id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2025 """Particle coordinate is NaN"" error in ISOLDE 1.0b2" dkreitle@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.8 (2018-12-17) Description Running simulation in ISOLDE. Particle coordinate is nan error that stops simulation. (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py"", line 338, in __init__ self.init_available_from_cache(logger) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py"", line 445, in init_available_from_cache abc.load_from_cache() File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/available.py"", line 61, in load_from_cache b = _build_bundle(d) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/available.py"", line 242, in _build_bundle keywords = _extract_extra_keywords(keywords) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/installed.py"", line 270, in _extract_extra_keywords all_kwds = [k.strip() for k in kwds.split(',')] AttributeError: 'list' object has no attribute 'split' UCSF ChimeraX version: 0.8 (2018-12-17) How to cite UCSF ChimeraX > toolshed show ISOLDE before.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for before.pdb #1 --- Chain | Description A | predicted microcompartment protein before.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for before.pdb --- Chain | Description 1.3/A | predicted microcompartment protein > toolshed show ""File History"" > toolshed show ""Side View"" > help help:user/tools/modelpanel.html Exception ignored in: > Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/opengl.py"", line 2509, in __del__ raise RuntimeError('OpenGL texture was not deleted before core.graphics.Texture destroyed') RuntimeError: OpenGL texture was not deleted before core.graphics.Texture destroyed Exception ignored in: > Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/opengl.py"", line 1743, in __del__ % self.name) RuntimeError: OpenGL framebuffer mask was not deleted before core.graphics.Framebuffer destroyed > close session > open /Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.pdb Chain information for NpsA_32_refine_30_ISOLDE.pdb #1 --- Chain | Description A | No description available > open NpsA_32_refine_30_ISOLDE.mtz File not found: NpsA_32_refine_30_ISOLDE.mtz > open NpsA_32_refine_30_ISOLDE.mtz structureModel #1 File not found: NpsA_32_refine_30_ISOLDE.mtz > open ~/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_2mFo- DFc.ccp4 structureModel #1 Opened NpsA_32_refine_30_2mFo-DFc.ccp4, grid size 80,87,114, pixel 0.934,0.915,0.921, shown at level 3.2, step 1, values float32 > toolshed show ISOLDE Chain information for NpsA_32_refine_30_ISOLDE.pdb --- Chain | Description 1.3/A | No description available > hide selAtoms ribbons > open ~/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_2mFo- DFc.ccp4 structureModel #1 Opened NpsA_32_refine_30_2mFo-DFc.ccp4, grid size 80,87,114, pixel 0.934,0.915,0.921, shown at level 3.2, step 1, values float32 Bad residue number: match Doing nothing > addh hbond true No usable SEQRES records for NpsA_32_refine_30_ISOLDE.pdb (#1.3) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLN 9 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 ALA 504 402 hydrogen bonds /A ALA 504 is not terminus, removing H atom from 'C' 3830 hydrogens added > hide H > hide #!2.1 models > close #2 > close #1.3 > close #1.2 > close #1.1.1.1 > close #1 > open 2bbv Summary of feedback from opening 2bbv fetched from pdb --- notes | Fetching compressed mmCIF 2bbv from http://files.rcsb.org/download/2bbv.cif Fetching CCD U from http://ligand-expo.rcsb.org/reports/U/U/U.cif Fetching CCD C from http://ligand-expo.rcsb.org/reports/C/C/C.cif Fetching CCD A from http://ligand-expo.rcsb.org/reports/A/A/A.cif Fetching CCD LEU from http://ligand-expo.rcsb.org/reports/L/LEU/LEU.cif Fetching CCD THR from http://ligand-expo.rcsb.org/reports/T/THR/THR.cif Fetching CCD ARG from http://ligand-expo.rcsb.org/reports/A/ARG/ARG.cif Fetching CCD SER from http://ligand-expo.rcsb.org/reports/S/SER/SER.cif Fetching CCD GLN from http://ligand-expo.rcsb.org/reports/G/GLN/GLN.cif Fetching CCD PRO from http://ligand-expo.rcsb.org/reports/P/PRO/PRO.cif Fetching CCD GLY from http://ligand-expo.rcsb.org/reports/G/GLY/GLY.cif Fetching CCD ALA from http://ligand-expo.rcsb.org/reports/A/ALA/ALA.cif Fetching CCD PHE from http://ligand-expo.rcsb.org/reports/P/PHE/PHE.cif Fetching CCD LYS from http://ligand-expo.rcsb.org/reports/L/LYS/LYS.cif Fetching CCD CYS from http://ligand-expo.rcsb.org/reports/C/CYS/CYS.cif Fetching CCD ASP from http://ligand-expo.rcsb.org/reports/A/ASP/ASP.cif Fetching CCD ASN from http://ligand-expo.rcsb.org/reports/A/ASN/ASN.cif Fetching CCD ILE from http://ligand-expo.rcsb.org/reports/I/ILE/ILE.cif