KeyError matching selected regions

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
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 "C:\\\Users\\\sarson-lawrence.k\\\OneDrive -
> wehi.edu.au\\\GCSF_paper\\\gp130_figure.cxs"

Log from Mon Nov 13 10:50:01 2023UCSF 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 8d82

8d82 title:  
Cryo-EM structure of human IL-6 signaling complex in detergent: model
containing full extracellular domains [more info...]  
  
Chain information for 8d82 #1  
---  
Chain | Description | UniProt  
A E | Interleukin-6 receptor subunit beta | IL6RB_HUMAN 23-700  
C G | Soluble interleukin-6 receptor subunit alpha | IL6RA_HUMAN 20-331  
D H | Interleukin-6 | IL6_HUMAN 30-212  
  
Non-standard residues in 8d82 #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> set bgColor white

> hide atoms

> show cartoons

> show surfaces

> transparency70

Unknown command: transparency70  

> transparency 70

Drag select of 8d82_E SES surface, 137124 of 595960 triangles, 149 residues  
Drag select of 8d82_A SES surface, 146645 of 599374 triangles, 150 residues  

> select up

1547 atoms, 1592 bonds, 192 residues, 2 models selected  

> select up

4803 atoms, 4940 bonds, 595 residues, 2 models selected  

> select up

17366 atoms, 17850 bonds, 2146 residues, 2 models selected  

> select down

4803 atoms, 4940 bonds, 595 residues, 7 models selected  

> color (#!1 & sel) #abffb8ff

> color (#!1 & sel) #8fffb4ff

Drag select of 8d82_E SES surface, 81034 of 595960 triangles, 107 residues  

> select up

1182 atoms, 1213 bonds, 145 residues, 2 models selected  

> select up

4803 atoms, 4940 bonds, 595 residues, 2 models selected  

> color (#!1 & sel) #f6ffbbff

> color (#!1 & sel) #bbffdaff

> color (#!1 & sel) #bcf4ffff

> color (#!1 & sel) #d3f8ffff

> color (#!1 & sel) #cddaffff

> color (#!1 & sel) #b7cdffff

> color (#!1 & sel) #98deffff

> color (#!1 & sel) #1d83ffff

> color (#!1 & sel) #6557ffff

> color (#!1 & sel) #107cffff

> color (#!1 & sel) #0f7bffff

> color (#!1 & sel) #1e96ffff

> color (#!1 & sel) #3a8fffff

> color (#!1 & sel) #57ffddff

> color (#!1 & sel) #4efff9ff

> color (#!1 & sel) #3ec2ffff

> select clear

> color #92caffff

> undo

Drag select of 8d82_E SES surface, 106540 of 595960 triangles, 122 residues  

> select up

1740 atoms, 1785 bonds, 217 residues, 2 models selected  

> select up

4803 atoms, 4940 bonds, 595 residues, 2 models selected  

> color (#!1 & sel) #aee9ffff

> color (#!1 & sel) #8fe7ffff

> color (#!1 & sel) #8fecffff

> color (#!1 & sel) #86f5ffff

> color (#!1 & sel) #81eaffff

> color (#!1 & sel) #75e8ffff

Drag select of 8d82_A SES surface, 60902 of 599374 triangles, 75 residues  

> select up

1076 atoms, 1100 bonds, 130 residues, 2 models selected  

> select up

4803 atoms, 4940 bonds, 595 residues, 2 models selected  

> select up

17366 atoms, 17850 bonds, 2146 residues, 2 models selected  

> select down

4803 atoms, 4940 bonds, 595 residues, 7 models selected  

> color (#!1 & sel) #a1ffbcff

> color (#!1 & sel) #89ffbaff

> color (#!1 & sel) #6bff90ff

> select clear

> transparency 70

Drag select of 8d82_D SES surface, 8395 of 180946 triangles, 4 residues  

> select up

247 atoms, 252 bonds, 30 residues, 2 models selected  

> select up

1358 atoms, 1376 bonds, 169 residues, 2 models selected  

> select up

17366 atoms, 17850 bonds, 2146 residues, 2 models selected  

> select down

1358 atoms, 1376 bonds, 169 residues, 7 models selected  

> color (#!1 & sel) #ff54a1ff

Drag select of 8d82_H SES surface, 10887 of 181260 triangles, 14 residues  

> select up

406 atoms, 410 bonds, 49 residues, 2 models selected  

> select up

1358 atoms, 1376 bonds, 169 residues, 2 models selected  

> color (#!1 & sel) #ffb254ff

> color (#!1 & sel) #ff54a4ff

> color (#!1 & sel) #ffb254ff

> color (#!1 & sel) #ff54a1ff

> select clear

> transparency 70

> save C:\Users\sarson-lawrence.k\Desktop\image38.png supersample 3

> save C:\Users\sarson-lawrence.k\Desktop\image39.png supersample 3

> save "C:/Users/sarson-lawrence.k/OneDrive -
> wehi.edu.au/GCSF_paper/gp130_figure.cxs"

