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Opened 4 months ago
Closed 3 months ago
#18085 closed defect (nonchimerax)
Boltz subprocess: Access is denied
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.10rc202506130232 (2025-06-13 02:32:35 UTC)
Description
I am trying to run Boltz through ChimeraX and am receiving a permissions error. All folders in this directory are read/write though. Thank you!!
Log:
UCSF ChimeraX version: 1.10rc202506130232 (2025-06-13)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:/Users/AnthonyGizzi/Downloads/fold_a11_01/fold_a11_01_model_4.cif
Chain information for fold_a11_01_model_4.cif #1
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> open C:/Users/AnthonyGizzi/Downloads/fold_a11_326/fold_a11_326_model_4.cif
Chain information for fold_a11_326_model_4.cif #2
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_a11_01_model_4.cif, chain A (#1) with
fold_a11_326_model_4.cif, chain A (#2), sequence alignment score = 1886.6
RMSD between 260 pruned atom pairs is 0.265 angstroms; (across all 365 pairs:
17.232)
> ui tool show "Render/Select by Attribute"
[Repeated 1 time(s)]
> ui tool show "Modeller Comparative"
[Repeated 1 time(s)]
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #2/A
Alignment identifier is 2/A
> select #1/A:173-174
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #1/A:173-174
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #1/A:175
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:174-175
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/A:174
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:174
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/A:174
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:174
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> select #1/A:180
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:180
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/A:180
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:180
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> select #1/A:182
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:182
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/A:182
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:182
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> select #1/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:190-191
23 atoms, 24 bonds, 2 residues, 1 model selected
> show sel target ab
> select #2/A:190
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:190-191
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel target ab
> ui tool show "Show Sequence Viewer"
> sequence chain #1/C
Alignment identifier is 1/C
> select #1/B
62 atoms, 61 bonds, 10 residues, 1 model selected
> show sel target ab
> select #2/B
62 atoms, 61 bonds, 10 residues, 1 model selected
> show sel target ab
> open C:/Users/AnthonyGizzi/Downloads/fold_1131_11v/fold_1131_11v_model_4.cif
Chain information for fold_1131_11v_model_4.cif #3
---
Chain | Description
A | .
B | .
C | .
D | .
Computing secondary structure
> matchmaker #3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_a11_01_model_4.cif, chain A (#1) with
fold_1131_11v_model_4.cif, chain C (#3), sequence alignment score = 1492.5
RMSD between 276 pruned atom pairs is 0.326 angstroms; (across all 276 pairs:
0.326)
> ui tool show ViewDockX
No suitable models found for ViewDockX
> ui tool show Contacts
> select add #3
6833 atoms, 6998 bonds, 884 residues, 2 models selected
> select add #2
10710 atoms, 10969 bonds, 1371 residues, 2 models selected
> select subtract #2
6771 atoms, 6937 bonds, 874 residues, 1 model selected
> hide #2 models
> hide #1 models
> contacts interModel false ignoreHiddenModels true
5029 contacts
> hide #4 models
> show #4 models
> hide #4 models
> contacts interModel false intraModel false ignoreHiddenModels true
No contacts
> contacts interModel false intraMol false ignoreHiddenModels true
378 contacts
> contacts ignoreHiddenModels true
5029 contacts
> contacts ignoreHiddenModels true
5029 contacts
> show #4 models
> select add #4
6771 atoms, 6937 bonds, 5029 pseudobonds, 874 residues, 2 models selected
> select subtract #4
6771 atoms, 6937 bonds, 874 residues, 1 model selected
> ui tool show Contacts
> contacts interModel false intraModel false ignoreHiddenModels true
No contacts
> contacts interModel false intraMol false ignoreHiddenModels true
378 contacts
> contacts intraMol false ignoreHiddenModels true
378 contacts
> contacts intraMol false ignoreHiddenModels true
378 contacts
> contacts ignoreHiddenModels true
5029 contacts
> hide #4 models
> ui tool show H-Bonds
> hbonds reveal true
4041 hydrogen bonds found
> hbonds interModel false reveal true
1679 hydrogen bonds found
> hbonds interModel false intraModel false reveal true
0 hydrogen bonds found
> hbonds interModel false intraModel false intraMol false reveal true
0 hydrogen bonds found
> hbonds interModel false intraModel false intraMol false intraRes false
> reveal true
0 hydrogen bonds found
> hbonds interModel false intraModel false intraMol false intraRes false
> reveal true
0 hydrogen bonds found
> hide #5 models
> show #5 models
> hbonds intraModel false reveal true
2362 hydrogen bonds found
> hbonds intraModel false intraMol false intraRes false reveal true
2362 hydrogen bonds found
> hbonds intraModel false intraMol false intraRes false reveal true
2362 hydrogen bonds found
> hbonds interModel false intraMol false intraRes false reveal true
98 hydrogen bonds found
> hbonds interModel false intraMol false intraRes false