Fetching CCD GLU from http://ligand-expo.rcsb.org/reports/G/GLU/GLU.cif Fetching CCD VAL from http://ligand-expo.rcsb.org/reports/V/VAL/VAL.cif Fetching CCD TYR from http://ligand-expo.rcsb.org/reports/T/TYR/TYR.cif Fetching CCD TRP from http://ligand-expo.rcsb.org/reports/T/TRP/TRP.cif Fetching CCD MET from http://ligand-expo.rcsb.org/reports/M/MET/MET.cif Fetching CCD HIS from http://ligand-expo.rcsb.org/reports/H/HIS/HIS.cif Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif Fetching CCD HOH from http://ligand-expo.rcsb.org/reports/H/HOH/HOH.cif 2bbv title: The refined three-dimensional structure of an insect virus At 2.8 angstroms resolution [more info...] Chain information for 2bbv #1 --- Chain | Description A B C | protein (black beetle virus capsid protein) D E F | protein (black beetle virus capsid protein) N | RNA (5'-R(*up*CP*up*up*ap*up*ap*up*CP*U)-3') Non-standard residues in 2bbv #1 --- CA — calcium ion 2bbv mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame 6| crystal asymmetric unit, crystal frame Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide solvent > show solvent > hide solvent could not retrieve bundle list from toolshed Unknown command: bgcolor black > set bgColor black > show selAtoms ribbons > hide selAtoms surfaces > hide selAtoms > hide selAtoms surfaces > show selAtoms ribbons > hide selAtoms ribbons > show selAtoms surfaces > hide selAtoms surfaces > show selAtoms > close #1 > open 1a0m fromDatabase eds Summary of feedback from opening 1a0m fetched from eds --- note | Fetching map 1a0m from http://www.ebi.ac.uk/pdbe/coordinates/files/1a0m.ccp4 Opened 1a0m.ccp4, grid size 97,101,88, pixel 0.37,0.37,0.367, shown at level 2.28, step 1, values float32 > open 1a0m Summary of feedback from opening 1a0m fetched from pdb --- notes | Fetching compressed mmCIF 1a0m from http://files.rcsb.org/download/1a0m.cif Fetching CCD NH2 from http://ligand-expo.rcsb.org/reports/N/NH2/NH2.cif 1a0m title: 1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...] Chain information for 1a0m #2 --- Chain | Description A B | α-conotoxin [TYR15]-epi Non-standard residues in 1a0m #2 --- NH2 — amino group > hide ribbons > show atoms Expected a keyword > volume #1 level 2.0 style mesh > close > open /Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30.pdb Summary of feedback from opening /Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2019-05-01 Time 15:14:02 EDT -0400 (1556738042.71 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : /Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/rosetta_refine_13/NpsA_32_refine_11_rosetta_phenix_001.mtz 38 messages similar to the above omitted Chain information for NpsA_32_refine_30.pdb #1 --- Chain | Description A | No description available > open /Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.mtz Must specify a structure model to associate with crystallographic data Must specify a structure model to associate with crystallographic data > open ~/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.mtz Must specify a structure model to associate with crystallographic data > open ~/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.mtz NpsA_32_refine_30 Must specify a structure model to associate with crystallographic data > open ~/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.mtz NpsA_32_refine_30.pdb Must specify a structure model to associate with crystallographic data > open ~/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.mtz model #1 Must specify a structure model to associate with crystallographic data > open /Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_2mFo- DFc.ccp4 Opened NpsA_32_refine_30_2mFo-DFc.ccp4, grid size 80,87,114, pixel 0.934,0.915,0.921, shown at level 3.2, step 1, values float32 > close > open /Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.pdb Chain information for NpsA_32_refine_30_ISOLDE.pdb #1 --- Chain | Description A | No description available > open /Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE Missing filename suffix /Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE Missing filename suffix /Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE > open /Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.ccp4 Opened NpsA_32_refine_30_ISOLDE.ccp4, grid size 85,92,129, pixel 0.692,0.703,0.691, shown at level 3.21, step 1, values float32 > toolshed show ISOLDE Chain information for NpsA_32_refine_30_ISOLDE.pdb --- Chain | Description 1.3/A | No description available > set bgColor white Bad residue number: match Doing nothing > addh hbond true No usable SEQRES records for NpsA_32_refine_30_ISOLDE.pdb (#1.3) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLN 9 