

> key borderColor default

> select add #1

5982 atoms, 6117 bonds, 764 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.68226,-0.44723,-0.57837,-92.73,-0.27235,-0.88961,0.36663,20.892,-0.67849,-0.092618,-0.72875,85.021

> select subtract #1

1 model selected  

> color byattribute r:seq_rmsd #!1-2 target sabc palette
> 1,#0fc7cf:3,white:16.6231,#9e205e

11991 atoms, 1528 residues, 2 surfaces, atom seq_rmsd range 4.68 to 24.1  

> color byattribute r:seq_rmsd #!1-2 target sabc palette
> 1,#0fc7cf:3,white:5,#9e205e

11991 atoms, 1528 residues, 2 surfaces, atom seq_rmsd range 4.68 to 24.1  

> show #!2 models

> select add #1

5982 atoms, 6117 bonds, 764 residues, 2 models selected  

> select add #2

11991 atoms, 12264 bonds, 1528 residues, 4 models selected  

> color byattribute r:seq_rmsd #!1-2 target sabc palette
> 1,#0fc7cf:3,white:5,#9e205e

11991 atoms, 1528 residues, 2 surfaces, atom seq_rmsd range 4.68 to 24.1  

> color byattribute r:seq_rmsd #!1-2 target sabc palette
> 1,#0fc7cf:3,white:5,#9e205e

11991 atoms, 1528 residues, 2 surfaces, atom seq_rmsd range 4.68 to 24.1  

> color byattribute r:seq_rmsd #!1-2 target sabc palette
> 1,#0fc7cf:3,white:5,#9e205e

11991 atoms, 1528 residues, 2 surfaces, atom seq_rmsd range 4.68 to 24.1  

> ui mousemode right select

> select clear

> select add #1

5982 atoms, 6117 bonds, 764 residues, 2 models selected  

> select subtract #1.1

1 model selected  

> select add #1

5982 atoms, 6117 bonds, 764 residues, 2 models selected  

> ui tool show "Render By Attribute"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 756, in _set_value_cb  
self._redraw_cb()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 646, in _redraw_cb  
self._bins = left + filled_bins + right  
ValueError: operands could not be broadcast together with shapes (48,) (253,)  
  
ValueError: operands could not be broadcast together with shapes (48,) (253,)  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 646, in _redraw_cb  
self._bins = left + filled_bins + right  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 179, in <lambda>  
if event.modifiers() & mod_key_info("shift")[0] else
self._select_marker_cb(event)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 714, in _select_marker_cb  
self._set_sel_marker(marker, drag_start=event)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 743, in _set_sel_marker  
self._last_mouse_xy = self._abs_xy((drag_start.scenePos().x(),
drag_start.scenePos().y()))  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 179, in <lambda>  
if event.modifiers() & mod_key_info("shift")[0] else
self._select_marker_cb(event)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 714, in _select_marker_cb  
self._set_sel_marker(marker, drag_start=event)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 743, in _set_sel_marker  
self._last_mouse_xy = self._abs_xy((drag_start.scenePos().x(),
drag_start.scenePos().y()))  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.12.7
OpenGL renderer: AMD Radeon Pro Vega 56 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac Pro
      Model Identifier: iMacPro1,1
      Processor Name: 8-Core Intel Xeon W
      Processor Speed: 3.2 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 1 MB
      L3 Cache: 11 MB
      Hyper-Threading Technology: Enabled
      Memory: 128 GB
      System Firmware Version: 1968.120.12.0.0 (iBridge: 20.16.5060.0.0,0)
      OS Loader Version: 577~170

Software:

    System Software Overview:

      System Version: macOS 13.4.1 (22F82)
      Kernel Version: Darwin 22.5.0
      Time since boot: 6 days, 2 hours, 14 minutes

Graphics/Displays:

    Radeon Pro Vega 56:

      Chipset Model: Radeon Pro Vega 56
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x6867
      Revision ID: 0x0000
      ROM Revision: 113-D0500D-114
      VBIOS Version: 113-D05001A1XL-018
      Option ROM Version: 113-D05001A1XL-018
      EFI Driver Version: 01.01.114
      Metal Support: Metal 3
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        LG HDR 4K:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440 @ 30.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 202NTGY36703
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0