98 hydrogen bonds found
> show #4 models
> hide #4 models
> select add #3
6771 atoms, 6937 bonds, 5076 pseudobonds, 874 residues, 3 models selected
> select subtract #3
Nothing selected
> select add #3
6771 atoms, 6937 bonds, 5076 pseudobonds, 874 residues, 3 models selected
> hide (#!3 & sel) target a
> hbonds interModel false intraMol false intraRes false
98 hydrogen bonds found
> hbonds interModel false intraMol false intraRes false reveal true
98 hydrogen bonds found
> hbonds interModel false intraRes false reveal true
1670 hydrogen bonds found
> hide (#!3 & sel) target a
> hbonds interModel false intraMol false intraRes false reveal true
98 hydrogen bonds found
> select subtract #4
6771 atoms, 6937 bonds, 874 residues, 1 model selected
> select add #3
6771 atoms, 6937 bonds, 5076 pseudobonds, 874 residues, 3 models selected
> select subtract #3
Nothing selected
> select #3/B
62 atoms, 61 bonds, 6 pseudobonds, 10 residues, 2 models selected
> show (#!3 & sel) target ab
> color (#!3 & sel) byelement
> color (#!3 & sel) byhetero
> select add #3
6771 atoms, 6937 bonds, 5076 pseudobonds, 874 residues, 3 models selected
> select subtract #3
Nothing selected
> select #3/B
62 atoms, 61 bonds, 6 pseudobonds, 10 residues, 2 models selected
> color (#!3 & sel) byelement
> color (#!3 & sel) byhetero
> color (#!3 & sel) hot pink
> color (#!3 & sel) byhetero
> select add #4
62 atoms, 61 bonds, 5029 pseudobonds, 10 residues, 2 models selected
> select add #3
6771 atoms, 6937 bonds, 5076 pseudobonds, 874 residues, 3 models selected
> select subtract #3
Nothing selected
> show #!1 models
> hide #!3 models
> hide #5 models
> show #5 models
> select add #1
3944 atoms, 4039 bonds, 26 pseudobonds, 497 residues, 2 models selected
> hide (#!1 & sel) target a
> show #!2 models
> select add #2
7883 atoms, 8071 bonds, 51 pseudobonds, 994 residues, 4 models selected
> hide (#!1-2 & sel) target a
[Repeated 1 time(s)]
> hide #5 models
> show #5 models
> hide #5 models
> show #!3 models
> select subtract #2
3944 atoms, 4039 bonds, 26 pseudobonds, 497 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #1.1 models
> hide #2.1 models
> hide #3.1 models
> show #3.1 models
> ui tool show "Modeller Comparative"
> select add #1
3944 atoms, 4039 bonds, 26 pseudobonds, 497 residues, 2 models selected
> select add #2
7883 atoms, 8071 bonds, 51 pseudobonds, 994 residues, 4 models selected
No alignments chosen for modeling
> select subtract #2.1
7883 atoms, 8071 bonds, 26 pseudobonds, 994 residues, 3 models selected
> select subtract #1.1
7883 atoms, 8071 bonds, 994 residues, 2 models selected
> select add #1
7883 atoms, 8071 bonds, 26 pseudobonds, 994 residues, 3 models selected
> select add #2
7883 atoms, 8071 bonds, 51 pseudobonds, 994 residues, 4 models selected
> select subtract #1
3939 atoms, 4032 bonds, 25 pseudobonds, 497 residues, 2 models selected
> select subtract #2
Nothing selected
> select #1/B
62 atoms, 61 bonds, 10 residues, 1 model selected
> show sel target ab
> color sel byhetero
> color sel byelement
> select #2/B
62 atoms, 61 bonds, 10 residues, 1 model selected
> show sel target ab
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #2/A
Alignment identifier is 2/A
> sequence chain #3/A
Alignment identifier is 3/A
> select #1/A:174
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:174
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel target ab
> select #1/A:180
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:180
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> select #1/A:182
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:182
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel target ab
> select #1/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:190-191
23 atoms, 24 bonds, 2 residues, 1 model selected
> show sel target ab
> select #2/A:174
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:174
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/A:74-76,81-108,162-173,176-198,200-203,278-280,308-341
860 atoms, 867 bonds, 107 residues, 1 model selected
> select #2/A:180
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:180
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/A:182
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:182
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> select #2/A:190
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:190-191
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel target ab
> ui mousemode right select
> select #1/C:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:151
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/C:151
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel target ab
> select #3/C:147@CG
1 atom, 1 residue, 1 model selected
> select clear
> select #3/C:147@CD
1 atom, 1 residue, 1 model selected
> select clear
> select #2/A:182@CB
1 atom, 1 residue, 1 model selected
> select #1/A:182
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/C:168
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel target ab
> hide #!2 models
> hide #!1 models
> show #!1 models
> ui tool show Contacts
> mlp sel
Map values for surface "fold_1131_11v_model_4.cif_C SES surface": minimum
-29.04, mean -5.84, maximum 22.77
To also show corresponding color key, enter the above mlp command and add key
true
> select add #3
6771 atoms, 6937 bonds, 5076 pseudobonds, 874 residues, 4 models selected
> mlp sel
Map values for surface "fold_1131_11v_model_4.cif_A SES surface": minimum
-29.9, mean -7.673, maximum 20.29