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 ALA 504 402 hydrogen bonds /A ALA 504 is not terminus, removing H atom from 'C' 3830 hydrogens added > hide H Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/delayed_reaction.py"", line 65, in callback self.ff(*self.ff_args) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1460, in _update_coordinates_and_repeat self.atoms.coords = th.coords File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 294, in coords f(self._c_pointer, n, pointer(coords)) RuntimeError: Particle coordinate is nan Error processing trigger ""new frame"": Particle coordinate is nan: RuntimeError: Particle coordinate is nan File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 294, in coords f(self._c_pointer, n, pointer(coords)) See log for complete Python traceback. Traceback (most recent call last): File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/isolde.py"", line 2482, in _start_sim_or_toggle_pause self.pause_sim_toggle() File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/isolde.py"", line 2680, in pause_sim_toggle self.sim_manager.toggle_pause() File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 678, in toggle_pause self.pause = not self.pause File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 657, in pause self.sim_handler.pause = flag File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1555, in pause self._resume() File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1450, in _resume self._repeat_step() File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1441, in _repeat_step th.thread_finished, self._update_coordinates_and_repeat, final_args) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/delayed_reaction.py"", line 56, in delayed_reaction initiator_func(*initiator_args) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 186, in minimize f(self._c_pointer, tolerance, max_iterations) RuntimeError: Particle coordinate is nan RuntimeError: Particle coordinate is nan File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 186, in minimize f(self._c_pointer, tolerance, max_iterations) See log for complete Python traceback. Traceback (most recent call last): File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/isolde.py"", line 2482, in _start_sim_or_toggle_pause self.pause_sim_toggle() File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/isolde.py"", line 2680, in pause_sim_toggle self.sim_manager.toggle_pause() File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 678, in toggle_pause self.pause = not self.pause File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 657, in pause self.sim_handler.pause = flag File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1555, in pause self._resume() File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1450, in _resume self._repeat_step() File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1441, in _repeat_step th.thread_finished, self._update_coordinates_and_repeat, final_args) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/delayed_reaction.py"", line 56, in delayed_reaction initiator_func(*initiator_args) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 186, in minimize f(self._c_pointer, tolerance, max_iterations) RuntimeError: Particle coordinate is nan RuntimeError: Particle coordinate is nan File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 186, in minimize f(self._c_pointer, tolerance, max_iterations) See log for complete Python traceback. > close > open /Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.pdb Chain information for NpsA_32_refine_30_ISOLDE.pdb #1 --- Chain | Description A | No description available > addh hbond true No usable SEQRES records for NpsA_32_refine_30_ISOLDE.pdb (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLN 9 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 ALA 504 402 hydrogen bonds /A ALA 504 is not terminus, removing H atom from 'C' 3830 hydrogens added > addh hbond true No usable SEQRES records for NpsA_32_refine_30_ISOLDE.pdb (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLN 9 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 ALA 504 376 hydrogen bonds /A ALA 504 is not terminus, removing H atom from 'C' 0 hydrogens added Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide H > show selAtoms ribbons > open /Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_2mFo- DFc.ccp4 Opened NpsA_32_refine_30_2mFo-DFc.ccp4, grid size 80,87,114, pixel 0.934,0.915,0.921, shown at level 3.2, step 1, values float32 > toolshed show ISOLDE Chain information for NpsA_32_refine_30_ISOLDE.pdb --- Chain | Description 1.3/A | No description available > hide selAtoms ribbons Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/delayed_reaction.py"", line 