AddH: unexpected None residue in sequence

[lpravda@…]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.7 (2018-07-28)
Description
Steps to reproduce error:

open 1tqn from pdbe_updated
addh hbond false



Log:
UCSF ChimeraX version: 0.7 (2018-07-28)  
OpenGL version: 4.1 ATI-1.68.20  
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine  
OpenGL vendor: ATI Technologies Inc.  
How to cite UCSF ChimeraX  

open 1tqn fromDatabase pdbe_updated

Summary of feedback from opening 1tqn fetched from pdbe_updated  
---  
notes | No PDBx fixed column width tables  
No PDBx keywords  
  
Chain information for 1tqn #1  
---  
Chain | Description  
A | cytochrome P450 3A4  
  
1tqn mmCIF Assemblies | 1| author_defined_assembly | 2|
software_defined_assembly  

1tqn citation:    Yano, J.K., Wester, M.R., Schoch, G.A., Griffin, K.J.,
Stout, C.D., Johnson, E.F. (2004). The Structure of Human Microsomal
Cytochrome P450 3A4 Determined by X-ray Crystallography to 2.05-A Resolution.
J. Biol. Chem., 279, 38091-38094. PMID: 15258162. DOI: 10.1074/jbc.C400293200  
Opened mmCIF data containing 3999 atoms and 3908 bonds  

addh hbond false

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 205, 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 2561, 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 116, in simple_add_hydrogens  
    fake_N, fake_C = _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 375, 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 42, 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 100, in guess_termini  
    if cross_residue(n_term, 'N'):  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/util.py", line 133, in cross_residue  
    a = res.find_atom(at_name)  
AttributeError: 'NoneType' object has no attribute 'find_atom'  
  

AttributeError: 'NoneType' object has no attribute 'find_atom'  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/util.py", line 133, in cross_residue  
a = res.find_atom(at_name)  
  
See log for complete Python traceback.  
  
If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and
describe what you were doing and include a copy of the contents of the log.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  




OpenGL version: 4.1 ATI-1.68.20
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Eric Pettersen]

Thanks for reporting this. The new set_input_seq_info() API wasn't setting from_seqres to true. Fix available in next daily build.