Needleman-Wunsch error

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-13.4-arm64-arm-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/dsouthworth/Desktop/AsymState1model_V1.cxs

Opened cryosparc_P48_J4278_005_volume_map_sharp.mrc as #3, grid size
360,360,360, pixel 0.834, shown at level 0.22, step 1, values float32  
Log from Mon Apr 7 16:35:01 2025 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/dsouthworth/Desktop/Southworth Lab/Results/CHIP+FabH1/ROSETTA
> Relax/FINAL/AsymmCHIP_State1/4277/OUTPUT/PHENIX/State1_FINAL_4277_real_space_refined_002.pdb"

Chain information for State1_FINAL_4277_real_space_refined_002.pdb #1  
---  
Chain | Description  
A E | No description available  
B F | No description available  
C | No description available  
D | No description available  
  

> style stick

Changed 15780 atom styles  

> show cartoons

> hide atoms

> open "/Users/dsouthworth/Desktop/Southworth Lab/Results/CHIP+FabH1/ROSETTA
> Relax/FINAL/State1_core_epitope/FINAL_FINAL/FINAL FINAL
> FINAL/H1_111224_6.pdb"

Chain information for H1_111224_6.pdb #2  
---  
Chain | Description  
C | No description available  
D | No description available  
E | No description available  
  

> open "/Users/dsouthworth/Desktop/Southworth Lab/Results/CHIP+FabH1/ROSETTA
> Relax/FINAL/State1_core_epitope/FINAL_FINAL/FINAL FINAL
> FINAL/cryosparc_P48_J4278_005_volume_map_sharp.mrc"

Opened cryosparc_P48_J4278_005_volume_map_sharp.mrc as #3, grid size
360,360,360, pixel 0.834, shown at level 0.0516, step 2, values float32  

> volume #3 step 1

> volume #3 level 0.2205

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> volume #3 color silver

> volume #3 color #c0c0c064

> volume #3 color #c0c0c088

> volume #3 color #009051

> volume #3 color #00905148

> surface dust #3 size 8.34

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #!3 models

> select #1/B

137 atoms, 136 bonds, 9 residues, 1 model selected  

> delete #1/B

> delete #1/F

> lighting shadows false

> select #1/A:23

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

> select #1/A:24

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/A:268

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

> select #1/E:268

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

> hide #2 models

> select #1/E:184

17 atoms, 17 bonds, 1 residue, 1 model selected  

> show #2 models

> hide #1 models

> select #2/E:268

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

> select add #2

4618 atoms, 4671 bonds, 308 residues, 1 model selected  

> select subtract #2

Nothing selected  

> show #1 models

> 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 H1_111224_6.pdb, chain D (#2) with
State1_FINAL_4277_real_space_refined_002.pdb, chain D (#1), sequence alignment
score = 573  
RMSD between 113 pruned atom pairs is 0.666 angstroms; (across all 121 pairs:
1.931)  
  

> open "/Users/dsouthworth/Desktop/Southworth Lab/Results/CHIP+FabH1/ROSETTA
> Relax/againfittingto_2117/2C2L_ABEF_oneH1.pdb"

Chain information for 2C2L_ABEF_oneH1.pdb #4  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
E F | No description available  
  

> style stick

Changed 31334 atom styles  

> show cartoons

> hide atoms

> hide #2 models

> color #4 #531b93ff

> matchmaker #4 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 State1_FINAL_4277_real_space_refined_002.pdb, chain A (#1) with
2C2L_ABEF_oneH1.pdb, chain A (#4), sequence alignment score = 1406.3  
RMSD between 246 pruned atom pairs is 1.080 angstroms; (across all 281 pairs:
1.620)  
  

> hide #4 models

> show #4 models

> close #4

> open /Users/dsouthworth/Downloads/2C2L_ABEF.pdb

Chain information for 2C2L_ABEF.pdb #4  
---  
Chain | Description  
A B | No description available  
E F | No description available  
  

> hide #4 models

> show #4 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> matchmaker #4 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 State1_FINAL_4277_real_space_refined_002.pdb, chain A (#1) with
2C2L_ABEF.pdb, chain A (#4), sequence alignment score = 1406.3  
RMSD between 246 pruned atom pairs is 1.080 angstroms; (across all 281 pairs:
1.620)  
  

> delete #4/F

> delete #4/E

> hide #1,4 atoms

> show #1,4 atoms

> hide H

> color #1 #ff40ffff

> show #2 models

> hide #4 models

> hide #1-2 atoms

> split #2

Split H1_111224_6.pdb (#2) into 3 models  
Chain information for H1_111224_6.pdb C #2.1  
---  
Chain | Description  
C | No description available  
  
Chain information for H1_111224_6.pdb D #2.2  
---  
Chain | Description  
D | No description available  
  
Chain information for H1_111224_6.pdb E #2.3  
---  
Chain | Description  
E | No description available  
  