65, in callback self.ff(*self.ff_args) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1460, in _update_coordinates_and_repeat self.atoms.coords = th.coords File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 294, in coords f(self._c_pointer, n, pointer(coords)) RuntimeError: Particle coordinate is nan Error processing trigger ""new frame"": Particle coordinate is nan: RuntimeError: Particle coordinate is nan File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 294, in coords f(self._c_pointer, n, pointer(coords)) See log for complete Python traceback. > close > open /Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.pdb Chain information for NpsA_32_refine_30_ISOLDE.pdb #1 --- Chain | Description A | No description available > open /Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_2mFo- DFc.ccp4 Opened NpsA_32_refine_30_2mFo-DFc.ccp4, grid size 80,87,114, pixel 0.934,0.915,0.921, shown at level 3.2, step 1, values float32 > toolshed show ISOLDE Chain information for NpsA_32_refine_30_ISOLDE.pdb --- Chain | Description 1.3/A | No description available > hide selAtoms ribbons Bad residue number: match Doing nothing > addh hbond true No usable SEQRES records for NpsA_32_refine_30_ISOLDE.pdb (#1.3) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLN 9 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 ALA 504 402 hydrogen bonds /A ALA 504 is not terminus, removing H atom from 'C' 3830 hydrogens added > hide H reverting to start Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/delayed_reaction.py"", line 65, in callback self.ff(*self.ff_args) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1460, in _update_coordinates_and_repeat self.atoms.coords = th.coords File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 294, in coords f(self._c_pointer, n, pointer(coords)) RuntimeError: Particle coordinate is nan Error processing trigger ""new frame"": Particle coordinate is nan: RuntimeError: Particle coordinate is nan File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 294, in coords f(self._c_pointer, n, pointer(coords)) See log for complete Python traceback. > close > open /Users/dkreitler/Xray/Projects/NpsA-312AAA-Nterm/NpsA- N_14/phenix/Refine_19/NpsA-N_14_refine_19.pdb Summary of feedback from opening /Users/dkreitler/Xray/Projects/NpsA-312AAA- Nterm/NpsA-N_14/phenix/Refine_19/NpsA-N_14_refine_19.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2019-04-25 Time 12:39:44 EDT -0400 (1556210384.29 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : /Users/dkreitler/Xray/Projects/NpsA-312AAA-Nterm/NpsA- N_14/data/NpsA-N_14_2_truncate-unique.mtz 31 messages similar to the above omitted Chain information for NpsA-N_14_refine_19.pdb #1 --- Chain | Description A | No description available B | No description available > open /Users/dkreitler/Xray/Projects/NpsA-312AAA-Nterm/NpsA- N_14/phenix/Refine_19/NpsA-N_14_refine_19_2mFo-DFc.ccp4 Opened NpsA-N_14_refine_19_2mFo-DFc.ccp4, grid size 176,180,232, pixel 0.5,0.493,0.503, shown at level 3.56, step 1, values float32 > toolshed show ISOLDE Chain information for NpsA-N_14_refine_19.pdb --- Chain | Description 1.3/A | No description available 1.3/B | No description available > addh hbond true No usable SEQRES records for NpsA-N_14_refine_19.pdb (#1.3) chain A; guessing termini instead No usable SEQRES records for NpsA-N_14_refine_19.pdb (#1.3) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A TYR 8, /B TYR 8 Chain-initial residues that are not actual N termini: /A PRO 320 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 401, /A ALA 312, /B VAL 401 2386 hydrogen bonds /A VAL 401 is not terminus, removing H atom from 'C' /A ALA 312 is not terminus, removing H atom from 'C' /B VAL 401 is not terminus, removing H atom from 'C' 7168 hydrogens added > hide H > hide selAtoms ribbons > hide selAtoms > show selAtoms > open /Users/dkreitler/Xray/Projects/NpsA-312AAA-Nterm/NpsA- N_14/phenix/Refine_19/NpsA-N_14_refine_19_2mFo-DFc.ccp4 Opened NpsA-N_14_refine_19_2mFo-DFc.ccp4, grid size 176,180,232, pixel 0.5,0.493,0.503, shown at level 3.56, step 1, values float32 > toolshed show ISOLDE Map is too large for fast cubic interpolation on the GPU! Switching to slower, more memory-efficient implementation. Map is too large for fast cubic interpolation on the GPU! Switching to slower, more memory-efficient implementation. Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/mouse_modes/mousemodes.py"", line 448, in _wheel_event f.wheel(MouseEvent(event)) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 263, in wheel rep, levels = adjust_threshold_level(v, step, self.symmetrical) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 277, in adjust_threshold_level new_levels[-1] = (max(l,1.01*ms.maximum),b) NameError: name 'ms' is not defined NameError: name 'ms' is not defined File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 277, in adjust_threshold_level new_levels[-1] = (max(l,1.01*ms.maximum),b) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/mouse_modes/mousemodes.py"", line 448, in _wheel_event f.wheel(MouseEvent(event)) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 263, in wheel rep, levels = adjust_threshold_level(v, step, self.symmetrical) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 277, in adjust_threshold_level new_levels[-1] = (max(l,1.01*ms.maximum),b) NameError: name 'ms' is not defined NameError: name 'ms' is not defined File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 277, in adjust_threshold_level new_levels[-1] = (max(l,1.01*ms.maximum),b) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/mouse_modes/mousemodes.py"", line 448, in _wheel_event f.wheel(MouseEvent(event)) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 263, in wheel rep, levels = adjust_threshold_level(v, step, self.symmetrical) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 277, in adjust_threshold_level new_levels[-1] = (max(l,1.01*ms.maximum),b) NameError: name 'ms' is not defined NameError: name 'ms' is not defined File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 277, in adjust_threshold_level new_levels[-1] = (max(l,1.01*ms.maximum),b) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/mouse_modes/mousemodes.py"", line 448, in _wheel_event f.wheel(MouseEvent(event)) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 263, in wheel rep, levels = adjust_threshold_level(v, step, self.symmetrical) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 277, in adjust_threshold_level new_levels[-1] = (max(l,1.01*ms.maximum),b) NameError: name 'ms' is not defined NameError: name 'ms' is not defined File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 277, in adjust_threshold_level new_levels[-1] = (max(l,1.01*ms.maximum),b) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/mouse_modes/mousemodes.py"", line 448, in _wheel_event f.wheel(MouseEvent(event)) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 263, in wheel rep, levels = adjust_threshold_level(v, step, self.symmetrical) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 277, in adjust_threshold_level new_levels[-1] = (max(l,1.01*ms.maximum),b) NameError: name 'ms' is not defined NameError: name 'ms' is not defined File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 277, in adjust_threshold_level new_levels[-1] = (max(l,1.01*ms.maximum),b) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/mouse_modes/mousemodes.py"", line 448, in _wheel_event f.wheel(MouseEvent(event)) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 263, in wheel rep, levels = adjust_threshold_level(v, step, self.symmetrical) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 277, in adjust_threshold_level new_levels[-1] = (max(l,1.01*ms.maximum),b) NameError: name 'ms' is not defined NameError: name 'ms' is not defined File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 277, in adjust_threshold_level new_levels[-1] = (max(l,1.01*ms.maximum),b) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/mouse_modes/mousemodes.py"", line 448, in _wheel_event f.wheel(MouseEvent(event)) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 263, in wheel rep, levels = adjust_threshold_level(v, step, self.symmetrical) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 277, in adjust_threshold_level new_levels[-1] = (max(l,1.01*ms.maximum),b) NameError: name 'ms' is not defined NameError: name 'ms' is not defined File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/clipper/mousemodes.py"", line 277, in adjust_threshold_level new_levels[-1] = (max(l,1.01*ms.maximum),b) See log for complete Python traceback. > close > open /Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.pdb Chain information for NpsA_32_refine_30_ISOLDE.pdb #1 --- Chain | Description A | No description available > open /Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_2mFo- DFc.ccp4 Opened NpsA_32_refine_30_2mFo-DFc.ccp4, grid size 80,87,114, pixel 0.934,0.915,0.921, shown at level 3.2, step 1, values float32 > toolshed show ISOLDE Chain information for NpsA_32_refine_30_ISOLDE.pdb --- Chain | Description 1.3/A | No description available Bad residue number: match Adding hydrogens No usable SEQRES records for NpsA_32_refine_30_ISOLDE.pdb (#1.3) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLN 9 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 ALA 504 402 hydrogen bonds /A ALA 504 is not