AddH: no lone pairs on acceptor

[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 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.

[Eric Pettersen]

Fixed by implementing tau test for aniline as an acceptor so that it can't be declared as both and acceptor and donor to the same atom.