——— End of log from Mon Nov 13 10:50:01 2023 ———

opened ChimeraX session  

> open "C:/Users/sarson-lawrence.k/OneDrive - wehi.edu.au/GCSF_paper/GCSF-
> GCSFR_Isolde_kaiseal_11_symmetry.pdb"

Chain information for GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C D | No description available  
  

> hide atoms

> ui tool show Matchmaker

> 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 GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain B (#2) with 8d82,
chain A (#1), sequence alignment score = 814.5  
RMSD between 106 pruned atom pairs is 0.844 angstroms; (across all 550 pairs:
11.340)  
  
Drag select of 8d82_G SES surface, 70051 of 302790 triangles, 71 residues  

> select up

667 atoms, 684 bonds, 88 residues, 2 models selected  

> select up

2382 atoms, 2459 bonds, 299 residues, 2 models selected  

> select up

17366 atoms, 17850 bonds, 2146 residues, 2 models selected  

> select down

2382 atoms, 2459 bonds, 299 residues, 7 models selected  

> hide sel cartoons

> select clear

> hide surfaces

Drag select of 53 residues  

> select up

708 atoms, 723 bonds, 95 residues, 2 models selected  

> select up

2382 atoms, 2459 bonds, 299 residues, 2 models selected  

> hide sel cartoons

Drag select of 3 residues  

> select up

91 atoms, 91 bonds, 12 residues, 2 models selected  

> select up

1358 atoms, 1376 bonds, 169 residues, 2 models selected  

> select up

17366 atoms, 17850 bonds, 2146 residues, 2 models selected  

> select down

1358 atoms, 1376 bonds, 169 residues, 7 models selected  

> hide sel cartoons

Drag select of 3 residues  

> select up

96 atoms, 95 bonds, 13 residues, 2 models selected  

> select up

1358 atoms, 1376 bonds, 169 residues, 2 models selected  

> select up

17366 atoms, 17850 bonds, 2146 residues, 2 models selected  

> select down

1358 atoms, 1376 bonds, 169 residues, 7 models selected  

> hide sel cartoons

> select add #1

17366 atoms, 17850 bonds, 2146 residues, 2 models selected  

> select subtract #1

6 models selected  

> hide #!1 models

Drag select of 41 residues  

> select up

1159 atoms, 1168 bonds, 80 residues, 1 model selected  

> select up

2546 atoms, 2570 bonds, 168 residues, 1 model selected  

> hide sel cartoons

Drag select of 11 residues  

> select up

626 atoms, 631 bonds, 43 residues, 1 model selected  

> select up

2543 atoms, 2568 bonds, 168 residues, 1 model selected  

> select up

23503 atoms, 23865 bonds, 1528 residues, 1 model selected  

> select down

2543 atoms, 2568 bonds, 168 residues, 1 model selected  

> hide sel cartoons

Drag select of 99 residues, 1 pseudobonds  

> select up

2166 atoms, 2193 bonds, 1 pseudobond, 139 residues, 2 models selected  

> select up

7902 atoms, 8032 bonds, 1 pseudobond, 502 residues, 2 models selected  

> select up

8016 atoms, 8149 bonds, 1 pseudobond, 510 residues, 2 models selected  

> select up

9371 atoms, 9527 bonds, 1 pseudobond, 596 residues, 2 models selected  

> select up

23503 atoms, 23865 bonds, 4 pseudobonds, 1528 residues, 2 models selected  

> select down

9371 atoms, 9527 bonds, 1 pseudobond, 596 residues, 2 models selected  

> hide sel cartoons

> show #!1 models

> undo

> redo

> color #2 #2630ebff

Drag select of 90 residues  

> select up

765 atoms, 785 bonds, 96 residues, 2 models selected  

> select up

4803 atoms, 4940 bonds, 595 residues, 2 models selected  

> select up

17366 atoms, 17850 bonds, 2146 residues, 2 models selected  

> select down

4803 atoms, 4940 bonds, 595 residues, 7 models selected  

> hide sel cartoons

> matchmaker #1/E to #2/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82,
chain E (#1), sequence alignment score = 803.3  
RMSD between 161 pruned atom pairs is 1.190 angstroms; (across all 550 pairs:
13.959)  
  

