"Access violation" filtering Collection

[amith.rangarajan@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22000
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here) I tried to select carbon atoms of the ligand in order to color them using sel command 
sel ligand & C .


Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> cd C:\Users\arangarajan\Documents\0-workdir\082021

Current working directory is: C:\Users\arangarajan\Documents\0-workdir\082021  

> open C:/Users/arangarajan/Documents/0-workdir/082021/2p0w-prepped.pdb

2p0w-prepped.pdb title:  
Human histone acetyltransferase 1 (HAT1) [more info...]  
  
Chain information for 2p0w-prepped.pdb #1  
---  
Chain | Description  
A | No description available  
P | No description available  
  
Non-standard residues in 2p0w-prepped.pdb #1  
---  
ACO — acetyl coenzyme *A  
  

> open
> C:/Users/arangarajan/Documents/0-workdir/082021/sitemap_1/sitemap_1_out.maegz

Chain information for sitemap_1_out.maegz  
---  
Chain | Description  
2.6/A | No description available  
2.6/P | No description available  
  
Opened sitemap_1_out.maegz containing 6 structures (5768 atoms, 5621 bonds)  

> hide #!2 models

> hide #1 models

> show #!2 models

> set bgColor white

> windowsize 600 500

> lighting soft

> graphics silhouettes true width 1

> color /A cornflower blue

> color /p light salmon

> transparency 95 target s

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 904, in find_matches  
f(session, models, results)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\selectors.py", line 26, in <lambda>  
reg(e.name, lambda ses, models, results, sym=e.name: _element_selector(sym,
models, results), logger, desc="%s (element)" % e.name)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\selectors.py", line 49, in _element_selector  
atoms = m.atoms.filter(m.atoms.element_names == symbol)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
OSError: exception: access violation reading 0xFFFFFFFFFFFFFFFF  
  
Error executing selector 'C':  
OSError: exception: access violation reading 0xFFFFFFFFFFFFFFFF  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 904, in find_matches  
f(session, models, results)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\selectors.py", line 26, in <lambda>  
reg(e.name, lambda ses, models, results, sym=e.name: _element_selector(sym,
models, results), logger, desc="%s (element)" % e.name)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\selectors.py", line 49, in _element_selector  
atoms = m.atoms.filter(m.atoms.element_names == symbol)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
OSError: exception: access violation reading 0xFFFFFFFFFFFFFFFF  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 280, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2812, in run  
prev_annos = self._process_positional_arguments()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2588, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2447, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 1272, in parse  
objects = aspec.evaluate(session)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 1055, in evaluate  
right_results = self._right_spec.evaluate(  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 1042, in evaluate  
results = self._left_spec.evaluate(  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 964, in evaluate  
return self.find_matches(session, models, results, ordered)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 967, in find_matches  
self._specifier.find_matches(session, models, results, ordered)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 908, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  
grako.exceptions.FailedSemantics: error evaluating selector C  
  
grako.exceptions.FailedSemantics: error evaluating selector C  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 908, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  
  
See log for complete Python traceback.  
  

> select ligand

170 atoms, 174 bonds, 2 residues, 2 models selected  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 904, in find_matches  
f(session, models, results)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\selectors.py", line 26, in <lambda>  
reg(e.name, lambda ses, models, results, sym=e.name: _element_selector(sym,
models, results), logger, desc="%s (element)" % e.name)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\selectors.py", line 49, in _element_selector  
atoms = m.atoms.filter(m.atoms.element_names == symbol)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
OSError: exception: access violation reading 0xFFFFFFFFFFFFFFFF  
  
Error executing selector 'C':  
OSError: exception: access violation reading 0xFFFFFFFFFFFFFFFF  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 904, in find_matches  
f(session, models, results)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\selectors.py", line 26, in <lambda>  
reg(e.name, lambda ses, models, results, sym=e.name: _element_selector(sym,
models, results), logger, desc="%s (element)" % e.name)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\selectors.py", line 49, in _element_selector  
atoms = m.atoms.filter(m.atoms.element_names == symbol)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
OSError: exception: access violation reading 0xFFFFFFFFFFFFFFFF  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 280, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2812, in run  
prev_annos = self._process_positional_arguments()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2588, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2447, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 1272, in parse  
objects = aspec.evaluate(session)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 1055, in evaluate  
right_results = self._right_spec.evaluate(  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 1042, in evaluate  
results = self._left_spec.evaluate(  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 964, in evaluate  
return self.find_matches(session, models, results, ordered)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 967, in find_matches  
self._specifier.find_matches(session, models, results, ordered)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 908, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  
grako.exceptions.FailedSemantics: error evaluating selector C  
  
grako.exceptions.FailedSemantics: error evaluating selector C  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 908, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  
  
See log for complete Python traceback.  
  

