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#5402 closed defect (fixed)

ctypes access violation

Reported by:	amith.rangarajan@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Core	Version:
Keywords:		Cc:	Tom Goddard
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.22471
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
when sel ligand& C --- it throws this error.
same error occurs if i sel the ligands with model numbers also.
I am not able to share the files without permission from my collaborators.

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  

> open C:/Users/arangarajan/Documents/0-workdir/101121/6GIL-
> INITIAL_tophits_with_sitepoints.mae

Chain information for 6GIL-INITIAL_tophits_with_sitepoints.mae  
---  
Chain | Description  
1.1/A 1.1/B | No description available  
1.1/D | No description available  
  
Opened 6GIL-INITIAL_tophits_with_sitepoints.mae containing 3 structures (5939
atoms, 6009 bonds)  

> hide #1.3.1 models

> hide #1.3.2 models

> show #1.3.2 models

> hide #1.3.3 models

> show #1.3.3 models

> hide #1.3.5 models

> show #1.3.5 models

> hide #1.3.6 models

> show #1.3.6 models

> hide #1.3.7 models

> show #1.3.7 models

> hide #1.3.8 models

> close session

> open
> C:/Users/arangarajan/Documents/0-workdir/101121/4ATK_tophits_with_sitepoints.mae

Chain information for 4ATK_tophits_with_sitepoints.mae  
---  
Chain | Description  
1.2/A 1.2/B | No description available  
1.2/C 1.2/D | No description available  
  
Opened 4ATK_tophits_with_sitepoints.mae containing 3 structures (3080 atoms,
3113 bonds)  

> hide #1.1 models

> hide #!1.3 models

> show #!1.3 models

> hide #!1.3 models

> hbonds #1.3.* restrict (#1.2 & /D,/C)

Invalid "restrict" argument: Expected one of 'any', 'both', or 'cross' or an
atoms specifier  

> hbonds #1.3.* restrict (#1.2 & /C,D)

8 hydrogen bonds found  

> show #!1.3 models

> hide #1.3.2 models

> hide #1.3.3 models

> show #1.3.3 models

> hide #1.3.3 models

> hide #1.3.4 models

> rename #2 DNA-HBONDS

> hide #2 models

> show #2 models

> hbonds #1.3.* restrict (#1.2 & /A,B)

8 hydrogen bonds found  

> hide #3 models

> show #3 models

> hide #3 models

> hide #2 models

> show #3 models

> hide #1.3.1 models

> show #1.3.1 models

> hide #1.3.1 models

> show #1.3.2 models

> show #1.3.3 models

> show #1.3.4 models

> show #2 models

> hide #2 models

> hide #3 models

> show #2 models

> hide #2 models

> hbonds #1.3.* restrict (#1.2 /A,B)

8 hydrogen bonds found  

> show #2 models

> show #3 models

> hide #3 models

> show #3 models

> delete #2,#3

Missing or invalid "atoms" argument: only initial part "#2" of atom specifier
valid  

> delete #2,#3

Missing or invalid "atoms" argument: only initial part "#2" of atom specifier
valid  

> select #2

8 pseudobonds, 1 model selected  

> delete sel

> close session

> open
> C:/Users/arangarajan/Documents/0-workdir/101121/4ATK_tophits_with_sitepoints.mae

Chain information for 4ATK_tophits_with_sitepoints.mae  
---  
Chain | Description  
1.2/A 1.2/B | No description available  
1.2/C 1.2/D | No description available  
  
Opened 4ATK_tophits_with_sitepoints.mae containing 3 structures (3080 atoms,
3113 bonds)  

> hide #1.1 models

> hide #1.2 models

> hide #!1.3 models

> show #!1.3 models

> hide #!1.3 models

> show #1.1 models

> hide #1.1 models

> show #1.2 models

> set bgColor white

> set bgColor white

> lighting soft

> graphics silhouettes true width 1

> lighting soft

> lighting soft

> lighting soft

> lighting soft

> color bychain

> select ~protein

1184 atoms, 1207 bonds, 37 residues, 8 models selected  

> color sel pale green

> ~select

Nothing selected  

> nucleotides slab

> show #1.1 models

> show #!1.3 models

> hide #!1.3 models

> hide #1.2 models

> show #1.2 models

> show #!1.3 models

> hide #!1.3 models

> show #!1.3 models

> select #1.3.#

Expected an objects specifier or a keyword  

> select #1.3.*

111 atoms, 115 bonds, 4 residues, 4 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 888, in parse  
return anno.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 #1.3.*

111 atoms, 115 bonds, 4 residues, 4 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.  
  
