Opened 22 months ago

Closed 22 months ago

#10435 closed defect (can't reproduce)

Crash in garbage collection while processing modeller results

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Structure Prediction Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.2.0-37-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007f03de7fc640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 324 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 622 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1392 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f03deffd640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f03df7fe640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f03dffff640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/selectors.py", line 415 in select
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f0424ff9640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f04257fa640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f0425ffb640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f04267fc640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f0427fff640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f0434ff1640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f04357f2640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f0435ff3640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f04367f4640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f0436ff5640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f04377f6640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f0437ff7640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f04387f8640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f0438ff9640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f04397fa640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f0439ffb640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f043a7fc640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f043affd640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f043b7fe640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f043bfff640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f04489f9640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f04491fa640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f04499fb640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f044a1fc640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00007f04f629db80 (most recent call first):
  Garbage-collecting
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/ctypes_support.py", line 34 in atom_pair
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 149 in get_prop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/modeller/common.py", line 434 in process_ok_models
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/modeller/common.py", line 603 in on_finish
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 717 in customEvent
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 58)
===== Log before crash start =====
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 2hyy format mmcif fromDatabase pdb

2hyy title:  
Human Abl kinase domain in complex with imatinib (STI571, Glivec) [more
info...]  
  
Chain information for 2hyy #1  
---  
Chain | Description | UniProt  
A B C D | Proto-oncogene tyrosine-protein kinase ABL1 | ABL1_HUMAN 228-500  
  
Non-standard residues in 2hyy #1  
---  
STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-
pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571; imatinib)  
  
2hyy mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
  

> interfaces ~solvent

4 buried areas: C A 499, B D 498, B A 443, D C 340  

> open 1gdi

Summary of feedback from opening 1gdi fetched from pdb  
---  
notes | Fetching compressed mmCIF 1gdi from
http://files.rcsb.org/download/1gdi.cif  
Fetching CCD HEM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/HEM/HEM.cif  
Fetching CCD CMO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/CMO/CMO.cif  
  
1gdi title:  
Crystal structure of ferric complexes of the yellow lupin leghemoglobin with
isoquinoline At 1.8 angstroms resolution (russian) [more info...]  
  
Chain information for 1gdi #2  
---  
Chain | Description | UniProt  
A | LEGHEMOGLOBIN (CARBONMONOXY) | LGB2_LUPLU 1-153  
  
Non-standard residues in 1gdi #2  
---  
CMO — carbon monoxide  
HEM — protoporphyrin IX containing Fe (HEME)  
  

> 1hbg

Unknown command: 1hbg  

> open 1hbg

Summary of feedback from opening 1hbg fetched from pdb  
---  
note | Fetching compressed mmCIF 1hbg from
http://files.rcsb.org/download/1hbg.cif  
  
1hbg title:  
Glycera dibranchiata hemoglobin. Structure and refinement At 1.5 angstroms
resolution [more info...]  
  
Chain information for 1hbg #3  
---  
Chain | Description | UniProt  
A | HEMOGLOBIN (CARBONMONOXY) | GLB1_GLYDI 1-147  
  
Non-standard residues in 1hbg #3  
---  
CMO — carbon monoxide  
HEM — protoporphyrin IX containing Fe (HEME)  
  

> preset "initial styles" "original look"

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> remove 2hyy

Unknown command: remove 2hyy  

> delete 2hyy

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete #1

> align help

Missing or invalid "atoms" argument: invalid atoms specifier  

> align #1 #2

Missing required "to_atoms" argument  

> align #1 toAtoms #2

Unequal number of atoms to pair, 0 and 1375  

> align #1 & :CA toAtoms #2 & :CA

No atoms paired for alignment  

> matchmaker #2 #3

Missing required "to" argument  

> matchmaker #2 to #3

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 1hbg, chain A (#3) with 1gdi, chain A (#2), sequence alignment
score = 226.6  
RMSD between 57 pruned atom pairs is 1.008 angstroms; (across all 137 pairs:
3.472)  
  

> remove solvent

Unknown command: remove solvent  

> delete solvent

> delete ligand

> delete ~protein

> matchmaker #2 to #3

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 1hbg, chain A (#3) with 1gdi, chain A (#2), sequence alignment
score = 226.6  
RMSD between 57 pruned atom pairs is 1.008 angstroms; (across all 137 pairs:
3.472)  
  

