Opened 6 years ago

Closed 6 years ago

#3178 closed defect (nonchimerax)

Error with GaudiViewX opening a .zip file

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
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:        Linux-5.3.0-51-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.94 (2020-04-08)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.94 (2020-04-08)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show GaudiViewX

/home/houda/Bureau/JD/Solutions/curc-4npw_157.zip is not a valid GAUDI result  
Traceback (most recent call last):  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gui.py", line 104, in handle_selection  
self.tm.gaudimain.display(model)  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gaudireader.py", line 111, in display  
self.session.models.add(self.models[key])  
KeyError: 'curc-4npw_157.zip'  
  
KeyError: 'curc-4npw_157.zip'  
  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gaudireader.py", line 111, in display  
self.session.models.add(self.models[key])  
  
See log for complete Python traceback.  
  

> ui autostart true GaudiViewX

Traceback (most recent call last):  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gui.py", line 97, in handle_selection  
self.tm.gaudimain.not_display(model)  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gaudireader.py", line 114, in not_display  
hide(self.session, self.models[key])  
KeyError: 'curc-4npw_157.zip'  
  
KeyError: 'curc-4npw_157.zip'  
  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gaudireader.py", line 114, in not_display  
hide(self.session, self.models[key])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gui.py", line 97, in handle_selection  
self.tm.gaudimain.not_display(model)  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gaudireader.py", line 114, in not_display  
hide(self.session, self.models[key])  
KeyError: 'curc-4npw_157.zip'  
  
KeyError: 'curc-4npw_157.zip'  
  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gaudireader.py", line 114, in not_display  
hide(self.session, self.models[key])  
  
See log for complete Python traceback.  
  

> ui autostart false GaudiViewX

> open /home/houda/Documents/structures/Complexe/4NPW_Complexe.pdb

Summary of feedback from opening
/home/houda/Documents/structures/Complexe/4NPW_Complexe.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 3
ASN A 7 1 5  
Start residue of secondary structure not found: HELIX 2 2 CYS A 8 ASN A 11 1 4  
Start residue of secondary structure not found: HELIX 3 3 VAL A 19 ALA A 25 1
7  
Start residue of secondary structure not found: HELIX 4 4 ALA A 30 ARG A 41 1
12  
Start residue of secondary structure not found: HELIX 5 5 LEU A 44 ARG A 47 1
4  
19 messages similar to the above omitted  
  
Chain information for 4NPW_Complexe.pdb  
---  
Chain | Description  
1.1/A | No description available  
  

> show target ab

> hide #* target a

> show target ab

> hide target a

> hide #* target a

> show target ab

> surface

> close session

> open /home/houda/Documents/structures/Complexe/4NPW_Complexe.pdb

Summary of feedback from opening
/home/houda/Documents/structures/Complexe/4NPW_Complexe.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 3
ASN A 7 1 5  
Start residue of secondary structure not found: HELIX 2 2 CYS A 8 ASN A 11 1 4  
Start residue of secondary structure not found: HELIX 3 3 VAL A 19 ALA A 25 1
7  
Start residue of secondary structure not found: HELIX 4 4 ALA A 30 ARG A 41 1
12  
Start residue of secondary structure not found: HELIX 5 5 LEU A 44 ARG A 47 1
4  
19 messages similar to the above omitted  
  
Chain information for 4NPW_Complexe.pdb  
---  
Chain | Description  
1.1/A | No description available  
  

> select #1.1/A:152

20 atoms, 20 bonds, 1 model selected  

> select up

201 atoms, 203 bonds, 1 model selected  

> select up

5200 atoms, 5257 bonds, 1 model selected  

> hide #* target a

> show sel target ab

> select clear

> toolshed show GaudiViewX

/home/houda/Bureau/JD/Solutions/curc-4npw_199.zip is not a valid GAUDI result  
Traceback (most recent call last):  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gui.py", line 104, in handle_selection  
self.tm.gaudimain.display(model)  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gaudireader.py", line 111, in display  
self.session.models.add(self.models[key])  
KeyError: 'curc-4npw_199.zip'  
  
KeyError: 'curc-4npw_199.zip'  
  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gaudireader.py", line 111, in display  
self.session.models.add(self.models[key])  
  
See log for complete Python traceback.  
  