> hide #2.3 models

> show #2.3 models

> open "/Users/dsouthworth/Desktop/Southworth Lab/Results/CHIP+FabH1/ROSETTA
> Relax/FINAL/State1_core_epitope/FINAL_FINAL/FINAL FINAL
> FINAL/H1_111224_6.pdb"

Chain information for H1_111224_6.pdb #5  
---  
Chain | Description  
C | No description available  
D | No description available  
E | No description available  
  

> close #2.2

> close #2.1

> hide #2.3 models

> hide #5 models

> show #2.3 models

> hide #!2 models

> show #!2 models

> matchmaker #2 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 State1_FINAL_4277_real_space_refined_002.pdb, chain A (#1) with
H1_111224_6.pdb E, chain E (#2.3), sequence alignment score = 381.5  
RMSD between 67 pruned atom pairs is 0.904 angstroms; (across all 77 pairs:
1.955)  
  

> hide #2.3 models

> show #2.3 models

> show #5 models

> hide #1 models

> hide #5 models

> show #5 models

> show #1 models

> select #1/A:227

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #2/A:227

Nothing selected  

> select #2/E:227

19 atoms, 18 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/A:227

19 atoms, 18 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide #2.3 models

> show #2.3 models

> hide sel atoms

> select add #1

15506 atoms, 15672 bonds, 1003 residues, 1 model selected  

> select subtract #1

Nothing selected  

> hide #1,5#2.3 atoms

> save /Users/dsouthworth/Desktop/FOrH1_models_040725.cxs includeMaps true

> select #1/A:227-500

1233 atoms, 1248 bonds, 77 residues, 1 model selected  

> combine #1

> hide #6 models

> hide #5 models

> show #5 models

> hide #5 models

> show #5 models

> select #1/A:227-500

1233 atoms, 1248 bonds, 77 residues, 1 model selected  

> delete sel

> hide #2.3 models

> show #2.3 models

> select #2/E:23-226

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

> delete sel

> combine #1,2

Remapping chain ID 'E' in H1_111224_6.pdb E #2.3 to 'F'  

> hide #1 models

> hide #!2 models

> hide #7 models

> show #7 models

> select #7/A:226@C

1 atom, 1 residue, 1 model selected  

> select #7/A:226@C #7/F:227@N

2 atoms, 2 residues, 1 model selected  

> ui tool show "Build Structure"

> bond sel reasonable false

Created 1 bond  

> select add #7

15484 atoms, 15649 bonds, 1002 residues, 1 model selected  

> select subtract #7

Nothing selected  

> select #7/E:227

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #5/E:227

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #5/E:228

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #7/E:228

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #5/E:22

Nothing selected  

> select #7/E:227

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #5/E:227

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #7/E:228

14 atoms, 14 bonds, 1 residue, 1 model selected  

> hide #5 models

> show #5 models

> select #7/E:228

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #7/E:226

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

> select #7/E:225

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #5/E:226

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

> select #5/E:227

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #7/E:226-400

1245 atoms, 1260 bonds, 78 residues, 1 model selected  

> combine #7

> hide #8 models

> select #7/E:226-400

1245 atoms, 1260 bonds, 78 residues, 1 model selected  

> delete sel

> select #7/E:226

Nothing selected  

> select #7/E:225

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #5/E:225

Nothing selected  

> select #5/E:226

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

> select #7/E:225@C #5/E:226@N

2 atoms, 2 residues, 2 models selected  

> combine #5,7

Remapping chain ID 'C' in combination #7 to 'F'  
Remapping chain ID 'D' in combination #7 to 'G'  
Remapping chain ID 'E' in combination #7 to 'H'  

> hide #7 models

> hide #5 models

> select add #5

4619 atoms, 4671 bonds, 309 residues, 2 models selected  

> select add #7

18857 atoms, 19059 bonds, 1232 residues, 2 models selected  

> select subtract #5

14239 atoms, 14388 bonds, 924 residues, 1 model selected  

> select subtract #7

Nothing selected  

> hide #9 models

> show #9 models

> select #9/E:225@C #9/E:226@N

1 atom, 1 residue, 1 model selected  

> select #9/H:225@C #9/E:226@N

2 atoms, 2 residues, 1 model selected  

> select #9/H:225@C #9/E:226@N

2 atoms, 2 residues, 1 model selected  

> ui tool show "Build Structure"

