Opened 6 years ago

Closed 6 years ago

#2630 closed defect (fixed)

Continuous clash monitoring: wrong # of args

Reported by: Elaine Meng Owned by: Eric Pettersen
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 (2019-12-02)
Description
traceback trying to use bond-rotation mouse mode with continuous clash checking

Commands:
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:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start toolshed show $1

> alias whereprefs info path user unversioned config

executed startup.cxc  
UCSF ChimeraX version: 0.91 (2019-12-02)  
© 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  
  
  

> view /a:248

> select /a:248

12 atoms, 12 bonds, 1 model selected  

> clashes sel restrict cross showDist true reveal true continuous true

No clashes  

> ui mousemode rightMode "bond rotation"

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/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
Error processing trigger "changes":  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
  
See log for complete Python traceback.  
  
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/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
Error processing trigger "changes":  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
  
See log for complete Python traceback.  
  
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/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
Error processing trigger "changes":  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
  
See log for complete Python traceback.  
  
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/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
Error processing trigger "changes":  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
  
See log for complete Python traceback.  
  
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/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
Error processing trigger "changes":  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
  
See log for complete Python traceback.  
  
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/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
Error processing trigger "changes":  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
  
See log for complete Python traceback.  
  
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/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
Error processing trigger "changes":  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
  
See log for complete Python traceback.  
  
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/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
Error processing trigger "changes":  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
  
See log for complete Python traceback.  
  
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/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
Error processing trigger "changes":  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
  
See log for complete Python traceback.  
  
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/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
Error processing trigger "changes":  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
  
See log for complete Python traceback.  
  
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/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
Error processing trigger "changes":  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
  
See log for complete Python traceback.  
  
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/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
Error processing trigger "changes":  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
  
See log for complete Python traceback.  
  
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/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
Error processing trigger "changes":  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
  
See log for complete Python traceback.  
  
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/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
Error processing trigger "changes":  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
  
See log for complete Python traceback.  
  
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/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
Error processing trigger "changes":  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
  
See log for complete Python traceback.  
  
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/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
Error processing trigger "changes":  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
  
See log for complete Python traceback.  
  

> torsion /A:248@CD1,CG,CB,CA -114.10

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/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
Error processing trigger "changes":  
TypeError: _cmd() takes 8 positional arguments but 31 were given  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/cmd.py", line 117, in changes_cb  
_cmd(*tuple(call_data))  
  
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 Eric Pettersen, 6 years ago

Component: Unassigned → Structure Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Continuous clash monitoring: wrong # of args

comment:2 by Eric Pettersen, 6 years ago

Resolution: → fixed
Status: accepted → closed
Note: See TracTickets for help on using tickets.