'CategorizedOptionsPanel' object has no attribute 'currentIndex'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.11.dev202505162204 (2025-05-16 22:04:29 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.11.dev202505162204 (2025-05-16)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> E:\VTechLab\Computation\2CuAhyBpC_dimer_crosslink\dimer_with_cu_a_b_model.cif
> format mmcif

Summary of feedback from opening
E:\VTechLab\Computation\2CuAhyBpC_dimer_crosslink\dimer_with_cu_a_b_model.cif  
---  
warnings | Unable to fetch template for 'ZL1P36A': will connect using distance criteria  
Unable to fetch template for 'ZL1P36B': will connect using distance criteria  
  
Chain information for dimer_with_cu_a_b_model.cif #1  
---  
Chain | Description  
A B | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'C')  

Computing secondary structure  

> open 8SY3 fromDatabase pdb format mmcif

Summary of feedback from opening 8SY3 fetched from pdb  
---  
note | Fetching compressed mmCIF 8sy3 from http://files.rcsb.org/download/8sy3.cif  
  
8sy3 title:  
Copper Complex of Peanut USP-type BURP Domain Peptide Cyclase [more info...]  
  
Chain information for 8sy3 #2  
---  
Chain | Description | UniProt  
A B | BURP domain-containing protein | A0A445DYW3_ARAHY 4-256  
  
Non-standard residues in 8sy3 #2  
---  
CU — copper (II) ion  
  

> ui tool show Matchmaker

> matchmaker #!2 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 dimer_with_cu_a_b_model.cif, chain A (#1) with 8sy3, chain A (#2),
sequence alignment score = 1206.5  
RMSD between 134 pruned atom pairs is 1.132 angstroms; (across all 209 pairs:
3.539)  
  

> matchmaker #!2 to #1 ssFraction 1.0

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 1  
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 dimer_with_cu_a_b_model.cif, chain A (#1) with 8sy3, chain A (#2),
sequence alignment score = 903  
RMSD between 136 pruned atom pairs is 1.202 angstroms; (across all 204 pairs:
5.274)  
  

> matchmaker #!2 to #1 ssFraction 0.0

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0  
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 dimer_with_cu_a_b_model.cif, chain A (#1) with 8sy3, chain A (#2),
sequence alignment score = 1361  
RMSD between 134 pruned atom pairs is 1.132 angstroms; (across all 209 pairs:
3.539)  
  

> matchmaker #!2 to #1 ssFraction 0.0

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0  
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 dimer_with_cu_a_b_model.cif, chain A (#1) with 8sy3, chain A (#2),
sequence alignment score = 1361  
RMSD between 134 pruned atom pairs is 1.132 angstroms; (across all 209 pairs:
3.539)  
  

> matchmaker #!2 to #1 ssFraction 0.4754

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.4754  
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 dimer_with_cu_a_b_model.cif, chain A (#1) with 8sy3, chain A (#2),
sequence alignment score = 1116.17  
RMSD between 134 pruned atom pairs is 1.132 angstroms; (across all 209 pairs:
3.539)  
  

> matchmaker #!2 to #1 ssFraction 0.4754

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.4754  
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 dimer_with_cu_a_b_model.cif, chain A (#1) with 8sy3, chain A (#2),
sequence alignment score = 1116.17  
RMSD between 134 pruned atom pairs is 1.132 angstroms; (across all 209 pairs:
3.539)  
  

> matchmaker #!2 to #1 ssFraction 0.4754

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.4754  
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 dimer_with_cu_a_b_model.cif, chain A (#1) with 8sy3, chain A (#2),
sequence alignment score = 1116.17  
RMSD between 134 pruned atom pairs is 1.132 angstroms; (across all 209 pairs:
3.539)  
  

> matchmaker #!2 to #1 ssFraction 0.4754 cutoffDistance 5.0

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.4754  
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 | 5  
  
Matchmaker dimer_with_cu_a_b_model.cif, chain A (#1) with 8sy3, chain A (#2),
sequence alignment score = 1116.17  
RMSD between 179 pruned atom pairs is 1.737 angstroms; (across all 209 pairs:
3.560)  
  

> matchmaker #!2 to #1 ssFraction 0.4754 cutoffDistance 5.0

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.4754  
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 | 5  
  
