id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3049 OpenMM coordinate update: RuntimeError: Release Object didny1@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 0.91 (2019-10-05) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.91 (2019-10-05) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open F:/cryoEM/UMOD/umod_fixedseq_cistem_172-coot-1.pdb Chain information for umod_fixedseq_cistem_172-coot-1.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available > open F:/cryoEM/UMOD/denmod_map.ccp4 Opened denmod_map.ccp4, grid size 133,77,185, pixel 1.45, shown at level 0.235, step 1, values float32 > toolshed show ISOLDE > set selectionWidth 4 Chain information for umod_fixedseq_cistem_172-coot-1.pdb --- Chain | Description 1.3/A | No description available 1.3/B | No description available 1.3/C | No description available Done loading forcefield > select clear > select clear Expected an objects specifier or a keyword > select #1.3.2 1 model selected > select #1.3.2 1 model selected > select #1.3 4046 atoms, 4137 bonds, 1 pseudobond, 6 models selected Bad residue number: match Adding hydrogens Summary of feedback from adding hydrogens to umod_fixedseq_cistem_172-coot-1.pdb #1.3 --- notes | No usable SEQRES records for umod_fixedseq_cistem_172-coot-1.pdb (#1.3) chain A; guessing termini instead No usable SEQRES records for umod_fixedseq_cistem_172-coot-1.pdb (#1.3) chain B; guessing termini instead No usable SEQRES records for umod_fixedseq_cistem_172-coot-1.pdb (#1.3) chain C; guessing termini instead Chain-initial residues that are actual N termini: /A LEU 329, /B VAL 450, /C ALA 326 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A GLY 584, /B GLY 584, /C ALA 445 246 hydrogen bonds /A GLY 584 is not terminus, removing H atom from 'C' /B GLY 584 is not terminus, removing H atom from 'C' /C ALA 445 is not terminus, removing H atom from 'C' 3938 hydrogens added Bad residue number: match Adding hydrogens Summary of feedback from adding hydrogens to umod_fixedseq_cistem_172-coot-1.pdb #1.3 --- notes | No usable SEQRES records for umod_fixedseq_cistem_172-coot-1.pdb (#1.3) chain A; guessing termini instead No usable SEQRES records for umod_fixedseq_cistem_172-coot-1.pdb (#1.3) chain B; guessing termini instead No usable SEQRES records for umod_fixedseq_cistem_172-coot-1.pdb (#1.3) chain C; guessing termini instead Chain-initial residues that are actual N termini: /A LEU 329, /B VAL 450, /C ALA 326 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A GLY 584, /B GLY 584, /C ALA 445 226 hydrogen bonds /A GLY 584 is not terminus, removing H atom from 'C' /B GLY 584 is not terminus, removing H atom from 'C' /C ALA 445 is not terminus, removing H atom from 'C' 0 hydrogens added Bad residue number: match Adding hydrogens Summary of feedback from adding hydrogens to umod_fixedseq_cistem_172-coot-1.pdb #1.3 --- notes | No usable SEQRES records for umod_fixedseq_cistem_172-coot-1.pdb (#1.3) chain A; guessing termini instead No usable SEQRES records for umod_fixedseq_cistem_172-coot-1.pdb (#1.3) chain B; guessing termini instead No usable SEQRES records for umod_fixedseq_cistem_172-coot-1.pdb (#1.3) chain C; guessing termini instead Chain-initial residues that are actual N termini: /A LEU 329, /B VAL 450, /C ALA 326 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A GLY 584, /B GLY 584, /C ALA 445 226 hydrogen bonds /A GLY 584 is not terminus, removing H atom from 'C' /B GLY 584 is not terminus, removing H atom from 'C' /C ALA 445 is not terminus, removing H atom from 'C' 0 hydrogens added Bad residue number: match Adding hydrogens Summary of feedback from adding hydrogens to umod_fixedseq_cistem_172-coot-1.pdb #1.3 --- notes | No usable SEQRES records for umod_fixedseq_cistem_172-coot-1.pdb (#1.3) chain A; guessing termini instead No usable SEQRES records for umod_fixedseq_cistem_172-coot-1.pdb (#1.3) chain B; guessing termini instead No usable SEQRES records for umod_fixedseq_cistem_172-coot-1.pdb (#1.3) chain C; guessing termini instead Chain-initial