id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5402 ctypes access violation amith.rangarajan@… Eric Pettersen "{{{ 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 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 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 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 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 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 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 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 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 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 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 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 }}} " defect closed normal Core fixed Tom Goddard all ChimeraX