> select ligand & "C"

Expected a keyword  

> select ligand & @C

2 atoms, 2 residues, 2 models selected  

> select :ACO @C

1 atom, 1 residue, 1 model selected  

> select :ACO & @C

1 atom, 1 residue, 1 model selected  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 904, in find_matches  
f(session, models, results)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\selectors.py", line 26, in <lambda>  
reg(e.name, lambda ses, models, results, sym=e.name: _element_selector(sym,
models, results), logger, desc="%s (element)" % e.name)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\selectors.py", line 49, in _element_selector  
atoms = m.atoms.filter(m.atoms.element_names == symbol)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
OSError: exception: access violation reading 0xFFFFFFFFFFFFFFFF  
  
Error executing selector 'C':  
OSError: exception: access violation reading 0xFFFFFFFFFFFFFFFF  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 904, in find_matches  
f(session, models, results)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\selectors.py", line 26, in <lambda>  
reg(e.name, lambda ses, models, results, sym=e.name: _element_selector(sym,
models, results), logger, desc="%s (element)" % e.name)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\selectors.py", line 49, in _element_selector  
atoms = m.atoms.filter(m.atoms.element_names == symbol)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
OSError: exception: access violation reading 0xFFFFFFFFFFFFFFFF  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 280, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2812, in run  
prev_annos = self._process_positional_arguments()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2588, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2447, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 1272, in parse  
objects = aspec.evaluate(session)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 1055, in evaluate  
right_results = self._right_spec.evaluate(  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 1042, in evaluate  
results = self._left_spec.evaluate(  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 964, in evaluate  
return self.find_matches(session, models, results, ordered)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 967, in find_matches  
self._specifier.find_matches(session, models, results, ordered)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 908, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  
grako.exceptions.FailedSemantics: error evaluating selector C  
  
grako.exceptions.FailedSemantics: error evaluating selector C  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 908, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  
  
See log for complete Python traceback.  
  

> select :ACO & @C

1 atom, 1 residue, 1 model selected  

> select :ACO

85 atoms, 87 bonds, 1 residue, 1 model selected  

> select :401

170 atoms, 174 bonds, 2 residues, 2 models selected  

> select :401 & @C

2 atoms, 2 residues, 2 models selected  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 904, in find_matches  
f(session, models, results)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\selectors.py", line 26, in <lambda>  
reg(e.name, lambda ses, models, results, sym=e.name: _element_selector(sym,
models, results), logger, desc="%s (element)" % e.name)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\selectors.py", line 49, in _element_selector  
atoms = m.atoms.filter(m.atoms.element_names == symbol)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
OSError: exception: access violation reading 0xFFFFFFFFFFFFFFFF  
  
Error executing selector 'C':  
OSError: exception: access violation reading 0xFFFFFFFFFFFFFFFF  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 904, in find_matches  
f(session, models, results)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\selectors.py", line 26, in <lambda>  
reg(e.name, lambda ses, models, results, sym=e.name: _element_selector(sym,
models, results), logger, desc="%s (element)" % e.name)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\selectors.py", line 49, in _element_selector  
atoms = m.atoms.filter(m.atoms.element_names == symbol)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
OSError: exception: access violation reading 0xFFFFFFFFFFFFFFFF  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 280, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2812, in run  
prev_annos = self._process_positional_arguments()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2588, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2447, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 1272, in parse  
objects = aspec.evaluate(session)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 1055, in evaluate  
right_results = self._right_spec.evaluate(  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 1042, in evaluate  
results = self._left_spec.evaluate(  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 964, in evaluate  
return self.find_matches(session, models, results, ordered)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 967, in find_matches  
self._specifier.find_matches(session, models, results, ordered)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 908, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  
grako.exceptions.FailedSemantics: error evaluating selector C  
  
grako.exceptions.FailedSemantics: error evaluating selector C  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\atomspec.py", line 908, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 470.76
OpenGL renderer: NVIDIA GeForce GTX 1650 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: XPS 15 9500
OS: Microsoft Windows 11 Pro (Build 22000)
Memory: 16,912,158,720
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-10875H CPU @ 2.30GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

[Tom Goddard]

I see you are using Windows-10-10.0.22000 which I think is a Windows 11 preview build. That is quite possibly the cause of this ChimeraX error. We have not tested on Windows 11 previews. The error is happening in the Python numpy module which is very widely used and it is hard to see how it could be the problem.

This ChimeraX bug is a memory access error (bad pointer) when trying to handle the atom specifier C. I tried reproducing it using PDB 2p0w in old pdb format executing all the same commands as shown in the log in this report using ChimeraX 1.2.5 on Windows 10 build 19041 (not Windows 11 preview) and it did not give any error. Possibly we could debug it if we had the actual files used

C:/Users/arangarajan/Documents/0-workdir/082021/2p0w-prepped.pdb

C:/Users/arangarajan/Documents/0-workdir/082021/sitemap_1/sitemap_1_out.maegz

Does the error happen again if you open these two files and try "select ligand & C"? If it does if you could email me (goddard@…) the files I will keep them private.

[Tom Goddard]

Fixed.

The maestro file contained atoms with element number -2. This did not cause a delayed crash when an operation that uses the element number is done like "select ligand & C" where it is looking for carbon as element number 6. I am not sure what it means that the maestro file has a negative atomic number, but I changed our reader to use hydrogen for those atoms. The same file crashed on Mac in the same way.

Eric, this took a few hours to debug causing a crash long after the model was opened. Could you put some sanity check into Element.get_element(atomic_number) so it raises an error for invalid atomic numbers? I would put this in but the code is cythonized and I'd rather not tamper with it since I have never used Cython.

[Eric Pettersen]

Okay it's in there. Put the check in the C++ layer, but Cython swallows the error thrown there, so also have to check in the Cython layer explicitly.

[goddard@…]

Thanks!  You can close the ticket.  I put a check in the Maestro reader so it will replace <= 0 atomic numbers with 1.