residues that are actual N termini: /A LEU 329, /B VAL 450, /C ALA 326 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A GLY 584, /B GLY 584, /C ALA 445 226 hydrogen bonds /A GLY 584 is not terminus, removing H atom from 'C' /B GLY 584 is not terminus, removing H atom from 'C' /C ALA 445 is not terminus, removing H atom from 'C' 0 hydrogens added Bad residue number: match Excluding residue > toolshed show ISOLDE Expected an objects specifier or a keyword Expected an objects specifier or a keyword Expected an objects specifier or a keyword Unknown command: 15 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. > select #1.3.3 1 model selected > select #1.3.3 1 model selected Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. QWidget::repaint: Recursive repaint detected Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. > hide #!1.2 models > show #!1.2 models > style sel stick Changed 19 atom styles > style sel sphere Changed 19 atom styles > style sel stick Changed 19 atom styles > select #1 7984 atoms, 8075 bonds, 1 pseudobond, 18 models selected > select #1 7984 atoms, 8075 bonds, 1 pseudobond, 18 models selected > select clear > select #1.3 7984 atoms, 8075 bonds, 1 pseudobond, 11 models selected > style sel stick Changed 7984 atom styles > hide sel atoms > show sel cartoons > hide sel cartoons > show sel cartoons > show sel cartoons > hide sel cartoons > show sel atoms > hbonds sel 345 hydrogen bonds found > hbonds sel 338 hydrogen bonds found Not saving entity_poly_seq for non-authoritative sequences > select #1.3 7984 atoms, 8075 bonds, 339 pseudobonds, 12 models selected Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\delayed_reaction.py"", line 65, in callback self.ff(*self.ff_args) File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1591, in _update_coordinates_and_repeat self.atoms.coords = th.coords File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 301, in coords f(self._c_pointer, n, pointer(coords)) RuntimeError: Release Object Error processing trigger ""new frame"": RuntimeError: Release Object File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 301, in coords f(self._c_pointer, n, pointer(coords)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\isolde.py"", line 2652, in _start_sim_or_toggle_pause self.pause_sim_toggle() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\isolde.py"", line 2876, in pause_sim_toggle self.sim_manager.toggle_pause() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 701, in toggle_pause self.pause = not self.pause File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 680, in pause self.sim_handler.pause = flag File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1686, in pause self._resume() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1581, in _resume self._repeat_step() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1572, in _repeat_step th.thread_finished, self._update_coordinates_and_repeat, final_args) File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\delayed_reaction.py"", line 56, in delayed_reaction initiator_func(*initiator_args) File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 161, in step f(self._c_pointer, steps, self._smoothing) RuntimeError: Release Object RuntimeError: Release Object File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 161, in step f(self._c_pointer, steps, self._smoothing) See log for complete Python traceback. Not saving entity_poly_seq for non-authoritative sequences Expected an objects specifier or a keyword Traceback (most recent call last): File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\isolde.py"", line 2652, in _start_sim_or_toggle_pause self.pause_sim_toggle() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\isolde.py"", line 2876, in pause_sim_toggle self.sim_manager.toggle_pause() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 701, in toggle_pause self.pause = not self.pause File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 680, in pause self.sim_handler.pause = flag