Opened 5 years ago

Closed 5 years ago

#3103 closed defect (can't reproduce)

Strudel Score can't write its own config file

Reported by: chimerax-bug-report@… Owned by:
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show "Strudel Score"

INTEGRATING  
Inject data called  
fill selectors called  
all chains (fill selectors) ['No chains found']  
Running: close all  

> close all

All chains (set data) ['A']  
active chain (set data) A  
Inject data called  
fill selectors called  
all chains (fill selectors) ['A']  
Y-RANGE Expanded  
active chain (update left) A  
Running: open
/Users/ardan/Downloads/T0102_correct_small_example/out_1.3/input/T0102.map  

> open
> /Users/ardan/Downloads/T0102_correct_small_example/out_1.3/input/T0102.map

Opened T0102.map, grid size 336,336,336, pixel 0.65, shown at level 1.29e-06,
step 2, values float32  
Running: volume #1 sdLevel 6 style mesh step 1  

> volume #1 sdLevel 6 style mesh step 1

Running: open
/Users/ardan/Downloads/T0102_correct_small_example/out_1.3/input/T0102EM010_1.cif  

> open
> /Users/ardan/Downloads/T0102_correct_small_example/out_1.3/input/T0102EM010_1.cif

Summary of feedback from opening
/Users/ardan/Downloads/T0102_correct_small_example/out_1.3/input/T0102EM010_1.cif  
---  
warning | Unknown polymer entity '1' near line 77  
  
Chain information for T0102EM010_1.cif #2  
---  
Chain | Description  
A | ?  
  
Running: style stick  

> style stick

Changed 1413 atom styles  
Running: size stickRadius 0.03  

> size stickRadius 0.03

Changed 1442 bond radii  
Running: ~ribbon  

> ~ribbon

Running: show atoms  

> show atoms

model_obj <Structure id=T0102EM010_1>  
Traceback (most recent call last):  
File "/Users/ardan/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/strudel_score/tool.py", line 149, in set_library  
with open(self.config_path, 'w') as f:  
PermissionError: [Errno 13] Permission denied:
'/Users/ardan/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/strudel_score/config.txt'  
  
PermissionError: [Errno 13] Permission denied:
'/Users/ardan/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/strudel_score/config.txt'  
  
File "/Users/ardan/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/strudel_score/tool.py", line 149, in set_library  
with open(self.config_path, 'w') as f:  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/ardan/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/strudel_score/tool.py", line 149, in set_library  
with open(self.config_path, 'w') as f:  
PermissionError: [Errno 13] Permission denied:
'/Users/ardan/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/strudel_score/config.txt'  
  
PermissionError: [Errno 13] Permission denied:
'/Users/ardan/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/strudel_score/config.txt'  
  
File "/Users/ardan/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/strudel_score/tool.py", line 149, in set_library  
with open(self.config_path, 'w') as f:  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/ardan/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/strudel_score/tool.py", line 149, in set_library  
with open(self.config_path, 'w') as f:  
PermissionError: [Errno 13] Permission denied:
'/Users/ardan/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/strudel_score/config.txt'  
  
PermissionError: [Errno 13] Permission denied:
'/Users/ardan/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/strudel_score/config.txt'  
  
File "/Users/ardan/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/strudel_score/tool.py", line 149, in set_library  
with open(self.config_path, 'w') as f:  
  
See log for complete Python traceback.  
  
All chains (set data) ['A']  
active chain (set data) A  
Y-RANGE Expanded  
active chain (update left) A  
Traceback (most recent call last):  
File "/Users/ardan/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/strudel_score/tool.py", line 184, in open_project  
folders = os.listdir(set_path)  
FileNotFoundError: [Errno 2] No such file or directory: ''  
  
FileNotFoundError: [Errno 2] No such file or directory: ''  
  
File "/Users/ardan/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/strudel_score/tool.py", line 184, in open_project  
folders = os.listdir(set_path)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.8.24
OpenGL renderer: AMD Radeon Pro Vega 16 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (1)

comment:1 by Eric Pettersen, 5 years ago

Component: UnassignedThird Party
Platform: all
Project: ChimeraX
Resolution: can't reproduce
Status: newclosed
Summary: ChimeraX bug report submissionStrudel Score can't write its own config file
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