> color #2 #eb9635ff

Drag select of 381 residues  

> select up

4737 atoms, 4827 bonds, 404 residues, 3 models selected  

> select up

10895 atoms, 11137 bonds, 1001 residues, 3 models selected  

> select down

4737 atoms, 4827 bonds, 404 residues, 3 models selected  

> hide sel cartoons

> undo

> select clear

Drag select of 400 residues  

> select up

4737 atoms, 3204 bonds, 404 residues, 3 models selected  

> select down

4683 atoms, 400 residues, 3 models selected  

> hide sel cartoons

> select clear

> save "C:/Users/sarson-lawrence.k/OneDrive -
> wehi.edu.au/GCSF_paper/GCSF_D3-D4_overlay_gp130.cxs"

Drag select of 150 residues  

> select up

2133 atoms, 2171 bonds, 180 residues, 3 models selected  

> select up

7754 atoms, 7943 bonds, 785 residues, 3 models selected  

> select clear

Drag select of 15 residues  

> select up

434 atoms, 439 bonds, 27 residues, 1 model selected  

> select up

1467 atoms, 1493 bonds, 94 residues, 1 model selected  

> select up

1485 atoms, 1510 bonds, 96 residues, 1 model selected  

> select up

2951 atoms, 3003 bonds, 190 residues, 1 model selected  

> select down

1485 atoms, 1510 bonds, 96 residues, 1 model selected  

> hide sel cartoons

Drag select of 2 residues  

> select up

150 atoms, 152 bonds, 10 residues, 1 model selected  

> select up

1484 atoms, 1510 bonds, 96 residues, 1 model selected  

> select up

1614 atoms, 1642 bonds, 105 residues, 1 model selected  

> select down

1484 atoms, 1510 bonds, 96 residues, 1 model selected  

> hide sel cartoons

Drag select of 98 residues  

> hide sel cartoons

Drag select of 95 residues  

> hide sel cartoons

> lighting full

> hide #!1 models

Drag select of 104 residues  

> show #!1 models

> hide #!2 models

Drag select of 102 residues  

> show #!2 models

> matchmaker #1/E & sel to #2/A pairing ss

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\tool.py", line 169, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda *args:
self.run_matchmaker(apply=True))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\tool.py", line 288, in run_matchmaker  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, 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 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 314, in match  
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,  
KeyError: <chimerax.atomic.molobject.StructureSeq object at
0x000002B0BEB168B0>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 314, in match  
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,  
  
See log for complete Python traceback.  
  

> matchmaker #1/E & sel to #2/A pairing ss

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\tool.py", line 169, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda *args:
self.run_matchmaker(apply=True))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\tool.py", line 288, in run_matchmaker  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, 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 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 314, in match  
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,  
KeyError: <chimerax.atomic.molobject.StructureSeq object at
0x000002B0C3ED60D0>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 314, in match  
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,  
  
See log for complete Python traceback.  
  

> matchmaker #!1 & sel 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 GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain B (#2) with 8d82,
chain E (#1), sequence alignment score = 119  
RMSD between 46 pruned atom pairs is 0.974 angstroms; (across all 97 pairs:
3.940)  
  

> matchmaker #1/E & sel to #2/A pairing ss

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\tool.py", line 169, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda *args:
self.run_matchmaker(apply=True))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\tool.py", line 288, in run_matchmaker  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, 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 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 314, in match  
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,  
KeyError: <chimerax.atomic.molobject.StructureSeq object at
0x000002B0C8F32A60>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 314, in match  
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,  
  
See log for complete Python traceback.  
  

> matchmaker #1/E to #2/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82,
chain E (#1), sequence alignment score = 803.3  
RMSD between 161 pruned atom pairs is 1.190 angstroms; (across all 550 pairs:
13.959)  
  

> select clear

Drag select of 34 residues  

> select up

771 atoms, 780 bonds, 50 residues, 1 model selected  

> select up

6092 atoms, 6197 bonds, 406 residues, 1 model selected  

> color #2 #eb1e4bff

> color #2 #eb0b47ff

> color #2 #eb2056ff

> color #2 #eb1e7aff

> color #2 #eb124cff

> color #2 #eb134dff

> select clear

> save C:\Users\sarson-lawrence.k\Desktop\image49.png supersample 3

> save "C:/Users/sarson-lawrence.k/OneDrive -
> wehi.edu.au/GCSF_paper/GCSF_D3-D4_overlay_gp130.cxs"

