id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1545 AddH: 'Atom' object has no attribute 'oslIdent' 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 5a93 Summary of feedback from opening 5a93 fetched from pdb --- warnings | Atom DA is not in the residue template for SER #28 in chain A Atom D is not in the residue template for VAL #29 in chain A Atom D is not in the residue template for GLN #30 in chain A Atom D is not in the residue template for GLN #31 in chain A Atom D is not in the residue template for GLN #32 in chain A Atom D is not in the residue template for LEU #33 in chain A 72 messages similar to the above omitted Atom DA is not in the residue template for PRO #107 in chain A Atom D is not in the residue template for ILE #108 in chain A Atom D is not in the residue template for ALA #109 in chain A Atom D is not in the residue template for GLU #110 in chain A Atom D is not in the residue template for LYS #111 in chain A Atom D is not in the residue template for HIS #112 in chain A 32 messages similar to the above omitted Atom DA is not in the residue template for PRO #145 in chain A Atom D is not in the residue template for ASP #146 in chain A Atom D is not in the residue template for LYS #147 in chain A Atom D is not in the residue template for VAL #148 in chain A Atom D is not in the residue template for THR #149 in chain A Atom D is not in the residue template for ALA #150 in chain A 16 messages similar to the above omitted Atom DA is not in the residue template for PRO #167 in chain A Atom D is not in the residue template for THR #168 in chain A Atom D is not in the residue template for LEU #169 in chain A Atom D is not in the residue template for ASN #170 in chain A Atom D is not in the residue template for THR #171 in chain A Atom D is not in the residue template for ALA #172 in chain A 1 messages similar to the above omitted Atom DA is not in the residue template for PRO #174 in chain A Atom D is not in the residue template for GLY #175 in chain A Atom D is not in the residue template for ASP #176 in chain A Atom DA is not in the residue template for PRO #177 in chain A Atom D is not in the residue template for ARG #178 in chain A Atom D is not in the residue template for ASP #179 in chain A Atom D is not in the residue template for THR #180 in chain A Atom D is not in the residue template for THR #181 in chain A Atom D is not in the residue template for THR #182 in chain A Atom DA is not in the residue template for PRO #183 in chain A Atom D is not in the residue template for LEU #184 in chain A Atom D is not in the residue template for ALA #185 in chain A Atom D is not in the residue template for MET #186 in chain A Atom D is not in the residue template for ALA #187 in chain A Atom D is not in the residue template for GLN #188 in chain A 37 messages similar to the above omitted Atom DA is not in the residue template for PRO #226 in chain A Atom D is not in the residue template for LYS #227 in chain A Atom D is not in the residue template for SER #228 in chain A Atom D is not in the residue template for TRP #229 in chain A Atom D is not in the residue template for VAL #230 in chain A Atom D is not in the residue template for VAL #231 in chain A 19 messages similar to the above omitted Atom DA is not in the residue template for PRO #252 in chain A Atom D is not in the residue template for GLU #254 in chain A Atom D is not in the residue template for ASN #255 in chain A Atom D is not in the residue template for HIS #256 in chain A Atom D is not in the residue template for ALA #257 in chain A Atom DA is not in the residue template for PRO #258 in chain A Atom D is not in the residue template for LEU #259 in chain A Atom D is not in the residue template for VAL #260 in chain A Atom D is not in the residue template for LEU #261 in chain A Atom D is not in the residue template for VAL #262 in chain A Atom D is not in the residue template for THR #263 in chain A 4 messages similar to the above omitted Atom DA is not in the residue template for PRO #268 in chain A Atom D is not in the residue template for GLU #269 in chain A Atom D is not in the residue template for GLN #270 in chain A Atom D is not in the residue template for LYS #271 in chain A Atom D is not in the residue template for ALA #272 in chain A Atom D is not in the residue template for GLU #273 in chain A 17 messages similar to the above omitted notes | Fetching compressed mmCIF 5a93 from http://files.rcsb.org/download/5a93.cif Fetching CCD CEF from http://ligand-expo.rcsb.org/reports/C/CEF/CEF.cif FYI: command is replacing existing command: ""lighting"" 5a93 title: 293K Joint X-ray Neutron with Cefotaxime: EXPLORING THE MECHANISM OF BETA- LACTAM RING PROTONATION IN THE CLASS A BETA-LACTAMASE ACYLATION MECHANISM USING NEUTRON AND X-RAY CRYSTALLOGRAPHY [more info...] Chain information for 5a93 #1 --- Chain | Description A | β-lactamase CTX-M-97 Non-standard residues in 5a93 #1 --- CEF — CEFOTAXIME, C3' cleaved, open, bound form SO4 — sulfate ion FYI: command is replacing existing command: ""addh"" > addh hbond true Termini for 5a93 (#1) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: /A SER 28 Chain-final residues that are actual C termini: /A PHE 290 Chain-final residues that are not actual C termini: 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 241, in add_hydrogens hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop, angle_slop=rec_angle_slop) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/hbonds/hbond.py"", line 637, in find_hbonds *tuple(arg_list + add_args)): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/hbonds/donor_geom.py"", line 137, in don_upsilon_tau sp2_O_upsilon_low, sp2_O_upsilon_high, sp2_O_theta, sp2_O_tau, tau_sym) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/hbonds/donor_geom.py"", line 239, in test_upsion_tau_acceptor 2 * len(bonded_pos), tau_sym, donor.oslIdent())) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/attr_registration.py"", line 39, in __getattr__ return look_in_class._attr_registration.get_attr(attr_name) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/attr_registration.py"", line 66, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Atom' object has no attribute 'oslIdent' AttributeError: 'Atom' object has no attribute 'oslIdent' File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/attr_registration.py"", line 66, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None 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