Opened 5 years ago

Closed 5 years ago

#3462 closed defect (fixed)

clashes: 'dict_values' object has no attribute 'sort'

Reported by: chimerax-bug-report@… 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:        Windows-10-10.0.18362
ChimeraX Version: 1.0rc202005222358 (2020-05-22 23:58:21 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0rc202005222358 (2020-05-22)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/q594r579/Documents/NatureComm2020/3j9cpore.pdb

Summary of feedback from opening
C:/Users/q594r579/Documents/NatureComm2020/3j9cpore.pdb  
---  
warning | Ignored bad PDB record found on line 23858  
END  
  
Chain information for 3j9cpore.pdb #1  
---  
Chain | Description  
A B C D E F G | No description available  
  

> open C:/Users/q594r579/Documents/NatureComm2020/Cola2_1.pdb

Summary of feedback from opening
C:/Users/q594r579/Documents/NatureComm2020/Cola2_1.pdb  
---  
warning | Ignored bad PDB record found on line 424  
END  
  
Chain information for Cola2_1.pdb #2  
---  
Chain | Description  
B | No description available  
  

> ui tool show Clashes

> clashes

1625 clashes  

> select #3

1625 pseudobonds, 1 model selected  

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> help help:user

> select #2/B:1-35

423 atoms, 439 bonds, 1 model selected  

> show sel atoms

> select #2/B:1-35

423 atoms, 439 bonds, 1 model selected  

> toolshed show

> hide sel atoms

> hide #2 models

> show #2 models

> ~select #2

Nothing selected  

> select #2

423 atoms, 439 bonds, 1 model selected  

> show sel atoms

> ~select #2

Nothing selected  

> select #3

1625 pseudobonds, 1 model selected  

> style sphere

Changed 24273 atom styles  

> style sphere

Changed 24273 atom styles  

> style ball

Changed 24273 atom styles  

> show cartoons

> style stick

Changed 24273 atom styles  

> hide #1 models

> show #1 models

> select #1

23850 atoms, 23967 bonds, 1570 pseudobonds, 2 models selected  

> select #3

1625 pseudobonds, 1 model selected  

> ~select #3

Nothing selected  

> select #3

1625 pseudobonds, 1 model selected  

> ~select #3

Nothing selected  

> undo

> undo

> undo

> style sphere

Changed 24273 atom styles  

> show surfaces

> toolshed show

> ui tool show Clashes

> clashes setAttrs true select true reveal true

1625 clashes  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0rc202005222358\bin\lib\site-
packages\chimerax\atomic\clashes\tool.py", line 55, in run_command  
run(self.session, " ".join(self.gui.get_command()))  
File "C:\Program Files\ChimeraX 1.0rc202005222358\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.0rc202005222358\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2802, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.0rc202005222358\bin\lib\site-
packages\chimerax\atomic\clashes\cmd.py", line 22, in cmd_clashes  
return _cmd(session, test_atoms, name, hbond_allowance, overlap_cutoff,
"clashes", color, radius, **kw)  
File "C:\Program Files\ChimeraX 1.0rc202005222358\bin\lib\site-
packages\chimerax\atomic\clashes\cmd.py", line 181, in _cmd  
clash_vals.sort()  
AttributeError: 'dict_values' object has no attribute 'sort'  
  
AttributeError: 'dict_values' object has no attribute 'sort'  
  
File "C:\Program Files\ChimeraX 1.0rc202005222358\bin\lib\site-
packages\chimerax\atomic\clashes\cmd.py", line 181, in _cmd  
clash_vals.sort()  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 25.20.100.6519
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: HP
Model: HP ProBook 450 G6
OS: Microsoft Windows 10 Enterprise (Build 18363)
Memory: 8,454,504,448
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8265U CPU @ 1.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (2)

comment:1 by pett, 5 years ago

Component: UnassignedStructure Analysis
Owner: set to pett
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionclashes: 'dict_values' object has no attribute 'sort'

comment:2 by pett, 5 years ago

Resolution: fixed
Status: acceptedclosed
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