> bond sel reasonable false

Created 1 bond  

> select add #9

18857 atoms, 19060 bonds, 1232 residues, 1 model selected  

> select subtract #9

Nothing selected  

> color #9 bychain

> select #9/C

1583 atoms, 1600 bonds, 110 residues, 1 model selected  

> select #9/C:1-123

1534 atoms, 1551 bonds, 107 residues, 1 model selected  

> select #9/C:124-300

49 atoms, 48 bonds, 3 residues, 1 model selected  

> delete sel

> select #9/F:1-123

1534 atoms, 1552 bonds, 107 residues, 1 model selected  

> select add #9

18808 atoms, 19011 bonds, 1229 residues, 1 model selected  

> select subtract #9

Nothing selected  

> combine #9

> hide #10 models

> select #9/F:1-123

1534 atoms, 1552 bonds, 107 residues, 1 model selected  

> delete sel

> hide #9 models

> show #9 models

> show #10 models

> hide #9 models

> select #10/C:120

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #10/F:120

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #10/C:120-300

64 atoms, 63 bonds, 4 residues, 1 model selected  

> select #10/C:121-300

57 atoms, 56 bonds, 3 residues, 1 model selected  

> select #10/C:121-300

57 atoms, 56 bonds, 3 residues, 1 model selected  

> delete sel

> select #10/F:122-300

1655 atoms, 1676 bonds, 111 residues, 1 model selected  

> select #10/F:121-300

1669 atoms, 1690 bonds, 112 residues, 1 model selected  

> select #10/F:1-120

1477 atoms, 1495 bonds, 104 residues, 1 model selected  

> delete sel

> select #10/F:121@N

1 atom, 1 residue, 1 model selected  

> select #10/C:120@C #10/F:121@N

2 atoms, 2 residues, 1 model selected  

> ui tool show "Build Structure"

> bond sel reasonable false

Created 1 bond  

> select add #10

17274 atoms, 17459 bonds, 1122 residues, 1 model selected  

> select subtract #10

Nothing selected  

> select #10/G

3314 atoms, 3356 bonds, 225 residues, 1 model selected  

> select add #10

17274 atoms, 17459 bonds, 1122 residues, 1 model selected  

> select #10/D

1812 atoms, 1834 bonds, 121 residues, 1 model selected  

> select #10/D:120

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #10/G:120

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #10/G:121

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #10/D:121

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #10/D:1-120

1728 atoms, 1750 bonds, 115 residues, 1 model selected  

> select #10/D:121-300

84 atoms, 83 bonds, 6 residues, 1 model selected  

> delete sel

> select #10/G:1-120

1743 atoms, 1765 bonds, 116 residues, 1 model selected  

> delete sel

> select #10/D:120@C #10/G:121@N

2 atoms, 2 residues, 1 model selected  

> ui tool show "Build Structure"

> bond sel reasonable false

Created 1 bond  

> select add #10

15447 atoms, 15610 bonds, 1000 residues, 1 model selected  

> select subtract #10

Nothing selected  

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> save /Users/dsouthworth/Desktop/AsymState1model_V1.cxs includeMaps true

——— End of log from Mon Apr 7 16:35:01 2025 ———

opened ChimeraX session  

> open /Users/dsouthworth/Desktop/AsymState1model_V1.pdb

Chain information for AsymState1model_V1.pdb #11  
---  
Chain | Description  
A | No description available  
C | No description available  
D | No description available  
H | No description available  
  

> matchmaker #11 to #10

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/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 730, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 394, in match  
score, s1, s2 = align(session, rseq, mseq,  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 67, in align  
score, seqs = NeedlemanWunsch.nw(ref, match,  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 50, in nw  
"".join([s1.ss_type(i) or ' ' for i in range(len(s1))]),  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 50, in
<listcomp>  
"".join([s1.ss_type(i) or ' ' for i in range(len(s1))]),  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1198, in ss_type  
r = self.residue_at(loc)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1166, in residue_at  
return convert.residue_or_none(f(self._c_pointer, index))  
IndexError: vector  
  
IndexError: vector  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1166, in residue_at  
return convert.residue_or_none(f(self._c_pointer, index))  
  
See log for complete Python traceback.  
  

> matchmaker #11 to #10

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/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 730, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 394, in match  
score, s1, s2 = align(session, rseq, mseq,  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 67, in align  
score, seqs = NeedlemanWunsch.nw(ref, match,  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 50, in nw  
"".join([s1.ss_type(i) or ' ' for i in range(len(s1))]),  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 50, in
<listcomp>  
"".join([s1.ss_type(i) or ' ' for i in range(len(s1))]),  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1198, in ss_type  
r = self.residue_at(loc)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1166, in residue_at  
return convert.residue_or_none(f(self._c_pointer, index))  
IndexError: vector  
  
IndexError: vector  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1166, in residue_at  
return convert.residue_or_none(f(self._c_pointer, index))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

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: MacBook Pro
      Model Identifier: Mac14,9
      Model Number: Z17K002HDLL/A
      Chip: Apple M2 Pro
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 32 GB
      System Firmware Version: 8422.121.1
      OS Loader Version: 8422.121.1

Software:

    System Software Overview:

      System Version: macOS 13.4 (22F66)
      Kernel Version: Darwin 22.5.0
      Time since boot: 41 days, 20 hours, 4 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 19
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


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-Clipper: 0.21.0
    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-ISOLDE: 1.6.0
    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