Matchmaker dimer_with_cu_a_b_model.cif, chain A (#1) with 8sy3, chain A (#2),
sequence alignment score = 1116.17  
RMSD between 179 pruned atom pairs is 1.737 angstroms; (across all 209 pairs:
3.560)  
  

> matchmaker #!2 to #1 ssFraction 0.4754 cutoffDistance 100.0

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.4754  
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 | 100  
  
Matchmaker dimer_with_cu_a_b_model.cif, chain A (#1) with 8sy3, chain A (#2),
sequence alignment score = 1116.17  
RMSD between 209 pruned atom pairs is 3.486 angstroms; (across all 209 pairs:
3.486)  
  

> matchmaker #!2 to #1 ssFraction 0.4754 cutoffDistance 500.0

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.4754  
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 | 500  
  
Matchmaker dimer_with_cu_a_b_model.cif, chain A (#1) with 8sy3, chain A (#2),
sequence alignment score = 1116.17  
RMSD between 209 pruned atom pairs is 3.486 angstroms; (across all 209 pairs:
3.486)  
  

> matchmaker #!2 to #1 ssFraction 0.4754 cutoffDistance 1.0

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.4754  
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 dimer_with_cu_a_b_model.cif, chain A (#1) with 8sy3, chain A (#2),
sequence alignment score = 1116.17  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> matchmaker #!1 to #2 ssFraction 0.4754 cutoffDistance 1.0

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.4754  
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 8sy3, chain A (#2) with dimer_with_cu_a_b_model.cif, chain A (#1),
sequence alignment score = 1116.17  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> matchmaker #!1 to #2 ssFraction 0.4754 cutoffDistance 1.0

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.4754  
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 8sy3, chain A (#2) with dimer_with_cu_a_b_model.cif, chain A (#1),
sequence alignment score = 1116.17  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> matchmaker #!1 to #2 ssFraction 0.4754 cutoffDistance 1.0

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.4754  
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 8sy3, chain A (#2) with dimer_with_cu_a_b_model.cif, chain A (#1),
sequence alignment score = 1116.17  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> matchmaker #!2 to #1 ssFraction 0.4754 cutoffDistance 1.0

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.4754  
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 dimer_with_cu_a_b_model.cif, chain A (#1) with 8sy3, chain A (#2),
sequence alignment score = 1116.17  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> matchmaker #!2 to #1/A pairing bs ssFraction 0.4754 cutoffDistance 1.0

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.4754  
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 dimer_with_cu_a_b_model.cif, chain A (#1) with 8sy3, chain A (#2),
sequence alignment score = 1116.17  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  
No reference and/or match structure/chain chosen  

> matchmaker #!1 to #2/A pairing bs ssFraction 0.4754 cutoffDistance 1.0

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.4754  
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 8sy3, chain A (#2) with dimer_with_cu_a_b_model.cif, chain A (#1),
sequence alignment score = 1116.17  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> matchmaker #!1 to #2/A pairing bs ssFraction 0.4754 cutoffDistance 1.0

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.4754  
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 8sy3, chain A (#2) with dimer_with_cu_a_b_model.cif, chain A (#1),
sequence alignment score = 1116.17  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> matchmaker #!1 to #2/B pairing bs ssFraction 0.4754 cutoffDistance 1.0

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.4754  
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 8sy3, chain B (#2) with dimer_with_cu_a_b_model.cif, chain A (#1),
sequence alignment score = 1084.79  
RMSD between 50 pruned atom pairs is 0.407 angstroms; (across all 200 pairs:
3.693)  
  

> matchmaker #!1 to #2/B pairing bs ssFraction 0.1476 cutoffDistance 1.0

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.1476  
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 8sy3, chain B (#2) with dimer_with_cu_a_b_model.cif, chain A (#1),
sequence alignment score = 1275.24  
RMSD between 50 pruned atom pairs is 0.407 angstroms; (across all 200 pairs:
3.693)  
  

> matchmaker #!1 to #2/B pairing bs alg Smith-Waterman ssFraction 0.1476
> cutoffDistance 1.0

