id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3065 ISOLDE simulation stopped: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer' josep.font@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Darwin-19.4.0-x86_64-i386-64bit ChimeraX Version: 0.92 (2020-02-05) Description Start a simulation of a trimer of 1200 residues to fix clashes. Clashes are fixed. I tried to stop the simulation to save the changes and got this error. Log: UCSF ChimeraX version: 0.92 (2020-02-05) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/pep/Desktop/Pep/papers/Crosslinkingpaper/cryoEmstructuresdeposition/TrimeriOFS/trimeriOFSfinal_7_isolde.pdb Chain information for trimeriOFSfinal_7_isolde.pdb #1 --- Chain | Description A B C | No description available > open > /Users/pep/Desktop/Pep/papers/Crosslinkingpaper/cryoEmstructuresdeposition/TrimeriOFS/trimermapfinal.mrc Opened trimermapfinal.mrc, grid size 256,256,256, pixel 0.986, shown at level 0.0154, step 1, values float32 > volume #2 level 0.03506 > toolshed show ISOLDE > set selectionWidth 4 Chain information for trimeriOFSfinal_7_isolde.pdb --- Chain | Description 1.1/A 1.1/B 1.1/C | No description available Done loading forcefield No template found for residue A501 (ASP) Adding hydrogens Summary of feedback from adding hydrogens to trimeriOFSfinal_7_isolde.pdb #1.1 --- notes | No usable SEQRES records for trimeriOFSfinal_7_isolde.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for trimeriOFSfinal_7_isolde.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for trimeriOFSfinal_7_isolde.pdb (#1.1) chain C; guessing termini instead Chain-initial residues that are actual N termini: /A LYS 6, /B LYS 6, /C LYS 6 Chain-initial residues that are not actual N termini: /A PRO 129, /B PRO 129, /C PRO 129 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A GLU 416, /A HIS 114, /B GLU 416, /B HIS 114, /C GLU 416, /C HIS 114 982 hydrogen bonds /A GLU 416 is not terminus, removing H atom from 'C' /A HIS 114 is not terminus, removing H atom from 'C' /B GLU 416 is not terminus, removing H atom from 'C' /B HIS 114 is not terminus, removing H atom from 'C' /C GLU 416 is not terminus, removing H atom from 'C' 1 messages similar to the above omitted 0 hydrogens added No template found for residue A501 (ASP) Excluding residue No template found for residue B501 (ASP) Excluding residue No template found for residue C501 (ASP) Excluding residue Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Users/pep/Library/Application Support/ChimeraX/0.92/site- packages/chimerax/isolde/delayed_reaction.py"", line 64, in callback if self.tf is None or self.tf(): File ""/Users/pep/Library/Application Support/ChimeraX/0.92/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 241, in thread_finished return f(self._c_pointer) AttributeError: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer' Error processing trigger ""new frame"": AttributeError: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer' File ""/Users/pep/Library/Application Support/ChimeraX/0.92/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 241, in thread_finished return f(self._c_pointer) See log for complete Python traceback. OpenGL version: 4.1 INTEL-14.5.22 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc. }}} " defect closed normal Third Party fixed all ChimeraX