> style stick

Changed 40869 atom styles  

> hide cartoons

> show cartoons

> undo

[Repeated 1 time(s)]Drag select of 397 residues  

> style sel stick

Changed 4451 atom styles  

> show sel cartoons

> style sel ball

Changed 4451 atom styles  

> select clear

> show atoms

> hide atoms

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides tube/slab shape box

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> help help:user

Drag select of 397 residues  

> ribbon

> undo

> licorice

Unknown command: licorice  

> cartoon style protein modeHelix default arrows false xsection oval width 1
> thickness 1

> select clear

> save C:\Users\sarson-lawrence.k\Desktop\image50.png supersample 3

> save "C:/Users/sarson-lawrence.k/OneDrive -
> wehi.edu.au/GCSF_paper/GCSF_D3-D4_overlay_gp130.cxs"

> style stick

Changed 40869 atom styles  

> show cartoons

> hide cartoons

> undo

[Repeated 1 time(s)]

> matchmaker #1/E to #2/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82,
chain E (#1), sequence alignment score = 803.3  
RMSD between 161 pruned atom pairs is 1.190 angstroms; (across all 550 pairs:
13.959)  
  

> matchmaker #1/E to #2/A pairing ss cutoffDistance 3.0

Parameters  
---  
Chain pairing | ss  
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 | 3  
  
Matchmaker GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82,
chain E (#1), sequence alignment score = 803.3  
RMSD between 191 pruned atom pairs is 1.481 angstroms; (across all 550 pairs:
13.865)  
  

> matchmaker #1/E to #2/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82,
chain E (#1), sequence alignment score = 803.3  
RMSD between 161 pruned atom pairs is 1.190 angstroms; (across all 550 pairs:
13.959)  
  

> ui tool show Matchmaker

> matchmaker #1/E to #2/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82,
chain E (#1), sequence alignment score = 803.3  
RMSD between 161 pruned atom pairs is 1.190 angstroms; (across all 550 pairs:
13.959)  
  

> matchmaker #1/E to #2/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82,
chain E (#1), sequence alignment score = 803.3  
RMSD between 161 pruned atom pairs is 1.190 angstroms; (across all 550 pairs:
13.959)  
  

> show cartoons

> matchmaker #1/E to #2/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82,
chain E (#1), sequence alignment score = 803.3  
RMSD between 161 pruned atom pairs is 1.190 angstroms; (across all 550 pairs:
13.959)  
  

> matchmaker #1/E to #2/A pairing ss cutoffDistance 4.0

Parameters  
---  
Chain pairing | ss  
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 | 4  
  
Matchmaker GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82,
chain E (#1), sequence alignment score = 803.3  
RMSD between 212 pruned atom pairs is 1.785 angstroms; (across all 550 pairs:
13.707)  
  

> matchmaker #1/E to #2/A pairing ss cutoffDistance 1.0

Parameters  
---  
Chain pairing | ss  
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 | 1  
  
Matchmaker GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82,
chain E (#1), sequence alignment score = 803.3  
RMSD between 65 pruned atom pairs is 0.704 angstroms; (across all 550 pairs:
14.072)  
  

> matchmaker #1/E to #2/A pairing ss cutoffDistance 10.0

Parameters  
---  
Chain pairing | ss  
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 | 10  
  
Matchmaker GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82,
chain E (#1), sequence alignment score = 803.3  
RMSD between 384 pruned atom pairs is 5.512 angstroms; (across all 550 pairs:
9.924)  
  
