IndexError showing MatchMaker alignment

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

> ui tool show Matchmaker

> open
> C:/Users/ACER/Documents/Pproteins/Paper/2024/modelos/Simples_full/P1a.pdb

Chain information for P1a.pdb #1  
---  
Chain | Description  
B | No description available  
  

> open C:/Users/ACER/Documents/Pproteins/modelos/anita/Minim/p1a_min.pdb

Chain information for p1a_min.pdb #2  
---  
Chain | Description  
? | No description available  
  

> matchmaker #2 to #1 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker P1a.pdb, chain B (#1) with p1a_min.pdb, chain (blank) (#2),
sequence alignment score = 472.7  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: P1a.pdb #1/B, p1a_min.pdb #2/?  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 10 pruned atom pairs is 1.362 angstroms; (across all 109 pairs:
25.038)  
  

> ui tool show Matchmaker

> matchmaker #2 to #1 alg Smith-Waterman matrix HSDM showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Smith-Waterman  
Similarity matrix | HSDM  
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 P1a.pdb (#1) with p1a_min.pdb (#2), sequence alignment score =
704.96  
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: P1a.pdb #1/B, p1a_min.pdb #2/?  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 10 pruned atom pairs is 1.362 angstroms; (across all 109 pairs:
25.038)  
  

> matchmaker #2 to #1 alg Smith-Waterman matrix HSDM showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Smith-Waterman  
Similarity matrix | HSDM  
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 P1a.pdb (#1) with p1a_min.pdb (#2), sequence alignment score =
704.96  
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: P1a.pdb #1/B, p1a_min.pdb #2/?  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3  
RMSD between 10 pruned atom pairs is 1.362 angstroms; (across all 109 pairs:
25.038)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/B #2/?

Alignment identifier is 1  

> select #1/B:1 #2/*:1

38 atoms, 36 bonds, 2 residues, 2 models selected  

> select #1/B:1-64 #2/*:1-64

1902 atoms, 1906 bonds, 128 residues, 2 models selected  
1 [ID: 1] region chains ,B [1-64] RMSD: 21.393  
  

> ui tool show Matchmaker

> matchmaker #2 & sel to #1 & sel alg Smith-Waterman matrix HSDM showAlignment
> true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Smith-Waterman  
Similarity matrix | HSDM  
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 P1a.pdb (#1) with p1a_min.pdb (#2), sequence alignment score =
405.559  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\match_maker\tool.py", line 171, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda *args:
self.run_matchmaker(apply=True))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\match_maker\tool.py", line 303, in run_matchmaker  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\match_maker\match.py", line 742, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\match_maker\match.py", line 547, in match  
residues[i] = r  
~~~~~~~~^^^  
IndexError: list assignment index out of range  
  
IndexError: list assignment index out of range  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\match_maker\match.py", line 547, in match  
residues[i] = r  
~~~~~~~~^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.13596 Core Profile Forward-Compatible Context 20.10.30.11 27.20.11030.11001
OpenGL renderer: AMD Radeon(TM) Vega 8 Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: es_AR.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: Acer
Model: Aspire A315-23
OS: Microsoft Windows 11 Home Single Language (Build 22631)
Memory: 10,671,370,240
MaxProcessMemory: 137,438,953,344
CPU: 8 AMD Ryzen 5 3500U with Radeon Vega Mobile Gfx  
OSLanguage: es-ES

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[pett]

Duplicate of #15758