> matchmaker #2 & /CA to #3 & /CA

No 'to' model specified  

> matchmaker #2 & @CA to #3 & @CA

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 1hbg, chain A (#3) with 1gdi, chain A (#2), sequence alignment
score = 226.6  
RMSD between 57 pruned atom pairs is 1.008 angstroms; (across all 137 pairs:
3.472)  
  

> matchmaker #2 @CA to #3 @CA

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 1hbg, chain A (#3) with 1gdi, chain A (#2), sequence alignment
score = 226.6  
RMSD between 57 pruned atom pairs is 1.008 angstroms; (across all 137 pairs:
3.472)  
  

> delete all

> open 4bkj

4bkj title:  
Crystal structure of the human DDR1 kinase domain in complex with imatinib
[more info...]  
  
Chain information for 4bkj #1  
---  
Chain | Description | UniProt  
A B | EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1 | DDR1_HUMAN 601-913  
  
Non-standard residues in 4bkj #1  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-
pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571; imatinib)  
  
4bkj mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> delete /b

> delete solvent

> delete ~protein

> delete all

> open 4bkj

4bkj title:  
Crystal structure of the human DDR1 kinase domain in complex with imatinib
[more info...]  
  
Chain information for 4bkj #1  
---  
Chain | Description | UniProt  
A B | EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1 | DDR1_HUMAN 601-913  
  
Non-standard residues in 4bkj #1  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-
pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571; imatinib)  
  
4bkj mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> delete ~protein & ~ligand

> delete /b

> delete ~protein & ~ligand

> delete help

Missing or invalid "atoms" argument: invalid atoms specifier  

> help delete

> delete @edo

> delete :edo

> coulombic

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/A MET 600  
/A ARG 602  
/A GLU 618  
/A GLN 620  
/A LYS 646  
/A LYS 663  
/A LYS 671  
/A ARG 686  
/A GLU 705  
/A ASP 720  
/A ARG 798  
/A LYS 819  
/A GLU 855  
/A GLU 893  
/A GLN 900  
/A ARG 903  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 4bkj_A SES surface #1.2: minimum, -24.77, mean -2.66,
maximum 8.64  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hbonds

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A ARG 903 NE  

288 hydrogen bonds found  

> contacts

1803 contacts  

> mlp

Map values for surface "4bkj_A SES surface": minimum -27.15, mean -4.034,
maximum 23.56  
To also show corresponding color key, enter the above mlp command and add key
true  

> delete ~protein

> coulombic

Coulombic values for 4bkj_A SES surface #1.2: minimum, -24.77, mean -2.66,
maximum 8.64  
To also show corresponding color key, enter the above coulombic command and
add key true  

> delete ~protein

> mlp

Map values for surface "4bkj_A SES surface": minimum -27.15, mean -4.034,
maximum 23.56  
To also show corresponding color key, enter the above mlp command and add key
true  

> rainbow

> show cartoons

> hide surfaces

> delete contacts

Missing or invalid "atoms" argument: invalid atoms specifier  

> hide contacts

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> contacts remove

Expected a keyword  

> contacts reset

Expected a keyword  

> contacts clear

Expected a keyword  

> clear contacts

Unknown command: clear contacts  

> coulombic

Coulombic values for 4bkj_A SES surface #1.2: minimum, -24.77, mean -2.66,
maximum 8.64  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp

Map values for surface "4bkj_A SES surface": minimum -27.15, mean -4.034,
maximum 23.56  
To also show corresponding color key, enter the above mlp command and add key
true  

> delete all

> clear log

Unknown command: clear log  

> log clear

> open 4bkj

4bkj title:  
Crystal structure of the human DDR1 kinase domain in complex with imatinib
[more info...]  
  
Chain information for 4bkj #1  
---  
Chain | Description | UniProt  
A B | EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1 | DDR1_HUMAN 601-913  
  
Non-standard residues in 4bkj #1  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-
pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571; imatinib)  
  
4bkj mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> select /B:600-913

2334 atoms, 2388 bonds, 2 pseudobonds, 297 residues, 2 models selected  

> delete sel

> delete :edo

> delete solvent

> delete /b

> hide ligand

> log clear

> delete all

No models chosen for saving  

> open 1hmr

Summary of feedback from opening 1hmr fetched from pdb  
---  
notes | Fetching compressed mmCIF 1hmr from
http://files.rcsb.org/download/1hmr.cif  
Fetching CCD ELA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/ELA/ELA.cif  
  
1hmr title:  
1.4 angstroms structural studies on human muscle fatty acid binding protein:
binding interactions with three saturated and unsaturated C18 fatty acids
[more info...]  
  
