AddH: 'Atom' object has no attribute 'oslIdent'

[lpravda@…]

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.

[Eric Pettersen]

Hydrogen-addition has its own internal bug reporting when "cannot happen" conditions are detected. That code, ported from Chimera1, had an old call in it. With that call fixed, it indirectly points out that the atom DZ3 in residue 73 of chain A is clearly incorrect. it is only 0.8 angstroms from atom DE3 and is nowhere near the correct tetrahedral position from NZ.