UnicodeDecodeError reading PDB file on Windows

[chimerax-bug-report@…]

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

[Eric Pettersen]

Would need the PDB file to figure out what codec is need on Windows.