File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1686, in pause self._resume() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1581, in _resume self._repeat_step() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1572, in _repeat_step th.thread_finished, self._update_coordinates_and_repeat, final_args) File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\delayed_reaction.py"", line 56, in delayed_reaction initiator_func(*initiator_args) File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 161, in step f(self._c_pointer, steps, self._smoothing) RuntimeError: Release Object RuntimeError: Release Object File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 161, in step f(self._c_pointer, steps, self._smoothing) See log for complete Python traceback. > close session > open F:\cryoEM\UMOD\umod_fixedseq_cistem_172-isolde2.cif format mmCIF Summary of feedback from opening F:\cryoEM\UMOD\umod_fixedseq_cistem_172-isolde2.cif --- warnings | Unknown polymer entity '1' near line 135 Unknown polymer entity '2' near line 4075 Unable to infer polymer connectivity due to unspecified label_seq_id for residue ""NAG"" near line 6114 Unknown polymer entity '3' near line 6170 Atom H1 is not in the residue template for LEU #329 in chain A Atom H1 is not in the residue template for VAL #450 in chain B Atom H11 is not in the residue template for NAG #585 in chain B Atom H1 is not in the residue template for ALA #326 in chain C Atom HD2 is not in the residue template for ASN #396 in chain C Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. notes | Fetching CCD NAG from http://ligand- expo.rcsb.org/reports/N/NAG/NAG.cif Fetching CCD BMA from http://ligand-expo.rcsb.org/reports/B/BMA/BMA.cif Fetching CCD MAN from http://ligand-expo.rcsb.org/reports/M/MAN/MAN.cif Chain information for umod_fixedseq_cistem_172-isolde2.cif #1 --- Chain | Description A | ? B | ? C | ? > open F:/cryoEM/UMOD/denmod_map.ccp4 Opened denmod_map.ccp4, grid size 133,77,185, pixel 1.45, shown at level 0.235, step 1, values float32 > toolshed show ISOLDE > set selectionWidth 4 Chain information for umod_fixedseq_cistem_172-isolde2.cif --- Chain | Description 1.3/A | ? 1.3/B | ? 1.3/C | ? Done loading forcefield > select #1.3 7984 atoms, 8075 bonds, 338 pseudobonds, 6 models selected Bad residue number: match Adding hydrogens Summary of feedback from adding hydrogens to umod_fixedseq_cistem_172-isolde2.cif #1.3 --- notes | No usable SEQRES records for umod_fixedseq_cistem_172-isolde2.cif (#1.3) chain A; guessing termini instead No usable SEQRES records for umod_fixedseq_cistem_172-isolde2.cif (#1.3) chain B; guessing termini instead No usable SEQRES records for umod_fixedseq_cistem_172-isolde2.cif (#1.3) chain C; guessing termini instead Chain-initial residues that are actual N termini: /A LEU 329, /B VAL 450, /C ALA 326 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A GLY 584, /B GLY 584, /C ALA 445 332 hydrogen bonds /A GLY 584 is not terminus, removing H atom from 'C' /B GLY 584 is not terminus, removing H atom from 'C' /C ALA 445 is not terminus, removing H atom from 'C' 0 hydrogens added Bad residue number: match Adding hydrogens Summary of feedback from adding hydrogens to umod_fixedseq_cistem_172-isolde2.cif #1.3 --- notes | No usable SEQRES records for umod_fixedseq_cistem_172-isolde2.cif (#1.3) chain A; guessing termini instead No usable SEQRES records for umod_fixedseq_cistem_172-isolde2.cif (#1.3) chain B; guessing termini instead No usable SEQRES records for umod_fixedseq_cistem_172-isolde2.cif (#1.3) chain C; guessing termini instead Chain-initial residues that are actual N termini: /A LEU 329, /B VAL 450, /C ALA 326 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A GLY 584, /B GLY 584, /C ALA 445 332 hydrogen bonds /A GLY 584 is not terminus, removing H atom from 'C' /B GLY 584 is not terminus, removing H atom from 'C' /C ALA 445 is not terminus, removing H atom from 'C' 0 hydrogens added Bad residue number: match Adding hydrogens Summary of feedback from adding hydrogens