AddH: skip falsely terminal heavy atoms of standard residues

[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 fails

Log:
UCSF ChimeraX version: 0.8 (2018-12-14)  
How to cite UCSF ChimeraX  

> open 2iab

Summary of feedback from opening 2iab fetched from pdb  
---  
notes | Fetching compressed mmCIF 2iab from
http://files.rcsb.org/download/2iab.cif  
Fetching CCD IPA from http://ligand-expo.rcsb.org/reports/I/IPA/IPA.cif  
  
FYI: command is replacing existing command: "lighting"  
2iab title:  
Crystal structure of a protein with FMN-binding split barrel fold
(NP_828636.1) from Streptomyces avermitilis at 2.00 A resolution [more
info...]  
  
Chain information for 2iab #1  
---  
Chain | Description  
A B | Hypothetical protein  
  
Non-standard residues in 2iab #1  
---  
IPA — isopropyl alcohol (2-propanol)  
  
2iab mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| software_defined_assembly  
  
  
FYI: command is replacing existing command: "addh"  

> addh hbond true

Termini for 2iab (#1) chain A determined from SEQRES records  
Termini for 2iab (#1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A THR 2, /B MSE 1  
Chain-final residues that are actual C termini: /A ASP 154  
Chain-final residues that are not actual C termini: /B LEU 151  

Unknown hybridization for atom (SE) of residue type MSE; not adding hydrogens
to it  

899 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 443, in add_hydrogens  
did_finish = _try_finish(end, hbond_info, finished, aro_amines, pruned_by,
processed)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/hbond.py", line 970, in _try_finish  
targets.append(_find_target(atom, at_pos, other, not is_acc, hbond_info,
finished))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/hbond.py", line 871, in _find_target  
to_bonded, coplanar=to_coplanar, toward=at_pos)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/bond_geom.py", line 73, in bond_positions  
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/bond_geom.py", line 129, in planar_pos  
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/bond_geom.py", line 231, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
ValueError: More than 2 coplanar positions specified!  
  
ValueError: More than 2 coplanar positions specified!  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/bond_geom.py", line 231, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
  
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]

Truncated arginine; duplicate of #1403