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Smith-Waterman  
Similarity matrix | BLOSUM-62  
SS fraction | 0.1476  
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 8sy3 (#2) with dimer_with_cu_a_b_model.cif (#1), sequence alignment
score = 1275.24  
RMSD between 50 pruned atom pairs is 0.407 angstroms; (across all 200 pairs:
3.693)  
  

> matchmaker #!1 to #2/B pairing bs alg Smith-Waterman ssFraction 0.1476
> matrix Grantham cutoffDistance 1.0

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Smith-Waterman  
Similarity matrix | Grantham  
SS fraction | 0.1476  
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 8sy3 (#2) with dimer_with_cu_a_b_model.cif (#1), sequence alignment
score = 23331.9  
RMSD between 5 pruned atom pairs is 0.510 angstroms; (across all 185 pairs:
12.736)  
  

> matchmaker #!1 to #2/B pairing bs alg Smith-Waterman ssFraction 0.1476
> matrix BLOSUM-30 cutoffDistance 1.0

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Smith-Waterman  
Similarity matrix | BLOSUM-30  
SS fraction | 0.1476  
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 8sy3 (#2) with dimer_with_cu_a_b_model.cif (#1), sequence alignment
score = 1656.27  
RMSD between 50 pruned atom pairs is 0.407 angstroms; (across all 200 pairs:
3.693)  
  

> ui mousemode right select

> select #1/A:78

4 atoms, 3 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/A:77

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

> show sel atoms

> select #1/A:79

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

> show sel atoms

> lighting flat

> set bgColor white

> graphics silhouettes false

> graphics silhouettes true

> set bgColor gray

> color bfactor sel

7 atoms, 1 residues, atom bfactor range 83.8 to 89  

> undo

> select clear

> color byhetero

> color bfactor

7242 atoms, 922 residues, atom bfactor range 22.1 to 310  

> undo

> matchmaker #!2 to #1/A pairing bs alg Smith-Waterman ssFraction 0.1476
> matrix BLOSUM-30 cutoffDistance 1.0

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Smith-Waterman  
Similarity matrix | BLOSUM-30  
SS fraction | 0.1476  
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 dimer_with_cu_a_b_model.cif (#1) with 8sy3 (#2), sequence alignment
score = 1666.01  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> matchmaker #!2 to #1/B pairing bs alg Smith-Waterman ssFraction 0.1476
> matrix BLOSUM-30 cutoffDistance 1.0

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Smith-Waterman  
Similarity matrix | BLOSUM-30  
SS fraction | 0.1476  
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 dimer_with_cu_a_b_model.cif (#1) with 8sy3 (#2), sequence alignment
score = 1666.01  
RMSD between 63 pruned atom pairs is 0.422 angstroms; (across all 209 pairs:
3.887)  
  

> matchmaker #!2 to #1/A & sel pairing bs alg Smith-Waterman ssFraction 0.1476
> matrix BLOSUM-30 cutoffDistance 1.0

No 'to' chains specified  

> matchmaker #!2 & sel to #1/A pairing bs alg Smith-Waterman ssFraction 0.1476
> matrix BLOSUM-30 cutoffDistance 1.0

No molecules/chains to match specified  
No reference and/or match structure/chain chosen  

> matchmaker #!2 to #1/A pairing bs alg Smith-Waterman ssFraction 0.1476
> matrix BLOSUM-30 cutoffDistance 1.0 showAlignment true

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Smith-Waterman  
Similarity matrix | BLOSUM-30  
SS fraction | 0.1476  
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 dimer_with_cu_a_b_model.cif (#1) with 8sy3 (#2), sequence alignment
score = 1666.01  
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: dimer_with_cu_a_b_model.cif
#1/A, 8sy3 #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> matchmaker #!2 to #1/A pairing bs alg Smith-Waterman ssFraction 0.1476
> matrix BLOSUM-30 cutoffDistance 1.0 showAlignment true

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Smith-Waterman  
Similarity matrix | BLOSUM-30  
SS fraction | 0.1476  
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 dimer_with_cu_a_b_model.cif (#1) with 8sy3 (#2), sequence alignment
score = 1666.01  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: dimer_with_cu_a_b_model.cif
#1/A, 8sy3 #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> matchmaker #!2 to #1/A pairing bs alg Smith-Waterman ssFraction 0.1476
> matrix BLOSUM-100 cutoffDistance 1.0 showAlignment true