to umod_fixedseq_cistem_172-isolde2.cif #1.3 --- notes | No usable SEQRES records for umod_fixedseq_cistem_172-isolde2.cif (#1.3) chain A; guessing termini instead No usable SEQRES records for umod_fixedseq_cistem_172-isolde2.cif (#1.3) chain B; guessing termini instead No usable SEQRES records for umod_fixedseq_cistem_172-isolde2.cif (#1.3) chain C; guessing termini instead Chain-initial residues that are actual N termini: /A LEU 329, /B VAL 450, /C ALA 326 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A GLY 584, /B GLY 584, /C ALA 445 332 hydrogen bonds /A GLY 584 is not terminus, removing H atom from 'C' /B GLY 584 is not terminus, removing H atom from 'C' /C ALA 445 is not terminus, removing H atom from 'C' 0 hydrogens added Bad residue number: match Adding hydrogens Summary of feedback from adding hydrogens to umod_fixedseq_cistem_172-isolde2.cif #1.3 --- notes | No usable SEQRES records for umod_fixedseq_cistem_172-isolde2.cif (#1.3) chain A; guessing termini instead No usable SEQRES records for umod_fixedseq_cistem_172-isolde2.cif (#1.3) chain B; guessing termini instead No usable SEQRES records for umod_fixedseq_cistem_172-isolde2.cif (#1.3) chain C; guessing termini instead Chain-initial residues that are actual N termini: /A LEU 329, /B VAL 450, /C ALA 326 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A GLY 584, /B GLY 584, /C ALA 445 332 hydrogen bonds /A GLY 584 is not terminus, removing H atom from 'C' /B GLY 584 is not terminus, removing H atom from 'C' /C ALA 445 is not terminus, removing H atom from 'C' 0 hydrogens added Bad residue number: match Adding hydrogens Summary of feedback from adding hydrogens to umod_fixedseq_cistem_172-isolde2.cif #1.3 --- notes | No usable SEQRES records for umod_fixedseq_cistem_172-isolde2.cif (#1.3) chain A; guessing termini instead No usable SEQRES records for umod_fixedseq_cistem_172-isolde2.cif (#1.3) chain B; guessing termini instead No usable SEQRES records for umod_fixedseq_cistem_172-isolde2.cif (#1.3) chain C; guessing termini instead Chain-initial residues that are actual N termini: /A LEU 329, /B VAL 450, /C ALA 326 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A GLY 584, /B GLY 584, /C ALA 445 332 hydrogen bonds /A GLY 584 is not terminus, removing H atom from 'C' /B GLY 584 is not terminus, removing H atom from 'C' /C ALA 445 is not terminus, removing H atom from 'C' 0 hydrogens added Bad residue number: match Adding hydrogens Summary of feedback from adding hydrogens to umod_fixedseq_cistem_172-isolde2.cif #1.3 --- notes | No usable SEQRES records for umod_fixedseq_cistem_172-isolde2.cif (#1.3) chain A; guessing termini instead No usable SEQRES records for umod_fixedseq_cistem_172-isolde2.cif (#1.3) chain B; guessing termini instead No usable SEQRES records for umod_fixedseq_cistem_172-isolde2.cif (#1.3) chain C; guessing termini instead Chain-initial residues that are actual N termini: /A LEU 329, /B VAL 450, /C ALA 326 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A GLY 584, /B GLY 584, /C ALA 445 332 hydrogen bonds /A GLY 584 is not terminus, removing H atom from 'C' /B GLY 584 is not terminus, removing H atom from 'C' /C ALA 445 is not terminus, removing H atom from 'C' 0 hydrogens added Bad residue number: match Excluding residue Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\delayed_reaction.py"", line 65, in callback self.ff(*self.ff_args) File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1591, in _update_coordinates_and_repeat self.atoms.coords = th.coords File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 301, in coords f(self._c_pointer, n, pointer(coords)) RuntimeError: Release Object Error processing trigger ""new frame"": RuntimeError: Release Object File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 301, in coords f(self._c_pointer, n, pointer(coords)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 450.12 OpenGL renderer: GeForce GTX 1070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Third Party 0.91 can't reproduce all ChimeraX