FoldSeek: Permission denied writing temp file

[23036745r@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.9rc202412030631 (2024-12-03 06:31:08 UTC)
Description
tools->similar structure->searching with foldseek 
promopted this error

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9rc202412030631 (2024-12-03)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/USER/OneDrive/Lab Documents/Log book/Log Acetyl coA
> carboxylase/Acc no.7
> coot/Manuscript_Figure/Publication_Models2/1.BC_SingleRing_C2.cif"

Summary of feedback from opening C:/Users/USER/OneDrive/Lab Documents/Log
book/Log Acetyl coA carboxylase/Acc no.7
coot/Manuscript_Figure/Publication_Models2/1.BC_SingleRing_C2.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' on line 229  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "15" on line 98  
Bad residue range for struct_conf "16" on line 99  
Invalid residue range for struct_conf "17": invalid entity "B", on line 100  
Invalid residue range for struct_conf "18": invalid entity "B", on line 101  
Invalid residue range for struct_conf "19": invalid entity "B", on line 102  
Invalid residue range for struct_conf "20": invalid entity "B", on line 103  
Invalid residue range for struct_conf "21": invalid entity "B", on line 104  
12 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "17 1": invalid entity "B", on line
197  
Invalid sheet range for struct_sheet_range "18 1": invalid entity "B", on line
198  
Invalid sheet range for struct_sheet_range "19 1": invalid entity "B", on line
199  
Invalid sheet range for struct_sheet_range "20 1": invalid entity "B", on line
200  
Invalid sheet range for struct_sheet_range "21 1": invalid entity "B", on line
201  
17 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' on line 8549  
Skipping chem_comp category: Missing column 'type' on line 8804  
  
Chain information for 1.BC_SingleRing_C2.cif #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C G | No description available  
D E | No description available  
  

> hide atoms

> show cartoons

> dssp

Computing secondary structure  

> ui tool show "Similar Structures"

> foldseek /B database afdb50

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9rc202412030631\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 238, in _search  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.9rc202412030631\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202412030631\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202412030631\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 37, in
foldseek_search  
FoldseekWebQuery(session, chain, database=database,  
File "C:\Program Files\ChimeraX 1.9rc202412030631\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 74, in __init__  
mmcif_string = _mmcif_as_string(chain)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202412030631\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 284, in
_mmcif_as_string  
write_mmcif(chain.structure.session, f.name, models = [structure])  
File "src\\\mmcif_write.pyx", line 168, in
chimerax.mmcif.mmcif_write.write_mmcif  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\USER\\\AppData\\\Local\\\Temp\\\foldseek_mmcif__z4sg1wd.cif'  
  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\USER\\\AppData\\\Local\\\Temp\\\foldseek_mmcif__z4sg1wd.cif'  
  
File "src\\\mmcif_write.pyx", line 168, in
chimerax.mmcif.mmcif_write.write_mmcif  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 560.94
OpenGL renderer: NVIDIA GeForce GTX 1660 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_HK.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7C95
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 17,102,540,800
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 5600X 6-Core Processor             
OSLanguage: en-US

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    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
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[pett]

Reported by Jackie

[Tom Goddard]

ChimeraX tried to write a temporary mmCIF atomic model file to send to the Foldseek server and it got a permission denied error writing the file.

PermissionError: [Errno 13] Permission denied:
'C:
\Users
\USER
\AppData
\Local
\Temp
\foldseek_mmcifz4sg1wd.cif'

Maybe the problem is related to Microsoft OneDrive. The temporary file path should definitely be writable. The path was created by a standard Python function asking for a temporary file path. So this seems like a problem on your computer. Besides OneDrive it may be possible that anti-virus software trying to scan the mmCIF file that ChimeraX is writing locks the file and prevents it from writing it all -- I think that is unlikely.

The first thing is to try Foldseek again and see if it happens consistently. Then try it without using OneDrive.

Let me know if you figure it out. I've seen this error reported once or twice and never found out what cause it.