id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1542 Handle microheterogenicity in PDB files lpravda@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-18.2.0-x86_64-i386-64bit ChimeraX Version: 0.8 (2018-12-14) Description protonation issue Log: UCSF ChimeraX version: 0.8 (2018-12-14) How to cite UCSF ChimeraX > open 2izq Summary of feedback from opening 2izq fetched from pdb --- warnings | Ignoring microheterogeneity for label_seq_id 11 in chain A Ignoring microheterogeneity for label_seq_id 11 in chain A Ignoring microheterogeneity for label_seq_id 11 in chain D Ignoring microheterogeneity for label_seq_id 11 in chain C Ignoring microheterogeneity for label_seq_id 11 in chain C 1 messages similar to the above omitted notes | Fetching compressed mmCIF 2izq from http://files.rcsb.org/download/2izq.cif Fetching CCD FVA from http://ligand-expo.rcsb.org/reports/F/FVA/FVA.cif Fetching CCD DLE from http://ligand-expo.rcsb.org/reports/D/DLE/DLE.cif Fetching CCD DVA from http://ligand-expo.rcsb.org/reports/D/DVA/DVA.cif Fetching CCD ETA from http://ligand-expo.rcsb.org/reports/E/ETA/ETA.cif Fetching CCD IOD from http://ligand-expo.rcsb.org/reports/I/IOD/IOD.cif Fetching CCD MOH from http://ligand-expo.rcsb.org/reports/M/MOH/MOH.cif FYI: command is replacing existing command: ""lighting"" 2izq title: Gramicidin D complex with KI [more info...] Chain information for 2izq #1 --- Chain | Description A C | gramicidin D A B C D | gramicidin D B D | gramicidin D Non-standard residues in 2izq #1 --- ETA — ethanolamine IOD — iodide ion MOH — methanol 2izq mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly FYI: command is replacing existing command: ""addh"" > addh hbond true Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/cmd_line/tool.py"", line 229, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 2585, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/cmd.py"", line 55, in cmd_addh add_h_func(session, structures, in_isolation=in_isolation, **prot_schemes) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/cmd.py"", line 160, in hbond_add_hydrogens _prep_add(session, structures, unknowns_info, **prot_schemes) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/cmd.py"", line 406, in _prep_add real_N, real_C, fake_N, fake_C = determine_termini(session, structures) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/util.py"", line 47, in determine_termini rn, rc, fn, fc = guess_termini(chain) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/util.py"", line 132, in guess_termini if res.number + 1 < next_res.number: AttributeError: 'NoneType' object has no attribute 'number' AttributeError: 'NoneType' object has no attribute 'number' File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/util.py"", line 132, in guess_termini if res.number + 1 < next_res.number: See log for complete Python traceback. OpenGL version: 4.1 ATI-2.4.9 OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect accepted minor Input/Output all ChimeraX