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.  
  

> color byhetero

> hide #1.2 models

> show #1.2 models

> hide #1.1 models

> select ligand

Nothing selected  

> select ligand & c

Expected a keyword  
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.  
  
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 471.35
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 Insider Preview (Build 22471)
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
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    Sphinx: 3.2.1
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    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
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    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
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    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

Change History (7)

comment:1 by Eric Pettersen, 4 years ago

Component:	Unassigned → Core
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → ctypes access violation

comment:2 by Eric Pettersen, 4 years ago

Status:	accepted → feedback

Hi Amith,

If you open that structure again in a new ChimeraX, does that error continue to happen? Is it only with that structure, or any structure? Can you try opening 2gbp and see if you get that error (I don't, in the 1.2.5 release)?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by Eric Pettersen, 4 years ago

Cc:	Tom Goddard added

in reply to: 4 ; follow-up: 4 comment:4 by Amith.Rangarajan@…, 4 years ago

Dear Eric,

Thanks for the response.

I opened 2gbp  and ran the same command( sel ligand & C) and it works fine.

The previous file that gave me the error was a schrodinger output maestro poseviewer file. i opened it with chimerax using the add on avaialble in the tool shed.

I have used chimera x to open maestro files successfully in the past and i am not sure why i got that error.

thanks
amith
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, October 14, 2021 10:57 AM
Cc: Rangarajan, Amith <Amith.Rangarajan@ucsf.edu>; PETTERSEN, ERIC <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #5402: ctypes access violation

#5402: ctypes access violation
-----------------------------------------+----------------------------
          Reporter:  amith.rangarajan@…  |      Owner:  Eric Pettersen
              Type:  defect              |     Status:  feedback
          Priority:  normal              |  Milestone:
         Component:  Core                |    Version:
        Resolution:                      |   Keywords:
        Blocked By:                      |   Blocking:
Notify when closed:                      |   Platform:  all
           Project:  ChimeraX            |
-----------------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => feedback


Comment:

 Hi Amith,
         If you open that structure again in a new ChimeraX, does that
 error continue to happen?  Is it only with that structure, or any
 structure?  Can you try opening 2gbp and see if you get that error (I
 don't, in the 1.2.5 release)?

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5402#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:5 by Tom Goddard, 4 years ago

The code raising the error is looking at atom element numbers. I recall several months ago an error involving element numbers read from a mol2 file that were negative. Maybe this is the same issue, negative element numbers in the maestro file. We fixed that in the daily build, so might be worth trying that.

Also I believe the maestro file reader has been included in ChimeraX 1.2.5 and more recent versions so you don't need the Toolshed plugin.

in reply to: 6 ; follow-up: 6 comment:6 by Amith.Rangarajan@…, 4 years ago

Dear Eric,

Thanks for the response.

I would try the daily build.

best
amith
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, October 14, 2021 12:23 PM
Cc: Rangarajan, Amith <Amith.Rangarajan@ucsf.edu>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; PETTERSEN, ERIC <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #5402: ctypes access violation

#5402: ctypes access violation
-----------------------------------------+----------------------------
          Reporter:  amith.rangarajan@…  |      Owner:  Eric Pettersen
              Type:  defect              |     Status:  feedback
          Priority:  normal              |  Milestone:
         Component:  Core                |    Version:
        Resolution:                      |   Keywords:
        Blocked By:                      |   Blocking:
Notify when closed:                      |   Platform:  all
           Project:  ChimeraX            |
-----------------------------------------+----------------------------

Comment (by Tom Goddard):

 The code raising the error is looking at atom element numbers.  I recall
 several months ago an error involving element numbers read from a mol2
 file that were negative.  Maybe this is the same issue, negative element
 numbers in the maestro file.  We fixed that in the daily build, so might
 be worth trying that.

 Also I believe the maestro file reader has been included in ChimeraX 1.2.5
 and more recent versions so you don't need the Toolshed plugin.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5402#comment:5>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:7 by Eric Pettersen, 4 years ago

Resolution:	→ fixed
Status:	feedback → closed

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