Opened 17 months ago
Closed 17 months ago
#15261 closed defect (can't reproduce)
UnicodeDecodeError reading PDB file on Windows
Reported by: | Owned by: | Eric Pettersen | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Input/Output | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.22631 ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:\Users\natal\Downloads\1g97.pdb format pdb 1g97.pdb title: S.pneumoniae GLMU complexed with udp-N-acetylglucosamine and MG2+ [more info...] Chain information for 1g97.pdb #1 --- Chain | Description | UniProt A | N-acetylglucosamine-1-phosphate uridyltransferase | Q97R46_STRPN 1-459 Non-standard residues in 1g97.pdb #1 --- MG — magnesium ion NA — sodium ion UD1 — uridine-diphosphate-N-acetylglucosamine > select helix 1011 atoms, 1015 bonds, 126 residues, 1 model selected > select subtract /A:244 1003 atoms, 1006 bonds, 125 residues, 1 model selected > select /A:243 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > color red > hide #!1 models > show #!1 models > color #1 #55ffffff > color #1 white > color #1 #aaaaffff > open C:/Users/natal/Downloads/2e28.pdb 2e28.pdb title: Crystal structure analysis of pyruvate kinase from bacillus stearothermophilus [more info...] Chain information for 2e28.pdb #2 --- Chain | Description | UniProt A | PK | KPYK_BACST 1-587 Non-standard residues in 2e28.pdb #2 --- SO4 — sulfate ion > open C:/Users/natal/Downloads/2e28.pdb 2e28.pdb title: Crystal structure analysis of pyruvate kinase from bacillus stearothermophilus [more info...] Chain information for 2e28.pdb #3 --- Chain | Description | UniProt A | PK | KPYK_BACST 1-587 Non-standard residues in 2e28.pdb #3 --- SO4 — sulfate ion > close session > open C:\Users\natal\Downloads\2e28.pdb format pdb 2e28.pdb title: Crystal structure analysis of pyruvate kinase from bacillus stearothermophilus [more info...] Chain information for 2e28.pdb #1 --- Chain | Description | UniProt A | PK | KPYK_BACST 1-587 Non-standard residues in 2e28.pdb #1 --- SO4 — sulfate ion > select sidechain 2600 atoms, 2042 bonds, 587 residues, 1 model selected > select coil 1526 atoms, 1508 bonds, 211 residues, 1 model selected > close session > open C:/Users/natal/Downloads/1rvv.pdb 1rvv.pdb title: Synthase/riboflavin synthase complex of bacillus subtilis [more info...] Chain information for 1rvv.pdb #1 --- Chain | Description | UniProt 1 2 3 4 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z | riboflavin synthase | RISB_BACSU 1-154 Non-standard residues in 1rvv.pdb #1 --- INI — 5-nitro-6-ribityl-amino-2,4(1H,3H)-pyrimidinedione PO4 — phosphate ion > select /D 1205 atoms, 1184 bonds, 191 residues, 1 model selected > select ~sel 34945 atoms, 34336 bonds, 5539 residues, 1 model selected > delete atoms sel > delete bonds sel > undo Undo failed, probably because structures have been modified. > close session > open C:\Users\natal\Downloads\1rvv.pdb format pdb 1rvv.pdb title: Synthase/riboflavin synthase complex of bacillus subtilis [more info...] Chain information for 1rvv.pdb #1 --- Chain | Description | UniProt 1 2 3 4 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z | riboflavin synthase | RISB_BACSU 1-154 Non-standard residues in 1rvv.pdb #1 --- INI — 5-nitro-6-ribityl-amino-2,4(1H,3H)-pyrimidinedione PO4 — phosphate ion > select /A 1208 atoms, 1184 bonds, 194 residues, 1 model selected > select /B 1201 atoms, 1184 bonds, 187 residues, 1 model selected > SELECT/A/B/C/D/E Unknown command: SELECT/A/B/C/D/E > SELECT /A/B/C/D/E Unknown command: SELECT /A/B/C/D/E > SELECT A/B/C/D/E Unknown command: SELECT A/B/C/D/E > select /A/B/C/D/E 6025 atoms, 5920 bonds, 955 residues, 1 model selected > select ~sel 30125 atoms, 29600 bonds, 4775 residues, 1 model selected > delete atoms sel > delete bonds sel > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 1rvv.pdb_A SES surface #1.1: minimum, -14.87, mean -2.09, maximum 8.34 Coulombic values for 1rvv.pdb_B SES surface #1.2: minimum, -14.56, mean -2.09, maximum 8.38 Coulombic values for 1rvv.pdb_C SES surface #1.3: minimum, -20.26, mean -2.09, maximum 8.35 Coulombic values for 1rvv.pdb_D SES surface #1.4: minimum, -15.53, mean -2.10, maximum 8.37 Coulombic values for 1rvv.pdb_E SES surface #1.5: minimum, -14.86, mean -2.08, maximum 8.36 To also show corresponding color key, enter the above coulombic command and add key true > coulombic Coulombic values for 1rvv.pdb_A SES surface #1.1: minimum, -14.87, mean -2.09, maximum 8.34 Coulombic values for 1rvv.pdb_B SES surface #1.2: minimum, -14.56, mean -2.09, maximum 8.38 Coulombic values for 1rvv.pdb_C SES surface #1.3: minimum, -20.26, mean -2.09, maximum 8.35 Coulombic values for 1rvv.pdb_D SES surface #1.4: minimum, -15.53, mean -2.10, maximum 8.37 Coulombic values for 1rvv.pdb_E SES surface #1.5: minimum, -14.86, mean -2.08, maximum 8.36 To also show corresponding color key, enter the above coulombic command and add key true > color bychain > coulombic Coulombic values for 1rvv.pdb_A SES surface #1.1: minimum, -14.87, mean -2.09, maximum 8.34 Coulombic values for 1rvv.pdb_B SES surface #1.2: minimum, -14.56, mean -2.09, maximum 8.38 Coulombic values for 1rvv.pdb_C SES surface #1.3: minimum, -20.26, mean -2.09, maximum 8.35 Coulombic values for 1rvv.pdb_D SES surface #1.4: minimum, -15.53, mean -2.10, maximum 8.37 Coulombic values for 1rvv.pdb_E SES surface #1.5: minimum, -14.86, mean -2.08, maximum 8.36 To also show corresponding color key, enter the above coulombic command and add key true > mlp Map values for surface "1rvv.pdb_A SES surface": minimum -28.22, mean -4.131, maximum 22.25 Map values for surface "1rvv.pdb_B SES surface": minimum -28.63, mean -4.115, maximum 22.14 Map values for surface "1rvv.pdb_C SES surface": minimum -28.18, mean -4.098, maximum 22.22 Map values for surface "1rvv.pdb_D SES surface": minimum -27.83, mean -4.107, maximum 23.34 Map values for surface "1rvv.pdb_E SES surface": minimum -28.28, mean -4.096, maximum 22.77 To also show corresponding color key, enter the above mlp command and add key true > color red > surface > ui tool show "Color Actions" > undo [Repeated 2 time(s)] > select ::name="ALA" 500 atoms, 415 bonds, 100 residues, 1 model selected > select ::name="ALA" 500 atoms, 415 bonds, 100 residues, 1 model selected > select ::name="ALA","GLY" Expected an objects specifier or a keyword > select ::name= ALA/GLY 500 atoms, 415 bonds, 100 residues, 1 model selected > select ::name= ALA/GLY/PRO/VAL/LEU/ILE/MET/PRO 500 atoms, 415 bonds, 100 residues, 1 model selected > color (#!1 & sel) cyan > select ::name= ALA/GLY/PRO/VAL/LEU/ILE/MET/PRO 500 atoms, 415 bonds, 100 residues, 1 model selected > color (#!1 & sel) lime > select ::name="GLY" 320 atoms, 240 bonds, 80 residues, 1 model selected > color (#!1 & sel) lime > select = ALA/GLY/PRO/VAL/LEU/ILE/MET/PRO Missing or invalid "objects" argument: invalid objects specifier > undo [Repeated 8 time(s)] > select = ALA/GLY/PRO/VAL/LEU/ILE/MET/PRO Missing or invalid "objects" argument: invalid objects specifier > select ALA/GLY/PRO/VAL/LEU/ILE/MET/PRO Expected an objects specifier or a keyword > select ALA/GLY/PRO/VAL/LEU/ILE/MET/PRO Expected an objects specifier or a keyword > select /ALA/GLY/PRO/VAL/LEU/ILE/MET/PRO Nothing selected > color lime > undo > select /ALA/GLY/PRO/VAL/LEU/ILE/MET/PRO Nothing selected > select /ALA/GLY/PRO/VAL/LEU/ILE/MET/PRO Nothing selected > select /ALA/GLY/PRO/VAL/LEU/ILE/MET/PRO Nothing selected > select /ALA/GLY/PRO/VAL/LEU/ILE/MET/PRO Nothing selected > select RESIDUES /ALA/GLY/PRO/VAL/LEU/ILE/MET/PRO Expected an objects specifier or a keyword > select /ALA/GLY/PRO/VAL/LEU/ILE/MET/PRO} Expected an objects specifier or a keyword > select ::name="ALA" 500 atoms, 415 bonds, 100 residues, 1 model selected > select ::name="GLY" 320 atoms, 240 bonds, 80 residues, 1 model selected > color (#!1 & sel) lime > select ::name="ALA" 500 atoms, 415 bonds, 100 residues, 1 model selected > color (#!1 & sel) lime > select "ALA" "GLY" "PRO" "VAL" "LEU" "ILE" "MET" "PRO" Expected an objects specifier or a keyword > select "ALA" Expected an objects specifier or a keyword > select ::name="ALA" 500 atoms, 415 bonds, 100 residues, 1 model selected > color (#!1 & sel) lime > select ::name="ALA" "GLY" "PRO" "VAL" "LEU" "ILE" "MET" "PRO" Expected a keyword > select ::name="ILE" 640 atoms, 570 bonds, 80 residues, 1 model selected > color (#!1 & sel) lime > ui tool show "Color Actions" > select ::name="LEU" 320 atoms, 290 bonds, 40 residues, 1 model selected > color (#!1 & sel) lime > select ::name="MET" 120 atoms, 105 bonds, 15 residues, 1 model selected > color (#!1 & sel) lime > select ::name="PRO" 105 atoms, 105 bonds, 15 residues, 1 model selected > color (#!1 & sel) lime > select ::name="VAL" 455 atoms, 395 bonds, 65 residues, 1 model selected > color (#!1 & sel) lime > select ::name="SER" 120 atoms, 100 bonds, 20 