#15983 closed defect (can't reproduce)

Cannot open PDB file for writing

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

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Your computer has Intel graphics driver 9565 with a known bug that
causes all Qt user interface panels to be blank. ChimeraX can partially fix
this but may make some panel titlebars and edges black. Hopefully newer Intel
graphics drivers will fix this.  
  
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> D:\\\WJF-709\\\ZNF384\\\ZNF384_complex_DNA\\\2024-9-20结构预测\\\fold_2024_05_16_10_22_znf384_3\\\fold_2024_05_16_10_22_znf384_3_model_0.cif

Chain information for fold_2024_05_16_10_22_znf384_3_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> save D:/WJF-709/ZNF384/ZNF384_complex_DNA/2024-9-20结构预测/ZNF384_3.pdb

Traceback (most recent call last):  
File "D:\Chimera-X\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 1541, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "D:\Chimera-X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "D:\Chimera-X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\Chimera-X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "D:\Chimera-X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "D:\Chimera-X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera-X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\Chimera-X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "D:\Chimera-X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "D:\Chimera-X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\atomic\pdb\\__init__.py", line 70, in save  
pdb.save_pdb(session, path, **kw)  
File "D:\Chimera-X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\atomic\pdb\pdb.py", line 119, in save_pdb  
(serial_numbering == "h36"), polymeric_res_names)  
OSError: Unable to open file
'D:/WJF-709/ZNF384/ZNF384_complex_DNA/2024-9-20结构预测/ZNF384_3.pdb' for writing  
  
OSError: Unable to open file
'D:/WJF-709/ZNF384/ZNF384_complex_DNA/2024-9-20结构预测/ZNF384_3.pdb' for writing  
  
File "D:\Chimera-X\ChimeraX 1.0\bin\lib\site-
packages\chimerax\atomic\pdb\pdb.py", line 119, in save_pdb  
(serial_numbering == "h36"), polymeric_res_names)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.9565
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel
Manufacturer: HUAWEI
Model: MACHD-WXX9
OS: Microsoft Windows 11 家庭中文版 (Build 22631)
Memory: 16,969,424,896
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (2)

comment:1 by pett, 13 months ago

Component: UnassignedInput/Output
Owner: set to pett
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionCannot open PDB file for writing

comment:2 by pett, 13 months ago

Resolution: can't reproduce
Status: acceptedclosed

Version 1.0; this throws IOError nowadays

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