Map values for surface "fold_1131_11v_model_4.cif_B SES surface": minimum
-23.16, mean -3.078, maximum 15.69
Map values for surface "fold_1131_11v_model_4.cif_C SES surface": minimum
-29.04, mean -5.84, maximum 22.77
Map values for surface "fold_1131_11v_model_4.cif_D SES surface": minimum
-26.14, mean -4.958, maximum 21.74
To also show corresponding color key, enter the above mlp command and add key
true
> volume planes z style image imageMode "full region"
No volumes specified
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right select
> hide #!3.2 models
> show #3.2 models
> hide #3.2 models
> hide #!3.5 models
> hide #!3.4 models
> ui mousemode right "clip rotate"
> ui mousemode right clip
[Repeated 1 time(s)]
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> select #3/A:216
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:216-219
48 atoms, 51 bonds, 9 pseudobonds, 4 residues, 2 models selected
> select #3/A:216
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:216
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:214
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:214
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:216
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:216
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:214-216
28 atoms, 28 bonds, 3 residues, 1 model selected
> save "C:/Users/AnthonyGizzi/OneDrive - Clasp
> Therapeutics/modeling/KRAS/A11/1131_A11_model.cxs"
> ui mousemode right "clip rotate"
> ui mousemode right clip
> select #3/A:218
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:218-219
24 atoms, 25 bonds, 1 pseudobond, 2 residues, 2 models selected
> select #3/A:241
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:241
4 atoms, 3 bonds, 1 residue, 1 model selected
> ui mousemode right "clip rotate"
> ui mousemode right clip
> hide #!3.3 models
> select #3/A:214
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:214
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (#!3 & sel) target ab
> select #3/A:217
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:216-217
24 atoms, 25 bonds, 2 residues, 1 model selected
> select #3/A:216
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:216
12 atoms, 12 bonds, 1 residue, 1 model selected
> show (#!3 & sel) target ab
> ui mousemode right "clip rotate"
> ui mousemode right clip
[Repeated 1 time(s)]
> ui mousemode right "clip rotate"
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "The operation
completed successfully."
> select #3/A:113
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:113
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (#!3 & sel) target ab
> label (#!3 & sel) text "{0.name} {0.number}{0.insertion_code}"
> hide (#!3 & sel) target a
> select #3/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:1-325
2384 atoms, 2438 bonds, 1565 pseudobonds, 325 residues, 2 models selected
> select #3/A:1-325
2384 atoms, 2438 bonds, 1565 pseudobonds, 325 residues, 2 models selected
> select #3/A:488
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:176-488
2314 atoms, 2366 bonds, 1476 pseudobonds, 313 residues, 2 models selected
> select #3/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:1-350
2572 atoms, 2629 bonds, 1764 pseudobonds, 350 residues, 2 models selected
> select #3/A:225
4 atoms, 3 bonds, 1 residue, 1 model selected
> show (#!3 & sel) target ab
> select #3/A:274
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:274
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:270
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:270
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:270
6 atoms, 5 bonds, 1 residue, 1 model selected
> show (#!3 & sel) target ab
> select #3/A:272
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:271-272
13 atoms, 12 bonds, 2 residues, 1 model selected
> show (#!3 & sel) target ab
> select #3/A:270
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:270-272
19 atoms, 18 bonds, 3 residues, 1 model selected
> select #3/A:306
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:306
7 atoms, 7 bonds, 1 residue, 1 model selected
> show (#!3 & sel) target ab
> select #3/A:299
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:299
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> select #3/A:307
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:307
6 atoms, 5 bonds, 1 residue, 1 model selected
> show (#!3 & sel) target ab
> select #3/A:308
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:308
4 atoms, 3 bonds, 1 residue, 1 model selected
> show (#!3 & sel) target ab
> select #3/A:309
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:309
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:304
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:304
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (#!3 & sel) target ab
> select #3/A:309
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:309
7 atoms, 6 bonds, 1 residue, 1 model selected
> show (#!3 & sel) target ab
> select #3/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> show (#!3 & sel) target ab
> select #3/A:304
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:303-304
16 atoms, 15 bonds, 1 pseudobond, 2 residues, 2 models selected
> show (#!3 & sel) target ab
Drag select of 3 atoms, 2 bonds, 1 residues
> select #3/A:216
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:216-219
48 atoms, 51 bonds, 9 pseudobonds, 4 residues, 2 models selected
> show (#!3 & sel) target ab
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "The operation
completed successfully."
