FoldSeek: Permission denied writing temp file

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:\Users\osull\OneDrive\Desktop\test_d7274_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
> format pdb

Chain information for
test_d7274_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> open "C:/Users/osull/OneDrive/Desktop/json
> imags/test_4c041_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"

Chain information for
test_4c041_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #2  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> ui tool show "Similar Structures"

> select #2/A:1-652

5341 atoms, 5464 bonds, 652 residues, 1 model selected  

> hide #2 models

> show #2 models

Must choose a chain in the similar structures panel before running search  

> foldseek #1/A

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 238, in _search  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.9\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 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 37, in
foldseek_search  
FoldseekWebQuery(session, chain, database=database,  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 74, in __init__  
mmcif_string = _mmcif_as_string(chain)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\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\\\osull\\\AppData\\\Local\\\Temp\\\foldseek_mmcif_657eh3ne.cif'  
  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\osull\\\AppData\\\Local\\\Temp\\\foldseek_mmcif_657eh3ne.cif'  
  
File "src\\\mmcif_write.pyx", line 168, in
chimerax.mmcif.mmcif_write.write_mmcif  
  
See log for complete Python traceback.  
  

> sequence search #1/A database afdb

Found 152 similar structures to
test_d7274_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #1/A in afdb
database using mmseqs2, name mm1  

> open A0A1D8PKB7 fromDatabase alphafold

Summary of feedback from opening A0A1D8PKB7 fetched from alphafold  
---  
notes | Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold A0A1D8PKB7 from
https://alphafold.ebi.ac.uk/files/AF-A0A1D8PKB7-F1-model_v4.cif  
  
Chain information for AlphaFold A0A1D8PKB7 #3  
---  
Chain | Description | UniProt  
A | Uncharacterized protein | A0A1D8PKB7_CANAL 1-536  
  
Color AlphaFold A0A1D8PKB7 by residue attribute pLDDT_score  
Deleted 46 C-terminal residues, 3 N-terminal residues.  
Alignment of A0A1D8PKB7 chain A to query has RMSD 0.962 using 359 of 462
paired residues within cutoff distance 2.0  

> hide #1 models

> show #1 models

> hide #2 models

> open A0A0D2HAR8 fromDatabase alphafold

Summary of feedback from opening A0A0D2HAR8 fetched from alphafold  
---  
note | Fetching compressed AlphaFold A0A0D2HAR8 from https://alphafold.ebi.ac.uk/files/AF-A0A0D2HAR8-F1-model_v4.cif  
  
Chain information for AlphaFold A0A0D2HAR8 #4  
---  
Chain | Description | UniProt  
A | Unplaced genomic scaffold supercont1.3, whole genome shotgun sequence | A0A0D2HAR8_9EURO 1-502  
  
Color AlphaFold A0A0D2HAR8 by residue attribute pLDDT_score  
Deleted 70 C-terminal residues.  
Alignment of A0A0D2HAR8 chain A to query has RMSD 1.05 using 304 of 419 paired
residues within cutoff distance 2.0  

> hide #3 models

> close

> open "C:/Users/osull/OneDrive/Desktop/json
> imags/test_0ca95_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_1a942_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_2b4cf_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_2bd82_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_2dc51_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_3ff73_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_4c041_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_4d34f_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_5dbb5_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_6e14e_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_7c193_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_7c293_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_7ec24_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_8e627_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_09c81_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_9c0a0_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_9f8ad_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_18e77_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_22c0f_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_34db1_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_38d0b_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_39e08_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_48ea8_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_59f61_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_66a38_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_70cb1_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_81b0f_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_99c93_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_143a0_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_333c7_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_355c3_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_405fc_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_455dd_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_0562d_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_646ff_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_699a0_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_857a2_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_896be_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_953fb_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_1126a_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_02065_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_03244_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_3399a_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_4465f_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_4591c_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_5527e_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_5530a_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_6371d_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_8006b_0_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_8477d_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_9329a_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_23222_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_31730_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_50169_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_66302_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_76834_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_81509_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_81571_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_87686_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_94303_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_99421_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_a0ee6_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_a4a35_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_a4a67_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_a05ec_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_a24ee_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_a27d7_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_a872c_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_b0b4d_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_b3d31_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_b7f7c_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_ba85b_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_bb8d1_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_bddfa_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_be98d_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_be177_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_c417b_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_c953c_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_c1765_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_c3900_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_cbeb0_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_cc665_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_ce56c_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_cea45_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_d3db8_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_d8d6f_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_d9fe1_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_d21e5_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_d3729_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_d7274_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_dbea7_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_dc1a1_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_dc775_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_dfff4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_e2e92_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_e48c2_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_e695c_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_edfce_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_ef8a2_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_f1bc0_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_f8224_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> "C:/Users/osull/OneDrive/Desktop/json
> imags/test_fb94c_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb"

Chain information for
test_0ca95_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for
test_1a942_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for
test_2b4cf_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #3  
---  
Chain | Description  
A | No description available  
  
Chain information for
test_2bd82_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #4  
---  
Chain | Description  
A | No description available  
  
Chain information for
test_2dc51_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #5  
---  
Chain | Description  
A | No description available  
  
Chain information for
test_3ff73_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #6  
---  
Chain | Description  
A | No description available  
  
Chain information for
test_4c041_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #7  
---  
Chain | Description  
A | No description available  
  
Chain information for
test_4d34f_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #8  
---  
Chain | Description  
A | No description available  
  
Chain information for
test_5dbb5_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #9  
---  
Chain | Description  
A | No description available  
  
Chain information for
test_6e14e_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #10  
---  
Chain | Description  
A | No description available  
  
Chain information for
test_7c193_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb #11  
---  
Chain | Description  
A | No description available  
  