residues, 1 model selected > color (#!1 & sel) yellow > select ::name="THR" 455 atoms, 405 bonds, 65 residues, 1 model selected > color (#!1 & sel) yellow > select ::name="CYS" 60 atoms, 50 bonds, 10 residues, 1 model selected > select ::name="CYS" 60 atoms, 50 bonds, 10 residues, 1 model selected > color (#!1 & sel) yellow > select ::name="GLN" 135 atoms, 120 bonds, 15 residues, 1 model selected > color (#!1 & sel) yellow > select ::name="ASN" 400 atoms, 350 bonds, 50 residues, 1 model selected > color (#!1 & sel) yellow > select ::name="LYS" 405 atoms, 370 bonds, 45 residues, 1 model selected > color (#!1 & sel) RED Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color (#!1 & sel) red > select ::name="ARG" 275 atoms, 250 bonds, 25 residues, 1 model selected > color (#!1 & sel) red > select ::name="HIS" 100 atoms, 100 bonds, 10 residues, 1 model selected > color (#!1 & sel) red > select ::name="ASP" 320 atoms, 280 bonds, 40 residues, 1 model selected > color (#!1 & sel) blue > select ::name="GLU" 410 atoms, 365 bonds, 45 residues, 1 model selected > color (#!1 & sel) blue > select ::name="PHE" 330 atoms, 330 bonds, 30 residues, 1 model selected > color (#!1 & sel) hot pink > select ::name="TYR" 180 atoms, 180 bonds, 15 residues, 1 model selected > color (#!1 & sel) hot pink > select ::name="TRP" 70 atoms, 75 bonds, 5 residues, 1 model selected > color (#!1 & sel) hot pink > close session > open C:/Users/natal/Downloads/1nqu.pdb 1nqu.pdb title: Crystal structure of lumazine synthase from aquifex aeolicus In complex with inhibitor: 6,7-dioxo-5H-8-ribitylaminolumazine [more info...] Chain information for 1nqu.pdb #1 --- Chain | Description | UniProt A B C D E | 6,7-dimethyl-8-ribityllumazine synthase | RISB_AQUAE 1-154 Non-standard residues in 1nqu.pdb #1 --- PO4 — phosphate ion RDL — 6,7-dioxo-5H-8-ribitylaminolumazine > select /A/B/C/D/E 6755 atoms, 6115 bonds, 1510 residues, 1 model selected > delete atoms sel > delete bonds sel > open C:\Users\natal\Downloads\1nqu.pdb format pdb 1nqu.pdb title: Crystal structure of lumazine synthase from aquifex aeolicus In complex with inhibitor: 6,7-dioxo-5H-8-ribitylaminolumazine [more info...] Chain information for 1nqu.pdb #1 --- Chain | Description | UniProt A B C D E | 6,7-dimethyl-8-ribityllumazine synthase | RISB_AQUAE 1-154 Non-standard residues in 1nqu.pdb #1 --- PO4 — phosphate ion RDL — 6,7-dioxo-5H-8-ribitylaminolumazine > select /A/B/D/E 5405 atoms, 4892 bonds, 1209 residues, 1 model selected > select ~sel & ##selected 1350 atoms, 1223 bonds, 301 residues, 1 model selected > delete atoms sel > delete bonds sel > select /A/B/C/D/E 5405 atoms, 4892 bonds, 1209 residues, 1 model selected > close session > open C:\Users\natal\Downloads\1rvv.pdb format pdb 1rvv.pdb title: Synthase/riboflavin synthase complex of bacillus subtilis [more info...] Chain information for 1rvv.pdb #1 --- Chain | Description | UniProt 1 2 3 4 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z | riboflavin synthase | RISB_BACSU 1-154 Non-standard residues in 1rvv.pdb #1 --- INI — 5-nitro-6-ribityl-amino-2,4(1H,3H)-pyrimidinedione PO4 — phosphate ion > close session > open C:\Users\natal\Downloads\1nqu.pdb format pdb 1nqu.pdb title: Crystal structure of lumazine synthase from aquifex aeolicus In complex with inhibitor: 6,7-dioxo-5H-8-ribitylaminolumazine [more info...] Chain information for 1nqu.pdb #1 --- Chain | Description | UniProt A B C D E | 6,7-dimethyl-8-ribityllumazine synthase | RISB_AQUAE 1-154 Non-standard residues in 1nqu.pdb #1 --- PO4 — phosphate ion RDL — 6,7-dioxo-5H-8-ribitylaminolumazine > select /A/B/C/D/E 6755 atoms, 6115 bonds, 1510 residues, 1 model selected > select ~sel & ##selected Nothing selected > save C:\Users\Public\Desktop\image1.png supersample 3 Permission denied writing file C:\Users\Public\Desktop\image1.png > mlp Map values for surface "1nqu.pdb_A SES surface": minimum -23.47, mean -3.782, maximum 21.94 Map values for surface "1nqu.pdb_B SES surface": minimum -24.66, mean -3.805, maximum 22.07 Map values for surface "1nqu.pdb_C SES surface": minimum -25.89, mean -3.842, maximum 22.51 Map values for surface "1nqu.pdb_D SES surface": minimum -24.77, mean -3.894, maximum 22.05 Map values for surface "1nqu.pdb_E SES surface": minimum -24.64, mean -3.807, maximum 22.12 To also show corresponding color key, enter the above mlp command and add key true > undo > select ::name="GLY" 300 atoms, 230 