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#7007 closed defect (duplicate)

Long atom spec crashes ChimeraX

Reported by:	wenxiang.cao@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Command Line	Version:
Keywords:		Cc:	chimera-programmers
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.22000
ChimeraX Version: 1.5.dev202205200152 (2022-05-20 01:52:55 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: stack overflow

Current thread 0x0000624c (most recent call first):
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\ast.py", line 129 in __hasattribute__
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\ast.py", line 138 in _safekey
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\ast.py", line 71 in set
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\ast.py", line 106 in __setitem__
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\ast.py", line 61 in upairs
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\ast.py", line 67 in update
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\ast.py", line 19 in __init__
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\ast.py", line 90 in copy
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 642 in _try
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\contextlib.py", line 119 in __enter__
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 679 in _choice
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\contextlib.py", line 119 in __enter__
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 688 in _optional
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\contextlib.py", line 119 in __enter__
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 427 in _part_range_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 409 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 458 in _call
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
  File "D:\program\ChimeraX 1.5.dev202205200152\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
  ...
===== Log before crash start =====
> open "F:/large files/Glen Hocky 22-05-12/Cofilactin-JunFan-periodic-
> nowater.pdb"

Chain information for Cofilactin-JunFan-periodic-nowater.pdb #1  
---  
Chain | Description  
A | No description available  
  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> select /A:2-166

56518 atoms, 57057 bonds, 3630 residues, 1 model selected  

> select /A:2-166

56518 atoms, 57057 bonds, 3630 residues, 1 model selected  

> select add #1

93970 atoms, 94237 bonds, 22 pseudobonds, 6608 residues, 3 models selected  

> select clear

> hide solvent

> select solvent

378 atoms, 378 residues, 1 model selected  

> hide sel

> select water

Expected an objects specifier or a keyword  

> select ions

279 atoms, 279 residues, 1 model selected  

> hide sel

> show sel

> show solvent

> select MG

Expected an objects specifier or a keyword  

> select :Mg

11 atoms, 11 residues, 1 model selected  

> select clear

> select :Mg

11 atoms, 11 residues, 1 model selected  

> select clear

> select :cla

268 atoms, 268 residues, 1 model selected  

> help help:user

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> select :cla

268 atoms, 268 residues, 1 model selected  

> hide sel

> hide solvent

> select :41-52

3928 atoms, 3894 bonds, 276 residues, 1 model selected  

> select :6-375

91934 atoms, 92466 bonds, 6211 residues, 1 model selected  

> select clear

> select :6-10

1402 atoms, 1375 bonds, 115 residues, 1 model selected  

> select :1-10

2727 atoms, 2695 bonds, 219 residues, 1 model selected  
Alignment identifier is 1/A  


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

Log:
UCSF ChimeraX version: 1.5.dev202205200152 (2022-05-20)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.14822 Core Profile Forward-Compatible Context 20.50.30.05 27.20.15030.5001
OpenGL renderer: AMD Radeon(TM) RX Vega 10 Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: en_US.cp936
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: HP
Model: HP Laptop 17-ca1xxx
OS: Microsoft Windows 11 Home (Build 22000)
Memory: 14,942,511,104
MaxProcessMemory: 137,438,953,344
CPU: 8 AMD Ryzen 7 3700U with Radeon Vega Mobile Gfx  
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.2
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.5.dev202205200152
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.20
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 23.0.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (7)

comment:1 by Eric Pettersen, 3 years ago

Cc:	chimera-programmers added
Component:	Unassigned → Command Line
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Long atom spec crashes ChimeraX

comment:2 by Eric Pettersen, 3 years ago

Status:	accepted → feedback

Hi Wenxiang,

Thanks for reporting this problem. Due to some limitations in ChimeraX's atom-spec parser, this crash can happen when executing a command with a long atom-spec argument. Do you remember what you were doing specifically when this crash occurred?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to: 3 ; follow-up: 3 comment:3 by wenxiang.cao@…, 3 years ago

Hi, Eric:

Thank you for following up my crash report. I don’t remember the exact command when the crashing happened. I was viewing a PDB structure with 22 molecules in it and with solvent, all in one chain. It is a huge structure. I was just viewing it in different ways and didn’t do any other things particular.

Sorry I am not able to provide more information.