Drag select of 127 residues  

> select up

1124 atoms, 1152 bonds, 147 residues, 2 models selected  

> select up

2382 atoms, 2459 bonds, 299 residues, 2 models selected  

> hide sel cartoons

Drag select of 159 residues  

> select up

1583 atoms, 1628 bonds, 204 residues, 2 models selected  

> select up

2382 atoms, 2459 bonds, 299 residues, 2 models selected  

> hide sel cartoons

Drag select of 64 residues  

> select up

1163 atoms, 1180 bonds, 120 residues, 3 models selected  

> select up

11221 atoms, 11462 bonds, 1001 residues, 3 models selected  

> select up

11453 atoms, 11695 bonds, 1018 residues, 3 models selected  

> select up

12705 atoms, 12972 bonds, 1097 residues, 3 models selected  

> select up

12819 atoms, 13089 bonds, 1105 residues, 3 models selected  

> select up

14174 atoms, 14467 bonds, 1191 residues, 3 models selected  

> select up

40869 atoms, 41715 bonds, 3674 residues, 3 models selected  

> select down

14174 atoms, 14467 bonds, 1191 residues, 8 models selected  

> hide sel cartoons

Drag select of 150 residues  

> select up

3229 atoms, 3259 bonds, 273 residues, 3 models selected  

> select up

3904 atoms, 3946 bonds, 337 residues, 3 models selected  

> select up

40869 atoms, 41715 bonds, 3674 residues, 3 models selected  

> select down

3904 atoms, 3946 bonds, 337 residues, 8 models selected  

> hide sel cartoons

Drag select of 97 residues  

> select up

2675 atoms, 2698 bonds, 220 residues, 3 models selected  

> select up

3901 atoms, 3944 bonds, 337 residues, 3 models selected  

> select up

40869 atoms, 41715 bonds, 3674 residues, 3 models selected  

> select down

3901 atoms, 3944 bonds, 337 residues, 8 models selected  

> hide sel cartoons

> ui tool show Matchmaker

> matchmaker #1/E to #2/A pairing ss cutoffDistance 10.0

Parameters  
---  
Chain pairing | ss  
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 | 10  
  
Matchmaker GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82,
chain E (#1), sequence alignment score = 803.3  
RMSD between 384 pruned atom pairs is 5.512 angstroms; (across all 550 pairs:
9.924)  
  

> matchmaker #1/E to #2/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82,
chain E (#1), sequence alignment score = 803.3  
RMSD between 161 pruned atom pairs is 1.190 angstroms; (across all 550 pairs:
13.959)  
  

> matchmaker #1/E to #2/A pairing ss cutoffDistance 3.0

Parameters  
---  
Chain pairing | ss  
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 | 3  
  
Matchmaker GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82,
chain E (#1), sequence alignment score = 803.3  
RMSD between 191 pruned atom pairs is 1.481 angstroms; (across all 550 pairs:
13.865)  
  

> save C:\Users\sarson-lawrence.k\Desktop\image53.png supersample 3

Drag select of 594 residues  
Drag select of 607 residues  

> matchmaker #1/E to #2/A pairing ss cutoffDistance 3.0

Parameters  
---  
Chain pairing | ss  
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 | 3  
  
Matchmaker GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82,
chain E (#1), sequence alignment score = 803.3  
RMSD between 191 pruned atom pairs is 1.481 angstroms; (across all 550 pairs:
13.865)  
  

> matchmaker #1/E to #2/A pairing ss cutoffDistance none

Parameters  
---  
Chain pairing | ss  
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  
No iteration  
  
Matchmaker GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82,
chain E (#1), sequence alignment score = 803.3  
RMSD between 550 atom pairs is 9.350 angstroms  
  

> matchmaker #1/E & sel to #2/A & sel pairing ss cutoffDistance none

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\tool.py", line 169, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda *args:
self.run_matchmaker(apply=True))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\tool.py", line 288, in run_matchmaker  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, 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 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 314, in match  
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,  
KeyError: <chimerax.atomic.molobject.StructureSeq object at
0x000002B0C7C42340>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 314, in match  
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,  
  
See log for complete Python traceback.  
  

> matchmaker #1/E to #2/A & sel pairing ss cutoffDistance none

Parameters  
---  
Chain pairing | ss  
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  
No iteration  
  
Matchmaker GCSF-GCSFR_Isolde_kaiseal_11_symmetry.pdb, chain A (#2) with 8d82,
chain E (#1), sequence alignment score = 411.3  
RMSD between 285 atom pairs is 4.210 angstroms  
  

> matchmaker #1/E & sel to #2/A pairing ss cutoffDistance none

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\tool.py", line 169, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda *args:
self.run_matchmaker(apply=True))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\tool.py", line 288, in run_matchmaker  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, 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 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 314, in match  
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,  
KeyError: <chimerax.atomic.molobject.StructureSeq object at
0x000002B0C7C59310>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\match_maker\match.py", line 314, in match  
score, s1, s2 = align(session, ref, match, final_matrix_name[match], alg,  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 20.19.15.5063
OpenGL renderer: Intel(R) HD Graphics 4600
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_AU.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 9020
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 8,493,617,152
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-4770 CPU @ 3.40GHz
OSLanguage: en-GB

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    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: 2023.5.7
    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
    comtypes: 1.1.14
    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: 2022.9.26
    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: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    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
    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
    pywin32: 305
    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
    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
    WMI: 1.5.1
    zipp: 3.15.0