terminus, removing H atom from 'C' 3830 hydrogens added > hide H > hide H > hide H Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/delayed_reaction.py"", line 65, in callback self.ff(*self.ff_args) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1460, in _update_coordinates_and_repeat self.atoms.coords = th.coords File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 294, in coords f(self._c_pointer, n, pointer(coords)) RuntimeError: Particle coordinate is nan Error processing trigger ""new frame"": Particle coordinate is nan: RuntimeError: Particle coordinate is nan File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 294, in coords f(self._c_pointer, n, pointer(coords)) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/delayed_reaction.py"", line 65, in callback self.ff(*self.ff_args) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1460, in _update_coordinates_and_repeat self.atoms.coords = th.coords File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 294, in coords f(self._c_pointer, n, pointer(coords)) RuntimeError: Particle coordinate is nan Error processing trigger ""new frame"": Particle coordinate is nan: RuntimeError: Particle coordinate is nan File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 294, in coords f(self._c_pointer, n, pointer(coords)) See log for complete Python traceback. reverting to start Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/delayed_reaction.py"", line 65, in callback self.ff(*self.ff_args) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1460, in _update_coordinates_and_repeat self.atoms.coords = th.coords File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 294, in coords f(self._c_pointer, n, pointer(coords)) RuntimeError: Particle coordinate is nan Error processing trigger ""new frame"": Particle coordinate is nan: RuntimeError: Particle coordinate is nan File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 294, in coords f(self._c_pointer, n, pointer(coords)) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/delayed_reaction.py"", line 65, in callback self.ff(*self.ff_args) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1460, in _update_coordinates_and_repeat self.atoms.coords = th.coords File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 294, in coords f(self._c_pointer, n, pointer(coords)) RuntimeError: Particle coordinate is nan Error processing trigger ""new frame"": Particle coordinate is nan: RuntimeError: Particle coordinate is nan File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 294, in coords f(self._c_pointer, n, pointer(coords)) See log for complete Python traceback. Traceback (most recent call last): File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/isolde.py"", line 2482, in _start_sim_or_toggle_pause self.pause_sim_toggle() File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/isolde.py"", line 2680, in pause_sim_toggle self.sim_manager.toggle_pause() File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 678, in toggle_pause self.pause = not self.pause File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 657, in pause self.sim_handler.pause = flag File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1555, in pause self._resume() File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1450, in _resume self._repeat_step() File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1441, in _repeat_step th.thread_finished, self._update_coordinates_and_repeat, final_args) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/delayed_reaction.py"", line 56, in delayed_reaction initiator_func(*initiator_args) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 186, in minimize f(self._c_pointer, tolerance, max_iterations) RuntimeError: Particle coordinate is nan RuntimeError: Particle coordinate is nan File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 186, in minimize f(self._c_pointer, tolerance, max_iterations) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/delayed_reaction.py"", line 65, in callback self.ff(*self.ff_args) File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1460, in _update_coordinates_and_repeat self.atoms.coords = th.coords File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 294, in coords f(self._c_pointer, n, pointer(coords)) RuntimeError: Particle coordinate is nan Error processing trigger ""new frame"": Particle coordinate is nan: RuntimeError: Particle coordinate is nan File ""/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 294, in coords f(self._c_pointer, n, pointer(coords)) See log for complete Python traceback. OpenGL version: 4.1 ATI-1.68.20 OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect closed normal Third Party fixed all ChimeraX