id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
2522	H-bonds tool's model-restriction option error	Elaine Meng	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-10-19)
Description
turning on ""Restrict to models"" option in H-bonds causes traceback upon Apply/OK.

Doesn't matter which structure.  Trying to run the calculation with the ""Restrict to models"" option turned on (and the one & only model highlighted in the chooser) gives the error.  

However, I suggest this option is both confusing and unneeded and could be removed from the GUI anyway.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-10-19)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 2gbp format mmCIF fromDatabase pdb

2gbp title:  
Sugar and signal-transducer binding sites of the escherichia coli galactose
chemoreceptor protein [more info...]  
  
Chain information for 2gbp #1  
---  
Chain | Description  
A | D-galactose/D-glucose binding protein  
  
Non-standard residues in 2gbp #1  
---  
BGC — β-D-glucose  
CA — calcium ion  
  
  

> toolshed show H-Bonds

Traceback (most recent call last):  
File
""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/tool.py"", line 50, in run_hbonds  
run(self.session, "" "".join(self.gui.get_command()))  
File
""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/gui.py"", line 227, in get_command  
atom_spec = concise_model_spec(models)  
TypeError: concise_model_spec() missing 1 required positional argument:
'models'  
  
TypeError: concise_model_spec() missing 1 required positional argument:
'models'  
  
File
""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/hbonds/gui.py"", line 227, in get_command  
atom_spec = concise_model_spec(models)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation

}}}
"	defect	closed	normal		Structure Analysis		fixed						all	ChimeraX