ChimeraX bug report submission

[Eric Pettersen]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-11-27)
Description
Showing labeled pseudobonds as part of interactive clash detection.  Found problem after fixing #2630.  To reproduce:

open 3w7f
view /a:248
sel /a:248
clashes sel restrict cross showDist t reveal t continuous t
ui mousemode rightMode "bond rotation"

...then use right mouse over bonds in Tyr 248

Log:
UCSF ChimeraX version: 0.91 (2019-11-27)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3w7f

3w7f title:  
Crystal structure of the C(30) carotenoid dehydrosqualene synthase from
staphylococcus aureus complexed with farnesyl thiopyrophosphate [more info...]  
  
Chain information for 3w7f #1  
---  
Chain | Description  
A B | Dehydrosqualene synthase  
  
Non-standard residues in 3w7f #1  
---  
FPS — S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen
thiodiphosphate (farnesyl thiopyrophosphate)  
MG — magnesium ion  
  
3w7f mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
  

> select /a:248

12 atoms, 12 bonds, 1 model selected  

> view /a:248

> clashes sel restrict cross showDist true reveal true continuous true

No clashes  

> ui mousemode rightMode "bond rotation"

Traceback (most recent call last):  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label3d.py", line 434, in _update_graphics_if_needed  
self._rebuild_label_graphics()  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label3d.py", line 446, in _rebuild_label_graphics  
va = self._label_vertices()  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label3d.py", line 516, in _label_vertices  
va = concatenate([l._label_rectangle(spos, cposd) for l in self._labels])  
ValueError: zero-dimensional arrays cannot be concatenated  
  
Error processing trigger "graphics update":  
ValueError: zero-dimensional arrays cannot be concatenated  
  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label3d.py", line 516, in _label_vertices  
va = concatenate([l._label_rectangle(spos, cposd) for l in self._labels])  
  
See log for complete Python traceback.  
  

> torsion /A:248@CD1,CG,CB,CA -79.80




OpenGL version: 4.1 ATI-2.11.21
OpenGL renderer: AMD Radeon Pro 575X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.