id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1540 AddH: no lone pairs on acceptor 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 5k99 Summary of feedback from opening 5k99 fetched from pdb --- warning | Atom H1 is not in the residue template for SER #-2 in chain A notes | Fetching compressed mmCIF 5k99 from http://files.rcsb.org/download/5k99.cif Fetching CCD XSN from http://ligand-expo.rcsb.org/reports/X/XSN/XSN.cif Fetching CCD AMP from http://ligand-expo.rcsb.org/reports/A/AMP/AMP.cif FYI: command is replacing existing command: ""lighting"" 5k99 title: Crystal structure of microcin immunity protein MccF from Bacillus anthracis in complex with McC [more info...] Chain information for 5k99 #1 --- Chain | Description A B | Microcin C7 self-immunity protein mccF C D | Microcin C Non-standard residues in 5k99 #1 --- AMP — adenosine monophosphate 5k99 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly FYI: command is replacing existing command: ""addh"" > addh hbond true Termini for 5k99 (#1) chain A determined from SEQRES records Termini for 5k99 (#1) chain D determined from SEQRES records Termini for 5k99 (#1) chain B determined from SEQRES records Termini for 5k99 (#1) chain C determined from SEQRES records Chain-initial residues that are actual N termini: /A SER -2 Chain-initial residues that are not actual N termini: /D ARG 2, /B MSE 1, /C ARG 2 Chain-final residues that are actual C termini: /A ILE 333, /D AMP 8, /B ILE 333, /C AMP 8 Chain-final residues that are not actual C termini: Unknown hybridization for atom (SE) of residue type MSE; not adding hydrogens to it 3421 hydrogen bonds 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 163, in hbond_add_hydrogens idatm_type, his_Ns, coordinations, in_isolation) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/hbond.py"", line 400, in add_hydrogens if not _can_accept(d, a, *hbond_info[a][-1][1:]): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/hbond.py"", line 897, in _can_accept raise ValueError(""No lone pairs on %s for %s to donate to"" % (acceptor, donor)) ValueError: No lone pairs on /D AMP 8 N6 for /D HOH 110 O to donate to ValueError: No lone pairs on /D AMP 8 N6 for /D HOH 110 O to donate to File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/hbond.py"", line 897, in _can_accept raise ValueError(""No lone pairs on %s for %s to donate to"" % (acceptor, donor)) 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 closed normal Structure Editing fixed all ChimeraX