> close session

Empty filename passed to function  

Traceback (most recent call last):  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gui.py", line 97, in handle_selection  
self.tm.gaudimain.not_display(model)  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gaudireader.py", line 114, in not_display  
hide(self.session, self.models[key])  
KeyError: 'curc-4npw_199.zip'  
  
KeyError: 'curc-4npw_199.zip'  
  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gaudireader.py", line 114, in not_display  
hide(self.session, self.models[key])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gui.py", line 97, in handle_selection  
self.tm.gaudimain.not_display(model)  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gaudireader.py", line 114, in not_display  
hide(self.session, self.models[key])  
KeyError: 'curc-4npw_199.zip'  
  
KeyError: 'curc-4npw_199.zip'  
  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gaudireader.py", line 114, in not_display  
hide(self.session, self.models[key])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gui.py", line 97, in handle_selection  
self.tm.gaudimain.not_display(model)  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gaudireader.py", line 114, in not_display  
hide(self.session, self.models[key])  
KeyError: 'curc-4npw_199.zip'  
  
KeyError: 'curc-4npw_199.zip'  
  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gaudireader.py", line 114, in not_display  
hide(self.session, self.models[key])  
  
See log for complete Python traceback.  
  

> close session

> close session

Traceback (most recent call last):  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gui.py", line 97, in handle_selection  
self.tm.gaudimain.not_display(model)  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gaudireader.py", line 114, in not_display  
hide(self.session, self.models[key])  
KeyError: 'curc-4npw_199.zip'  
  
KeyError: 'curc-4npw_199.zip'  
  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gaudireader.py", line 114, in not_display  
hide(self.session, self.models[key])  
  
See log for complete Python traceback.  
  

> toolshed show GaudiViewX

/home/houda/Bureau/JD/Solutions/curc-2itx_091.zip is not a valid GAUDI result  
Traceback (most recent call last):  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gui.py", line 104, in handle_selection  
self.tm.gaudimain.display(model)  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gaudireader.py", line 111, in display  
self.session.models.add(self.models[key])  
KeyError: 'curc-2itx_091.zip'  
  
KeyError: 'curc-2itx_091.zip'  
  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gaudireader.py", line 111, in display  
self.session.models.add(self.models[key])  
  
See log for complete Python traceback.  
  

> open "/home/houda/Bureau/PARAMETRIZATION/GA1 .mol2" format mol2

Summary of feedback from opening /home/houda/Bureau/PARAMETRIZATION/GA1 .mol2  
---  
warning | line 13: ignore unexpected line '~'  
  
Opened GA1 .mol2 containing 1 structures (1 atoms, 0 bonds)  

> close session

Traceback (most recent call last):  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gui.py", line 97, in handle_selection  
self.tm.gaudimain.not_display(model)  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gaudireader.py", line 114, in not_display  
hide(self.session, self.models[key])  
KeyError: 'curc-2itx_091.zip'  
  
KeyError: 'curc-2itx_091.zip'  
  
File "/home/houda/.local/share/ChimeraX/0.94/site-
packages/chimerax/gaudiviewx/gaudireader.py", line 114, in not_display  
hide(self.session, self.models[key])  
  
See log for complete Python traceback.  
  




OpenGL version: 4.5 (Core Profile) Mesa 19.2.8
OpenGL renderer: Mesa DRI Intel(R) Haswell Mobile 
OpenGL vendor: Intel Open Source Technology Center
Manufacturer: Hewlett-Packard
Model: HP ProBook 450 G2
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
CPU: 4 Intel(R) Core(TM) i5-4210U CPU @ 1.70GHz
Cache Size: 3072 KB
Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Haswell-ULT Integrated Graphics Controller [8086:0a16] (rev 0b)
	Subsystem: Hewlett-Packard Company Haswell-ULT Integrated Graphics Controller [103c:2248]
	Kernel driver in use: i915

Change History (2)

comment:1 by Eric Pettersen, 6 years ago

Component: Unassigned → Third Party
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Error with GaudiViewX opening a .zip file

comment:2 by Eric Pettersen, 6 years ago

Resolution: → nonchimerax
Status: accepted → closed
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