Opened 7 months ago

Closed 7 months ago

#17189 closed defect (can't reproduce)

Crash in chem_group on Windows

Reported by: julio.bonilla@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.10.dev202503210042 (2025-03-21 00:42:17 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Thread 0x000079c0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00006740 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005ebc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\connection.py", line 878 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005680 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000070c4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000051b0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000687c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000062f4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002dd4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00007230 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00006850 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000636c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000263c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00006c60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000073f0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00007f54 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00006fd8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00006ef4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\connection.py", line 878 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00006ed8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000756c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000079c4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00007d34 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000606c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000090c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00007d1c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00007d18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000747c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00007d28 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00007d20 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00007de8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000067e4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\chem_group\support.py", line 40 in call_c_plus_plus
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\chem_group\chem_group.py", line 233 in find_group
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\hbonds\hbond.py", line 771 in _find_acceptors
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\hbonds\hbond.py", line 498 in find_hbonds
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\hbonds\cmd.py", line 94 in cmd_hbonds
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3215 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 537 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 594 in run_expanded_command
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 340 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 421 in run_shortcut
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 403 in try_shortcut
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 1394 in run_provider
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\shortcuts\__init__.py", line 66 in run_provider
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 1419 in run_provider
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line 397 in run_provider
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\toolbar\tool.py", line 215 in callback
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.10.dev202503210042 (2025-03-21)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open q8fnj4 fromDatabase uniprot format uniprot

Summary of feedback from opening q8fnj4 fetched from uniprot  
---  
notes |   
UniProt identifier q8fnj4 maps to entry Q8FNJ4  
Alignment identifier is q8fnj4  
  
Opened UniProt q8fnj4  

> blastprotein q8fnj4:1 database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version None name bp1

Webservices job id: 6IUN13ZNB768874S  
Webservices job finished: 6IUN13ZNB768874S  
Alignment identifier is bp1 [1]  
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp1 [1]  

> open pdb:2C4N

2c4n title:  
NagD from E.coli K-12 strain [more info...]  
  
Chain information for 2c4n #1  
---  
Chain | Description | UniProt  
A | PROTEIN NAGD | NAGD_ECOLI 1-250  
  
Non-standard residues in 2c4n #1  
---  
MG — magnesium ion  
PO4 — phosphate ion  
  
2c4n mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
Associated 2c4n chain A to 2C4N_A with 0 mismatches  

> select /A

2034 atoms, 1965 bonds, 6 pseudobonds, 364 residues, 2 models selected  

> ui mousemode right select

Drag select of 67 atoms, 250 residues, 6 pseudobonds, 52 bonds  

> select clear

Drag select of 67 atoms, 250 residues, 6 pseudobonds, 52 bonds  

> ui tool show "Modeller Comparative"

> modeller comparative "bp1 [1]:2" numModels 3 fast false multichain false
> hetPreserve false hydrogens true waterPreserve false

Webservices job id: QK6X1OHBA5Y41WTC  
Webservices job finished: QK6X1OHBA5Y41WTC  
Modeller job (ID QK6X1OHBA5Y41WTC) finished  
Computing secondary structure  
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 2C4N_A, chain A (#1) with 2C4N_A, chain A (#), sequence alignment
score = 964.5  
RMSD between 15 pruned atom pairs is 1.324 angstroms; (across all 247 pairs:
8.623)  
  
Computing secondary structure  
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 2C4N_A, chain A (#1) with 2C4N_A, chain A (#), sequence alignment
score = 971.1  
RMSD between 18 pruned atom pairs is 1.430 angstroms; (across all 247 pairs:
8.552)  
  
Computing secondary structure  
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 2C4N_A, chain A (#1) with 2C4N_A, chain A (#), sequence alignment
score = 968.7  
RMSD between 17 pruned atom pairs is 1.309 angstroms; (across all 247 pairs:
8.505)  
  
Associated 2C4N_A chain A to 2C4N_A with 0 mismatches  
Chain information for 2C4N_A  
---  
Chain | Description  
2.1/A 2.2/A 2.3/A | No description available  
  

> hide #2.3 models

> hide #2.2 models

> ui tool show Matchmaker

> hide #!1 models

> hbonds #2.1 reveal true


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.10.dev202503210042 (2025-03-21)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 - Build 31.0.101.4887
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

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

Manufacturer: HP
Model: HP ProBook 450 15.6 inch G10 Notebook PC
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 16,794,292,224
MaxProcessMemory: 137,438,953,344
CPU: 12 13th Gen Intel(R) Core(TM) i7-1355U
OSLanguage: es-ES

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: 3.2.0
    build: 1.2.2.post1
    certifi: 2025.1.31
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.19.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.1
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.5
    ChimeraX-AtomicLibrary: 14.1.13
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202503210042
    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: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.5.2
    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
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    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: 1.5.18
    ChimeraX-ModelPanel: 1.5
    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: 2.7.7
    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: 1.1.2
    ChimeraX-ProfileGrids: 1.1
    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
    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: 1.44
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    coverage: 7.7.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.13
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.56.0
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    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: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    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: 4.3.7
    pluggy: 1.5.0
    prompt_toolkit: 3.0.50
    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: 3.2.1
    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: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2025.1
    pywin32: 310
    pyzmq: 26.3.0
    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: 75.8.2
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    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: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2025.1
    urllib3: 2.3.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.13
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 7 months ago

Component: Unassigned → Structure Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in chem_group on Windows

comment:2 by Eric Pettersen, 7 months ago

Resolution: → can't reproduce
Status: accepted → closed

Hi Julio,

Thanks for reporting this problem. So far we have been unable to reproduce it ourselves, but we will keep investigating. It seems to only happen on Windows and only with the daily build. So if you have access to a non-Windows machine or can use the 1.9 production release, you can avoid the problem for now. I will add you to the recipient list for the main ticket we have open for this problem.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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