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Smith-Waterman  
Similarity matrix | BLOSUM-100  
SS fraction | 0.1476  
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 dimer_with_cu_a_b_model.cif (#1) with 8sy3 (#2), sequence alignment
score = 2283.15  
Alignment identifier is 3  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3  
Hiding conservation header for alignment 3  
Chains used in RMSD evaluation for alignment 3: dimer_with_cu_a_b_model.cif
#1/A, 8sy3 #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> matchmaker #!2 to #1/A pairing bs alg Smith-Waterman ssFraction 0.1476
> matrix BLOSUM-100 cutoffDistance 1.0 gapExtend 6

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Smith-Waterman  
Similarity matrix | BLOSUM-100  
SS fraction | 0.1476  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 6  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 1  
  
Matchmaker dimer_with_cu_a_b_model.cif (#1) with 8sy3 (#2), sequence alignment
score = 2283.15  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> help help:user/tools/matchmaker.html

> matchmaker #!2 to #1/A pairing bs alg Smith-Waterman ssFraction 0.1476
> matrix BLOSUM-100 cutoffDistance 1.0 gapExtend 2

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Smith-Waterman  
Similarity matrix | BLOSUM-100  
SS fraction | 0.1476  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 2  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 1  
  
Matchmaker dimer_with_cu_a_b_model.cif (#1) with 8sy3 (#2), sequence alignment
score = 2283.15  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> matchmaker #!2 to #1/A pairing bs alg Smith-Waterman ssFraction 0.1476
> matrix BLOSUM-100 cutoffDistance 1.0 gapExtend 2 keepComputedSS true

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Smith-Waterman  
Similarity matrix | BLOSUM-100  
SS fraction | 0.1476  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 2  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 1  
  
Matchmaker dimer_with_cu_a_b_model.cif (#1) with 8sy3 (#2), sequence alignment
score = 2283.15  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> matchmaker #!2 to #1/A pairing bs alg Smith-Waterman ssFraction 0.8252
> matrix BLOSUM-100 cutoffDistance 1.0 gapExtend 2 keepComputedSS true

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Smith-Waterman  
Similarity matrix | BLOSUM-100  
SS fraction | 0.8252  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 2  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 1  
  
Matchmaker dimer_with_cu_a_b_model.cif (#1) with 8sy3 (#2), sequence alignment
score = 1140.71  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> matchmaker #!2 to #1/A pairing bs alg Smith-Waterman ssFraction 0.8252
> matrix BLOSUM-100 cutoffDistance 1.0 gapExtend 2 keepComputedSS true

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Smith-Waterman  
Similarity matrix | BLOSUM-100  
SS fraction | 0.8252  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 2  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 1  
  
Matchmaker dimer_with_cu_a_b_model.cif (#1) with 8sy3 (#2), sequence alignment
score = 1140.71  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> matchmaker #!2 to #1/B pairing bs alg Smith-Waterman ssFraction 0.8252
> matrix BLOSUM-100 cutoffDistance 1.0 gapExtend 2 keepComputedSS true

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Smith-Waterman  
Similarity matrix | BLOSUM-100  
SS fraction | 0.8252  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 2  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 1  
  
Matchmaker dimer_with_cu_a_b_model.cif (#1) with 8sy3 (#2), sequence alignment
score = 1140.71  
RMSD between 63 pruned atom pairs is 0.422 angstroms; (across all 209 pairs:
3.887)  
  

> matchmaker #!2 to #1 alg Smith-Waterman ssFraction 0.8252 matrix BLOSUM-100
> cutoffDistance 1.0 gapExtend 2 keepComputedSS true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Smith-Waterman  
Similarity matrix | BLOSUM-100  
SS fraction | 0.8252  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 2  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 1  
  
Matchmaker dimer_with_cu_a_b_model.cif (#1) with 8sy3 (#2), sequence alignment
score = 1140.71  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> matchmaker #!2 to #1 alg Smith-Waterman ssFraction 0.2296 matrix BLOSUM-100
> cutoffDistance 1.0 gapExtend 2 keepComputedSS true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Smith-Waterman  
Similarity matrix | BLOSUM-100  
SS fraction | 0.2296  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 2  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 1  
  
