id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18085 Boltz subprocess: Access is denied anthony@… Tom Goddard "{{{ 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 }}} " defect closed normal Structure Prediction nonchimerax all ChimeraX