Thank you very much!
Wenxiang



From: ChimeraX<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, June 3, 2022 12:18 PM
Cc: chimera-programmers@cgl.ucsf.edu<mailto:chimera-programmers@cgl.ucsf.edu>; pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>; Cao, Wenxiang<mailto:wenxiang.cao@yale.edu>
Subject: Re: [ChimeraX] #7007: Long atom spec crashes ChimeraX

#7007: Long atom spec crashes ChimeraX
-------------------------------------+----------------------
          Reporter:  wenxiang.cao@…  |      Owner:  pett
              Type:  defect          |     Status:  feedback
          Priority:  normal          |  Milestone:
         Component:  Command Line    |    Version:
        Resolution:                  |   Keywords:
        Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
           Project:  ChimeraX        |
-------------------------------------+----------------------
Changes (by pett):

 * status:  accepted => feedback


Comment:

 Hi Wenxiang,
         Thanks for reporting this problem.  Due to some limitations in
 ChimeraX's atom-spec parser, this crash can happen when executing a
 command with a long atom-spec argument.  Do you remember what you were
 doing specifically when this crash occurred?

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F7007%23comment%3A2&amp;data=05%7C01%7Cwenxiang.cao%40yale.edu%7C87383eff1907410a67b908da457cac36%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637898699020596789%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;sdata=KsSkSdp7lMNNd9Yz%2FHfKQaBdtBdzhArxB%2FHBR5UbIyU%3D&amp;reserved=0>
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comment:4 by Eric Pettersen, 3 years ago

Hi Wenxiang,

No worries, we can easily reproduce this problem ourselves. Was just wondering what you were doing because there are some mitigation strategies we can use to make the problem less likely to occur if we know where the long atom spec came from.

--Eric

in reply to: 5 ; follow-up: 5 comment:5 by wenxiang.cao@…, 3 years ago

Hi, Eric:

The pdb file was used in MD simulation, and may have something extra for the simulation. I can send you the pdb if you want. For example, it has HIC, HSE, HSD and other different histidine states, which chimeraX doesn’t recognize and uses “X” instead of “H” for sequencing.

Thanks!

Wenxiang



From: ChimeraX<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, June 6, 2022 2:42 PM
Cc: chimera-programmers@cgl.ucsf.edu<mailto:chimera-programmers@cgl.ucsf.edu>; pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>; Cao, Wenxiang<mailto:wenxiang.cao@yale.edu>
Subject: Re: [ChimeraX] #7007: Long atom spec crashes ChimeraX

#7007: Long atom spec crashes ChimeraX
-------------------------------------+----------------------
          Reporter:  wenxiang.cao@…  |      Owner:  pett
              Type:  defect          |     Status:  feedback
          Priority:  normal          |  Milestone:
         Component:  Command Line    |    Version:
        Resolution:                  |   Keywords:
        Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
           Project:  ChimeraX        |
-------------------------------------+----------------------

Comment (by pett):

 Hi Wenxiang,
         No worries, we can easily reproduce this problem ourselves.  Was
 just wondering what you were doing because there are some mitigation
 strategies we can use to make the problem less likely to occur if we know
 where the long atom spec came from.

 --Eric

--
Ticket URL: <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F7007%23comment%3A4&amp;data=05%7C01%7Cwenxiang.cao%40yale.edu%7Ced78e3bacf5c46010d4108da47ec52db%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637901377579297739%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;sdata=plD8egpfcPEhNV1zUnukpI%2BUGT3iFOY0FttLPUQUjSM%3D&amp;reserved=0>
ChimeraX <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&amp;data=05%7C01%7Cwenxiang.cao%40yale.edu%7Ced78e3bacf5c46010d4108da47ec52db%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637901377579297739%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;sdata=evoMDgLwSYryGXCqCApV1QCcRL7%2FF4EPulvW%2BLpFFqE%3D&amp;reserved=0>
ChimeraX Issue Tracker

comment:6 by Eric Pettersen, 3 years ago

Hi Wenxaing,

I don't need the PDB file. The crash isn't really related to the contents of the PDB file (other than it's hard to make a long atom spec from a small structure). BTW, if those histidines used the Amber-style protonation nomenclature (HIP, HIE, HID) then ChimeraX would recognize them as histidines.

--Eric

comment:7 by Eric Pettersen, 3 years ago

Resolution:	→ duplicate
Status:	feedback → closed

Adding reporter to cc list for main version of this ticket

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