Matchmaker dimer_with_cu_a_b_model.cif (#1) with 8sy3 (#2), sequence alignment
score = 2144.89  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> matchmaker #!2 to #1 ssFraction 0.2296 matrix BLOSUM-100 cutoffDistance 1.0
> gapExtend 2 keepComputedSS true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-100  
SS fraction | 0.2296  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 2  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 1  
  
Matchmaker dimer_with_cu_a_b_model.cif, chain A (#1) with 8sy3, chain A (#2),
sequence alignment score = 2144.89  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> matchmaker #!2 to #1 ssFraction 0.388 matrix BLOSUM-100 cutoffDistance 1.0
> gapExtend 2 keepComputedSS true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-100  
SS fraction | 0.388  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 2  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 1  
  
Matchmaker dimer_with_cu_a_b_model.cif, chain A (#1) with 8sy3, chain A (#2),
sequence alignment score = 1877.83  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> matchmaker #!2 to #1 ssFraction 0.388 matrix BLOSUM-30 cutoffDistance 1.0
> gapExtend 2 keepComputedSS true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-30  
SS fraction | 0.388  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 2  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 1  
  
Matchmaker dimer_with_cu_a_b_model.cif, chain A (#1) with 8sy3, chain A (#2),
sequence alignment score = 1434.74  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  

> matchmaker #!2 to #1 ssFraction 0.388 matrix BLOSUM-30 gapExtend 2
> keepComputedSS true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-30  
SS fraction | 0.388  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 2  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker dimer_with_cu_a_b_model.cif, chain A (#1) with 8sy3, chain A (#2),
sequence alignment score = 1434.74  
RMSD between 134 pruned atom pairs is 1.132 angstroms; (across all 209 pairs:
3.539)  
  

> matchmaker #!2 to #1 ssFraction 0.388 matrix BLOSUM-30 cutoffDistance 1.0
> gapExtend 2 keepComputedSS true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-30  
SS fraction | 0.388  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 2  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 1  
  
Matchmaker dimer_with_cu_a_b_model.cif, chain A (#1) with 8sy3, chain A (#2),
sequence alignment score = 1434.74  
RMSD between 62 pruned atom pairs is 0.417 angstroms; (across all 209 pairs:
3.899)  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11.dev202505162204\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 458, in _save  
for opt in self._get_actionable_options():  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202505162204\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 420, in
_get_actionable_options  
options = self.options_panel.options(self.options_panel.current_category())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202505162204\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 280, in current_category  
return self._tabs_widget.tabText(self.currentIndex())  
^^^^^^^^^^^^^^^^^  
AttributeError: 'CategorizedOptionsPanel' object has no attribute
'currentIndex'  
  
AttributeError: 'CategorizedOptionsPanel' object has no attribute
'currentIndex'  
  
File "C:\Program Files\ChimeraX 1.11.dev202505162204\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 280, in current_category  
return self._tabs_widget.tabText(self.currentIndex())  
^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11.dev202505162204\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 458, in _save  
for opt in self._get_actionable_options():  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202505162204\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 420, in
_get_actionable_options  
options = self.options_panel.options(self.options_panel.current_category())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.dev202505162204\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 280, in current_category  
return self._tabs_widget.tabText(self.currentIndex())  
^^^^^^^^^^^^^^^^^  
AttributeError: 'CategorizedOptionsPanel' object has no attribute
'currentIndex'  
  
AttributeError: 'CategorizedOptionsPanel' object has no attribute
'currentIndex'  
  
File "C:\Program Files\ChimeraX 1.11.dev202505162204\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 280, in current_category  
return self._tabs_widget.tabText(self.currentIndex())  
^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 581.29
OpenGL renderer: NVIDIA GeForce GTX 1650 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: LENOVO
Model: 20QV0007US
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 51,261,341,696
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.3.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.3.3
    build: 1.2.2.post1
    certifi: 2025.4.26
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.dev202505162204
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.46
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.10
    contourpy: 1.3.2
    coverage: 7.8.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.3.5
    pytest-cov: 6.1.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    pyzmq: 26.4.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5
    traitlets: 5.14.3
    typing_extensions: 4.13.2
    tzdata: 2025.2
    urllib3: 2.4.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1

[Eric Pettersen]

Duplicate of #18731