ChimeraX bug report submission

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.7 (2018-07-27)
Description
open 1fav
addh hbond false

gives the following error


Log:
UCSF ChimeraX version: 0.7 (2018-07-27)  
OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102  
OpenGL renderer: NVIDIA GeForce GTX 680MX OpenGL Engine  
OpenGL vendor: NVIDIA Corporation  
How to cite UCSF ChimeraX  

open 1fav format mmCIF fromDatabase pdb

Summary of feedback from opening 1fav fetched from pdb  
---  
notes | Used PDBx fixed column width tables to speed up reading mmCIF file  
Used PDBx keywords to speed up reading mmCIF file  
  
Chain information for 1fav #1  
---  
Chain | Description  
A | hiv-1 envelope protein chimera  
C | protein (transmembrane glycoprotein)  
  
1fav mmCIF Assemblies | 1| author_and_software_defined_assembly  

1fav citation:    Zhou, G., Ferrer, M., Chopra, R., Kapoor, T.M., Strassmaier,
T., Weissenhorn, W., Skehel, J.J., Oprian, D., Schreiber, S.L., Harrison,
S.C., Wiley, D.C. (2000). The structure of an HIV-1 specific cell entry
inhibitor in complex with the HIV-1 gp41 trimeric core. Bioorg.Med.Chem., 8,
2219-2227. PMID: 11026535. DOI: 10.1016/S0968-0896(00)00155-3  
Opened mmCIF data containing 888 atoms and 896 bonds  

show selAtoms

hide selAtoms ribbons

addh hbond false

Traceback (most recent call last):  
  File
"/Users/goddard/ucsf/chimerax/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
"/Users/goddard/ucsf/chimerax/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
"/Users/goddard/ucsf/chimerax/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
"/Users/goddard/ucsf/chimerax/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
"/Users/goddard/ucsf/chimerax/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
"/Users/goddard/ucsf/chimerax/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
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/util.py", line 112, in guess_termini  
    if cross_residue(c_term, 'C'):  
  File
"/Users/goddard/ucsf/chimerax/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
"/Users/goddard/ucsf/chimerax/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 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GTX 680MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation

[Tom Goddard]

Works in daily build.

My development build must not be up to date.

[Tom Goddard]

I rebuilt atomic before submitting this bug, and the error still happened.

Now I did a "make clean" then a "make install" in atomic and the error is fixed. It seems that "make install" in atomic does not update the module when it is out of date. I'll make a separate ticket for this -- it has burned me repeatedly.