[Repeated 13 time(s)]
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY2:" "The operation
completed successfully."
[Repeated 1 time(s)]
> select #3/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:1-425
3105 atoms, 3174 bonds, 2063 pseudobonds, 425 residues, 2 models selected
> ui tool show Boltz
> boltz predict protein #1/A protein #1/B protein #1/C name
> fold_a11_01_model_4.cif
Running Boltz prediction of 3 proteins with 497 residues on gpu
Using multiple sequence alignment server https://api.colabfold.com
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\boltz\boltz_gui.py", line 511, in _predict
self._run_prediction(options = ' '.join(options))
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\boltz\boltz_gui.py", line 528, in _run_prediction
br = run(self.session, cmd)
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10rc202506130232\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 1.10rc202506130232\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\boltz\predict.py", line 63, in boltz_predict
br.start(results_directory)
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\boltz\predict.py", line 217, in start
self._run_boltz_local()
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\boltz\predict.py", line 373, in _run_boltz_local
p = Popen(command, cwd = self._results_directory,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\subprocess.py",
line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\subprocess.py",
line 1538, in _execute_child
hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
PermissionError: [WinError 5] Access is denied
PermissionError: [WinError 5] Access is denied
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\subprocess.py",
line 1538, in _execute_child
hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> boltz predict protein #1/A protein #1/B protein #1/C name
> fold_a11_01_model_4.cif float16 true steering true
Running Boltz prediction of 3 proteins with 497 residues on gpu
Using multiple sequence alignment server https://api.colabfold.com
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\boltz\boltz_gui.py", line 511, in _predict
self._run_prediction(options = ' '.join(options))
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\boltz\boltz_gui.py", line 528, in _run_prediction
br = run(self.session, cmd)
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10rc202506130232\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 1.10rc202506130232\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\boltz\predict.py", line 63, in boltz_predict
br.start(results_directory)
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\boltz\predict.py", line 217, in start
self._run_boltz_local()
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\boltz\predict.py", line 373, in _run_boltz_local
p = Popen(command, cwd = self._results_directory,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\subprocess.py",
line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\subprocess.py",
line 1538, in _execute_child
hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
PermissionError: [WinError 5] Access is denied
PermissionError: [WinError 5] Access is denied
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\subprocess.py",
line 1538, in _execute_child
hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 560.94
OpenGL renderer: NVIDIA RTX 3500 Ada Generation Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: Precision 7680
OS: Microsoft Windows 11 Business (Build 26100)
Memory: 68,388,900,864
MaxProcessMemory: 137,438,953,344
CPU: 32 13th Gen Intel(R) Core(TM) i9-13950HX
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.4.0
build: 1.2.2.post1
certifi: 2025.6.15
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10rc202506130232
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 2.5.1
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: 1.6.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.19.1
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: 2.5.2
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: 1.45.1
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.10
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 310
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.4.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
WMI: 1.5.1
Change History (4)
comment:1 by , 4 months ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Boltz subprocess: Access is denied |
comment:2 by , 4 months ago
This "Access is denied" error from Windows is happening when ChimeraX tries to run Boltz as a subprocess. ChimeraX tries to create the Boltz input file in a new folder it makes ~/Desktop/boltz_<prediction_name>. Was that folder created? I see in the log a reference to OneDrive, the Microsoft cloud desktop which replaces your local ~/Desktop folder. My guess is that is the problem. ChimeraX tries to start Boltz in that newly created folder ~/Desktop/boltz_<prediction_name> but probably OneDrive has either hidden the local Desktop or made it unusable and that causes the "Access is denied".
If my theory is right you should press the Options button on the ChimeraX Boltz tool and enter a new Results Directory that is not in ~/Desktop. Alternatively you could turn off OneDrive so the local ~/Desktop location works.
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\subprocess.py",
line 1538, in _execute_child
hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
PermissionError: 5 Access is denied
comment:3 by , 4 months ago
Thank you very much for your input. I'll give this a try.
Many thanks,
Anthony
comment:4 by , 3 months ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
Perhaps using a different boltz results directory worked. No response from reporter.
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Reported by Anthony Gizzi