Chain information for
test_7c293_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #12  
---  
Chain | Description  
A | No description available  
  
Chain information for
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test_fb94c_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb #102  
---  
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A | No description available  
  
Computing secondary structure  
[Repeated 101 time(s)]

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> select ~sel & ##selected

Nothing selected  

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> log metadata #95

The model has no metadata

> log chains #95

Chain information for
test_e2e92_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb #95  
---  
Chain | Description  
A | No description available  
  

> log metadata #95

The model has no metadata

> log chains #95

Chain information for
test_e2e92_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb #95  
---  
Chain | Description  
A | No description available  
  

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> sequence search #1/A

RCSB sequence search no matches found  

> sequence search #1/A

RCSB sequence search no matches found  

> foldseek #1/A database afdb50

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 238, in _search  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.9\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 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 37, in
foldseek_search  
FoldseekWebQuery(session, chain, database=database,  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 74, in __init__  
mmcif_string = _mmcif_as_string(chain)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\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\\\osull\\\AppData\\\Local\\\Temp\\\foldseek_mmcif_w6js9iym.cif'  
  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\osull\\\AppData\\\Local\\\Temp\\\foldseek_mmcif_w6js9iym.cif'  
  
File "src\\\mmcif_write.pyx", line 168, in
chimerax.mmcif.mmcif_write.write_mmcif  
  
See log for complete Python traceback.  
  

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"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "The operation
completed successfully."  

[Repeated 11 time(s)]

> foldseek #1/A database afdb50

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 238, in _search  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.9\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 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 37, in
foldseek_search  
FoldseekWebQuery(session, chain, database=database,  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 74, in __init__  
mmcif_string = _mmcif_as_string(chain)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\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\\\osull\\\AppData\\\Local\\\Temp\\\foldseek_mmcif_hoadap6g.cif'  
  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\osull\\\AppData\\\Local\\\Temp\\\foldseek_mmcif_hoadap6g.cif'  
  
File "src\\\mmcif_write.pyx", line 168, in
chimerax.mmcif.mmcif_write.write_mmcif  
  
See log for complete Python traceback.  
  

> foldseek #1/A

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 238, in _search  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.9\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 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 37, in
foldseek_search  
FoldseekWebQuery(session, chain, database=database,  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 74, in __init__  
mmcif_string = _mmcif_as_string(chain)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\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\\\osull\\\AppData\\\Local\\\Temp\\\foldseek_mmcif_40prquti.cif'  
  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\osull\\\AppData\\\Local\\\Temp\\\foldseek_mmcif_40prquti.cif'  
  
File "src\\\mmcif_write.pyx", line 168, in
chimerax.mmcif.mmcif_write.write_mmcif  
  
See log for complete Python traceback.  
  

> sequence search #1/A database afdb

RCSB sequence search no matches found  

> similarstructures blast #1/A database afdb

Exception in thread Thread-34 (_run_function):  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\threading.py", line 1038, in
_bootstrap_inner  
self.run()  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\threading.py", line 975, in run  
self._target(*self._args, **self._kwargs)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\tasks.py", line 300, in _run_function  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\webservices\cxservices_job.py", line 148, in run  
reason = json.loads(e.body)["description"]  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\json\\__init__.py", line 346, in
loads  
return _default_decoder.decode(s)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\json\decoder.py", line 337, in
decode  
obj, end = self.raw_decode(s, idx=_w(s, 0).end())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\json\decoder.py", line 355, in
raw_decode  
raise JSONDecodeError("Expecting value", s, err.value) from None  
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)  

> sequence search #1/A database afdb

RCSB sequence search no matches found  

> sequence search #1/A

RCSB sequence search no matches found  

> save "C:/Users/osull/OneDrive/Desktop/json imags/images in chimera used for
> comparison .cxs"

> open A0A1D8PKB7 fromDatabase alphafold

Summary of feedback from opening A0A1D8PKB7 fetched from alphafold  
---  
note | Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
  
Chain information for AlphaFold A0A1D8PKB7 #103  
---  
Chain | Description | UniProt  
A | Uncharacterized protein | A0A1D8PKB7_CANAL 1-536  
  
Color AlphaFold A0A1D8PKB7 by residue attribute pLDDT_score  
Deleted 46 C-terminal residues, 3 N-terminal residues.  

> open Q9FWW6 fromDatabase alphafold

Summary of feedback from opening Q9FWW6 fetched from alphafold  
---  
note | Fetching compressed AlphaFold Q9FWW6 from https://alphafold.ebi.ac.uk/files/AF-Q9FWW6-F1-model_v4.cif  
  
Chain information for AlphaFold Q9FWW6 #104  
---  
Chain | Description | UniProt  
A | Flavin-containing monooxygenase FMO GS-OX-like 1 | GSXL1_ARATH 1-468  
  
Color AlphaFold Q9FWW6 by residue attribute pLDDT_score  
Deleted 116 C-terminal residues, 11 N-terminal residues.  

> hide #103 models

> hide #104 models

> foldseek #1/A database afdb50

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 238, in _search  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.9\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 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 37, in
foldseek_search  
FoldseekWebQuery(session, chain, database=database,  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\foldseek_search.py", line 74, in __init__  
mmcif_string = _mmcif_as_string(chain)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\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\\\osull\\\AppData\\\Local\\\Temp\\\foldseek_mmcif_wilu1ml0.cif'  
  
PermissionError: [Errno 13] Permission denied:
'C:\\\Users\\\osull\\\AppData\\\Local\\\Temp\\\foldseek_mmcif_wilu1ml0.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 - Build 30.0.101.1692
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

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

Manufacturer: LENOVO
Model: 82BH
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 16,969,424,896
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1

[Eric Pettersen]

Duplicate of #17050