Opened 6 years ago

Closed 6 years ago

#2522 closed defect (fixed)

H-bonds tool's model-restriction option error

Reported by: Elaine Meng Owned by: pett
Priority: normal Milestone:
Component: Structure Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

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

Change History (2)

comment:1 by pett, 6 years ago

Component: UnassignedStructure Analysis
Owner: set to pett
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionH-bonds tool's model-restriction option error

comment:2 by pett, 6 years ago

Resolution: fixed
Status: acceptedclosed
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