Handle microheterogenicity in PDB files

[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 2izq

Summary of feedback from opening 2izq fetched from pdb  
---  
warnings | Ignoring microheterogeneity for label_seq_id 11 in chain A  
Ignoring microheterogeneity for label_seq_id 11 in chain A  
Ignoring microheterogeneity for label_seq_id 11 in chain D  
Ignoring microheterogeneity for label_seq_id 11 in chain C  
Ignoring microheterogeneity for label_seq_id 11 in chain C  
1 messages similar to the above omitted  
notes | Fetching compressed mmCIF 2izq from
http://files.rcsb.org/download/2izq.cif  
Fetching CCD FVA from http://ligand-expo.rcsb.org/reports/F/FVA/FVA.cif  
Fetching CCD DLE from http://ligand-expo.rcsb.org/reports/D/DLE/DLE.cif  
Fetching CCD DVA from http://ligand-expo.rcsb.org/reports/D/DVA/DVA.cif  
Fetching CCD ETA from http://ligand-expo.rcsb.org/reports/E/ETA/ETA.cif  
Fetching CCD IOD from http://ligand-expo.rcsb.org/reports/I/IOD/IOD.cif  
Fetching CCD MOH from http://ligand-expo.rcsb.org/reports/M/MOH/MOH.cif  
  
FYI: command is replacing existing command: "lighting"  
2izq title:  
Gramicidin D complex with KI [more info...]  
  
Chain information for 2izq #1  
---  
Chain | Description  
A C | gramicidin D  
A B C D | gramicidin D  
B D | gramicidin D  
  
Non-standard residues in 2izq #1  
---  
ETA — ethanolamine  
IOD — iodide ion  
MOH — methanol  
  
2izq mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
  
FYI: command is replacing existing command: "addh"  

> addh hbond true

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 160, in hbond_add_hydrogens  
_prep_add(session, structures, unknowns_info, **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 406, in _prep_add  
real_N, real_C, fake_N, fake_C = determine_termini(session, structures)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/util.py", line 47, in determine_termini  
rn, rc, fn, fc = guess_termini(chain)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/util.py", line 132, in guess_termini  
if res.number + 1 < next_res.number:  
AttributeError: 'NoneType' object has no attribute 'number'  
  
AttributeError: 'NoneType' object has no attribute 'number'  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/util.py", line 132, in guess_termini  
if res.number + 1 < next_res.number:  
  
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]

ChimeraX will never handle microheterogenicity completely properly. The best it can do within its design paradigms is use only one of the alternatives at each microheterogenic position. The real solutions is separate files for each combination of alternatives.

At any rate, mmCIF already does use only one alternative at each, but apparently screws up the chain information. I will open a separate ticket for that. This ticket is for getting the PDB reader to skip alternatives, which it doesn't do yet.