Chain information for 1hmr #1  
---  
Chain | Description | UniProt  
A | MUSCLE FATTY ACID BINDING PROTEIN | FABPH_HUMAN 1-132  
  
Non-standard residues in 1hmr #1  
---  
ELA — 9-octadecenoic acid  
  

> delete solvent

> style spheres ligand

Expected a keyword  

> style sphere ligand

Expected a keyword  

> style sphere :ela

Expected a keyword  

> select :ela

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

> style sel sphere

Changed 20 atom styles  

> hide spheres

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> color green sel & @ca

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color green sel & @c?

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel & C salmon

> background white

Unknown command: background white  

> color background white

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> set bgColor white

> select clear

> addh

Summary of feedback from adding hydrogens to 1hmr #1  
---  
notes | Termini for 1hmr (#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A VAL 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A GLU 131  
124 hydrogen bonds  
/A GLU 131 is not terminus, removing H atom from 'C'  
1087 hydrogens added  
  

> color sel & C gray

> color :ela & C gray

> color protein brown

> color protein red

> color list

No custom colors.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> color protein saddle brown

> hide sticks

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide atoms

> show atoms

> hide atoms

> show :ela

> preset "overall look" "publication 2 (depth-cued)"

Using preset: Overall Look / Publication 2 (Depth-Cued)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes f
    lighting depthCue t

  

> save /home/marty/tmp/fabp.png width 1273 height 1010 supersample 3
> transparentBackground true

> save /home/marty/tmp/fabp.png width 1273 height 1010 supersample 4

> delete all

> load 1gdi 1hbg

Unknown command: load 1gdi 1hbg  

> load 1gdi,1hbg

Unknown command: load 1gdi,1hbg  

> load 1gdi

Unknown command: load 1gdi  

> open 1gdi 1hbg

1gdi title:  
Crystal structure of ferric complexes of the yellow lupin leghemoglobin with
isoquinoline At 1.8 angstroms resolution (russian) [more info...]  
  
Chain information for 1gdi #1  
---  
Chain | Description | UniProt  
A | LEGHEMOGLOBIN (CARBONMONOXY) | LGB2_LUPLU 1-153  
  
Non-standard residues in 1gdi #1  
---  
CMO — carbon monoxide  
HEM — protoporphyrin IX containing Fe (HEME)  
  
1hbg title:  
Glycera dibranchiata hemoglobin. Structure and refinement At 1.5 angstroms
resolution [more info...]  
  
Chain information for 1hbg #2  
---  
Chain | Description | UniProt  
A | HEMOGLOBIN (CARBONMONOXY) | GLB1_GLYDI 1-147  
  
Non-standard residues in 1hbg #2  
---  
CMO — carbon monoxide  
HEM — protoporphyrin IX containing Fe (HEME)  
  

> delete ~solvent

> open 1hmr

1hmr title:  
1.4 angstroms structural studies on human muscle fatty acid binding protein:
binding interactions with three saturated and unsaturated C18 fatty acids
[more info...]  
  
Chain information for 1hmr #3  
---  
Chain | Description | UniProt  
A | MUSCLE FATTY ACID BINDING PROTEIN | FABPH_HUMAN 1-132  
  
Non-standard residues in 1hmr #3  
---  
ELA — 9-octadecenoic acid  
  

> delete all

> open 1hmr

1hmr title:  
1.4 angstroms structural studies on human muscle fatty acid binding protein:
binding interactions with three saturated and unsaturated C18 fatty acids
[more info...]  
  