bonds, 75 residues, 1 model selected > color (#!1 & sel) yellow > select ::name="ALA" 475 atoms, 390 bonds, 95 residues, 1 model selected > color (#!1 & sel) yellow > select ::name="PRO" 140 atoms, 140 bonds, 20 residues, 1 model selected > color (#!1 & sel) yellow > select ::name="VAL" 385 atoms, 330 bonds, 55 residues, 1 model selected > color (#!1 & sel) yellow > select ::name="LEU" 600 atoms, 525 bonds, 75 residues, 1 model selected > color (#!1 & sel) yellow > select ::name="ILE" 600 atoms, 525 bonds, 75 residues, 1 model selected > color (#!1 & sel) yellow > select ::name="MET" 80 atoms, 70 bonds, 10 residues, 1 model selected > color (#!1 & sel) yellow > select ::name="GLY" 300 atoms, 230 bonds, 75 residues, 1 model selected > color (#!1 & sel) lime > select ::name="ALA" 475 atoms, 390 bonds, 95 residues, 1 model selected > color (#!1 & sel) lime > select ::name="PRO" 140 atoms, 140 bonds, 20 residues, 1 model selected > color (#!1 & sel) lime > select ::name="VAL" 385 atoms, 330 bonds, 55 residues, 1 model selected > color (#!1 & sel) lime > select ::name="LEU" 600 atoms, 525 bonds, 75 residues, 1 model selected > color (#!1 & sel) lime > select ::name="ILE" 600 atoms, 525 bonds, 75 residues, 1 model selected > color (#!1 & sel) lime > select ::name="VAL" 385 atoms, 330 bonds, 55 residues, 1 model selected > color (#!1 & sel) lime > select ::name="MET" 80 atoms, 70 bonds, 10 residues, 1 model selected > color (#!1 & sel) lime > select ::name="SER" 210 atoms, 175 bonds, 35 residues, 1 model selected > color (#!1 & sel) yellow > select ::name="THR" 245 atoms, 210 bonds, 35 residues, 1 model selected > color (#!1 & sel) yellow > select ::name="CYS" 30 atoms, 25 bonds, 5 residues, 1 model selected > color (#!1 & sel) yellow > select ::name="GLN" 90 atoms, 80 bonds, 10 residues, 1 model selected > color (#!1 & sel) yellow > select ::name="ASN" 160 atoms, 140 bonds, 20 residues, 1 model selected > color (#!1 & sel) yellow > select ::name="LYS" 315 atoms, 280 bonds, 35 residues, 1 model selected > color (#!1 & sel) red > select ::name="ARG" 610 atoms, 555 bonds, 55 residues, 1 model selected > color (#!1 & sel) red > select ::name="HIS" 200 atoms, 200 bonds, 20 residues, 1 model selected > color (#!1 & sel) red [Repeated 1 time(s)] > select ::name="ASP" 280 atoms, 245 bonds, 35 residues, 1 model selected > color (#!1 & sel) blue > select ::name="GLU" 630 atoms, 565 bonds, 70 residues, 1 model selected > color (#!1 & sel) blue > select ::name="PHE" 275 atoms, 275 bonds, 25 residues, 1 model selected > color (#!1 & sel) hot pink > select ::name="TYR" 120 atoms, 120 bonds, 10 residues, 1 model selected > color (#!1 & sel) hot pink > select ::name="TRP" 140 atoms, 150 bonds, 10 residues, 1 model selected > color (#!1 & sel) hot pink > undo > open "C:/Users/natal/Downloads/psicrofilico (1).pdb" Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\open_command\dialog.py", line 334, in _qt_safe run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + ("" File "C:\Program Files\ChimeraX\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\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 131, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 213, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 513, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 484, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\pdb\\__init__.py", line 45, in open return pdb.open_pdb(session, data, file_name, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\pdb\pdb.py", line 89, in open_pdb pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic, segid_chains, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "<frozen codecs>", line 322, in decode UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9 in position 94: invalid continuation byte UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9 in position 94: invalid continuation byte File "", line 322, in decode See log for complete Python traceback. > open C:/Users/natal/Downloads/psicrofilico.pdb Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\open_command\dialog.py", line 334, in _qt_safe run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + ("" File "C:\Program Files\ChimeraX\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\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 131, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 213, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 513, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 484, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\pdb\\__init__.py", line 45, in open return pdb.open_pdb(session, data, file_name, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\pdb\pdb.py", line 89, in open_pdb pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic, segid_chains, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "<frozen codecs>", line 322, in decode UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9 in position 94: invalid continuation byte UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9 in position 94: invalid continuation byte File "", line 322, in decode See log for complete Python traceback. > open C:/Users/natal/Downloads/psicrofilico.pdb Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\open_command\dialog.py", line 334, in _qt_safe run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + ("" File "C:\Program Files\ChimeraX\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\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 131, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 213, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 513, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 484, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\pdb\\__init__.py", line 45, in open return pdb.open_pdb(session, data, file_name, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\pdb\pdb.py", line 89, in open_pdb pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic, segid_chains, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "<frozen codecs>", line 322, in decode UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9 in position 94: invalid continuation byte UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9 in position 94: invalid continuation byte File "", line 322, in decode See log for complete Python traceback. > open C:/Users/natal/Downloads/6F677BBB-7D6C-4394-974D-D60B0FF77F12.pdf > open "C:/Users/natal/Downloads/psicrofilico (1).pdb" Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\open_command\dialog.py", line 334, in _qt_safe run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + ("" File "C:\Program Files\ChimeraX\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\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 131, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 213, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 513, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 484, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\pdb\\__init__.py", line 45, in open return pdb.open_pdb(session, data, file_name, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\pdb\pdb.py", line 89, in open_pdb pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic, segid_chains, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "<frozen codecs>", line 322, in decode UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9 in position 94: invalid continuation byte UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9 in position 94: invalid continuation byte File "", line 322, in decode See log for complete Python traceback. OpenGL version: 3.3.0 - Build 27.20.100.9565 OpenGL renderer: Intel(R) UHD Graphics OpenGL vendor: Intel Python: 3.11.2 Locale: es_AR.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: Acer Model: Aspire A315-56 OS: Microsoft Windows 11 Home Single Language (Build 22631) Memory: 8,368,807,936 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i3-1005G1 CPU @ 1.20GHz OSLanguage: es-MX Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 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-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 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 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 comtypes: 1.1.14 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 23.2 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pywin32: 305 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 WMI: 1.5.1
Change History (2)
comment:1 by , 17 months ago
Component: | Unassigned → Input/Output |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → UnicodeDecodeError reading PDB file on Windows |
comment:2 by , 17 months ago
Resolution: | → can't reproduce |
---|---|
Status: | accepted → closed |
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Would need the PDB file to figure out what codec is need on Windows.