Chain information for 1hmr #1  
---  
Chain | Description | UniProt  
A | MUSCLE FATTY ACID BINDING PROTEIN | FABPH_HUMAN 1-132  
  
Non-standard residues in 1hmr #1  
---  
ELA — 9-octadecenoic acid  
  

> delete solvent

> hide sticks

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> style :ela spheres

Expected a keyword  

> style spheres :ela

Expected a keyword  

> addh

Summary of feedback from adding hydrogens to 1hmr #1  
---  
notes | Termini for 1hmr (#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A VAL 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A GLU 131  
124 hydrogen bonds  
/A GLU 131 is not terminus, removing H atom from 'C'  
1087 hydrogens added  
  

> style :ela sphere

Changed 55 atom styles  

> color :ela & C gray

> color protein saddlebrown bornw

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color protein saddle brown

> style protein cartoon

Expected a keyword  

> select protein

2082 atoms, 2097 bonds, 131 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> undo

> hide protein atoms

> delete all

> open 1gdi 1hbg

1gdi title:  
Crystal structure of ferric complexes of the yellow lupin leghemoglobin with
isoquinoline At 1.8 angstroms resolution (russian) [more info...]  
  
Chain information for 1gdi #1  
---  
Chain | Description | UniProt  
A | LEGHEMOGLOBIN (CARBONMONOXY) | LGB2_LUPLU 1-153  
  
Non-standard residues in 1gdi #1  
---  
CMO — carbon monoxide  
HEM — protoporphyrin IX containing Fe (HEME)  
  
1hbg title:  
Glycera dibranchiata hemoglobin. Structure and refinement At 1.5 angstroms
resolution [more info...]  
  
Chain information for 1hbg #2  
---  
Chain | Description | UniProt  
A | HEMOGLOBIN (CARBONMONOXY) | GLB1_GLYDI 1-147  
  
Non-standard residues in 1hbg #2  
---  
CMO — carbon monoxide  
HEM — protoporphyrin IX containing Fe (HEME)  
  

> delete ~protein

> hide protein atoms

> 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 1hbg, chain A (#2) with 1gdi, chain A (#1), sequence alignment
score = 226.6  
RMSD between 57 pruned atom pairs is 1.008 angstroms; (across all 137 pairs:
3.472)  
  

> delete all

> open 4bkj

4bkj title:  
Crystal structure of the human DDR1 kinase domain in complex with imatinib
[more info...]  
  
Chain information for 4bkj #1  
---  
Chain | Description | UniProt  
A B | EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1 | DDR1_HUMAN 601-913  
  
Non-standard residues in 4bkj #1  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-
pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571; imatinib)  
  
4bkj mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> delete /b

> delete ~protein

> ui tool show "Dock Prep"

> ui tool show "Model Loops"

No alignments chosen for modeling  

> select all

2316 atoms, 2370 bonds, 2 pseudobonds, 295 residues, 2 models selected  
No alignments chosen for modeling  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> ui tool show "Model Loops"

> modeller refine 1/A:1:internal-missing numModels 5 fast false
> adjacentFlexible 1 protocol standard

Webservices job id: FSNV39UTJ80BIXAZ  
Modeller job (ID FSNV39UTJ80BIXAZ) finished  
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 4bkj, chain A (#1) with chain_A, chain A (#), sequence alignment
score = 1618.3  
RMSD between 295 pruned atom pairs is 0.046 angstroms; (across all 295 pairs:
0.046)  
  


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

Log:
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 525.147.05
OpenGL renderer: NVIDIA RTX A5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=cinnamon
XDG_SESSION_DESKTOP=cinnamon
XDG_CURRENT_DESKTOP=X-Cinnamon
DISPLAY=:0
Manufacturer: LENOVO
Model: 30E1CTO1WW
OS: Linux Mint 21.2 Victoria
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 AMD Ryzen Threadripper PRO 3945WX 12-Cores
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi       6.0Gi        32Gi       179Mi        23Gi        55Gi
	Swap:          4.7Gi       1.0Mi       4.7Gi

Graphics:
	61:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102GL [RTX A5000] [10de:2231] (rev a1)	
	Subsystem: Lenovo GA102GL [RTX A5000] [17aa:147e]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    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: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    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: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    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: 1.1.3
    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: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    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: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    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: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by pett, 22 months ago

Cc: Tom Goddard added
Component: Unassigned → Structure Prediction
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in garbage collection while processing modeller results

comment:2 by pett, 22 months ago

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

Was in "a1, a2 = b.atoms", specifically atomic.ctypes_support.atom_pair(p) when the garbage collection occurred. This crash and the coulombic crashes share a theme in that they were performing operations on atomic structures that had not yet been added to the session (or would never be), though I don't have a good idea how that would be relevant.

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