UnicodeDecodeError reading PDB file

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\Ahmed\Downloads\pdb2q3z.ent format pdb

pdb2q3z.ent title:  
Transglutaminase 2 undergoes large conformational change upon activation [more
info...]  
  
Chain information for pdb2q3z.ent #1  
---  
Chain | Description | UniProt  
A | transglutaminase 2 | TGM2_HUMAN 1-687  
X | polypeptide |   
  
Non-standard residues in pdb2q3z.ent #1  
---  
ACE — acetyl group  
NH2 — amino group  
ONL — 5-oxo-L-norleucine  
SO4 — sulfate ion  
  

> color #1 #7f71d2ff

> distance :277@SG :335@NE2

Distance between /A CYS 277 SG and HIS 335 NE2: 5.726Å  

> distance :335@NE2 :358@OD2

Distance between /A HIS 335 NE2 and ASP 358 OD2: 2.954Å  

> distance :277@SG :358@OD2

Distance between /A CYS 277 SG and ASP 358 OD2: 8.388Å  

> style stick

Changed 5519 atom styles  

> show :277,335,358

> represent sphere sel

Unknown command: represent sphere sel  
Drag select of 5 atoms, 21 residues, 5 bonds  

> select clear

> select add /A:277

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select add /A:335

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select add /A:358@OD2

17 atoms, 15 bonds, 3 residues, 1 model selected  

> color sel white

Drag select of 1 atoms, 7 residues, 1 bonds  

> select add /A:159

91 atoms, 29 bonds, 11 residues, 1 model selected  

> select clear

> select /A:277

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:335

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select /A:358

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel white

> label sel text "{0.name} {0.number}{0.insertion_code}"

> select add /A:335

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select add /A:277

24 atoms, 22 bonds, 3 residues, 1 model selected  

> label sel text "{0.name} {0.number}{0.insertion_code}"

> select /A:338

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:277

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select add /A:335

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select add /A:358

24 atoms, 22 bonds, 3 residues, 1 model selected  

> save "C:/Users/Ahmed/Downloads/New Folder2/ff.jpg" width 859 height 624
> supersample 3

> hide #!1 models

> hide #!2 models

> hide #2.1 models

> open C:/Users/Ahmed/Downloads/AF-Q8C8H8-F1-model_v4.pdb

AF-Q8C8H8-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for kyphoscoliosis peptidase (Q8C8H8) [more
info...]  
  
Chain information for AF-Q8C8H8-F1-model_v4.pdb #3  
---  
Chain | Description | UniProt  
A | kyphoscoliosis peptidase | KY_MOUSE 1-661  
  
Computing secondary structure  

> color #3 #dd637fff

> distance show true

Missing or invalid "objects" argument: invalid objects specifier  

> distance #3/A:225@SG #3/A:267@NE2

Distance between AF-Q8C8H8-F1-model_v4.pdb #3/A CYS 225 SG and HIS 267 NE2:
5.897Å  

> distance #3/A:267@NE2 #3/A:282@OD2

Distance between AF-Q8C8H8-F1-model_v4.pdb #3/A HIS 267 NE2 and ASP 282 OD2:
2.729Å  

> distance #3/A:225@SG #3/A:282@OD2

Distance between AF-Q8C8H8-F1-model_v4.pdb #3/A CYS 225 SG and ASP 282 OD2:
8.120Å  

> distance style stick

Expected a keyword  

> label size 2

> label color yellow

> distance style stick

Expected a keyword  

> label size 2

> label color yellow

> color hotpink target distance

Invalid "target" argument: Character 'd' is not an allowed target, must be one
of acrsbmpfl  

> show distances

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> distance #1:/A:225@SG #1:/A:267@NE2

Missing or invalid "objects" argument: only initial part "#1" of atom
specifier valid  

> distance #1:/A:267@NE2 #1:/A:282@OD2

Missing or invalid "objects" argument: only initial part "#1" of atom
specifier valid  

> distance #1:/A:225@SG #1:/A:282@OD2

Missing or invalid "objects" argument: only initial part "#1" of atom
specifier valid  

> distance color red

Missing or invalid "objects" argument: invalid objects specifier  

> label color yellow

> label size 2

> distance #3:/A:225@SG #3:/A:267@NE2

Missing or invalid "objects" argument: only initial part "#3" of atom
specifier valid  

> distance #3:/A:267@NE2 #3:/A:282@OD2

Missing or invalid "objects" argument: only initial part "#3" of atom
specifier valid  

> distance #3:/A:225@SG #3:/A:282@OD2

Missing or invalid "objects" argument: only initial part "#3" of atom
specifier valid  

> color red :225,267,282

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> label :225,267,282

Drag select of 6 residues  
Drag select of 11 residues  

> select clear

[Repeated 1 time(s)]

> select add #3/A:225

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select add #3/A:267

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select #3/A:225

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #3/A:267

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select add #3/A:225

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select add #3/A:282

24 atoms, 22 bonds, 3 residues, 1 model selected  

> color sel white

> label sel text "{0.name} {0.number}{0.insertion_code}"

> info atoms #3/A:225@SG

atom id #3/A:225@SG idatm_type S3  

> info atoms #3/A:267@NE2

atom id #3/A:267@NE2 idatm_type Npl  

> info atoms #3/A:282@OD2

atom id #3/A:282@OD2 idatm_type O2-  

> distance show true

Missing or invalid "objects" argument: invalid objects specifier  

> distance #3/A:225@SG #3/A:267@NE2

Distance already exists; modify distance properties with 'distance style'  

> distance #3/A:267@NE2 #3/A:282@OD2

Distance already exists; modify distance properties with 'distance style'  

> distance #3/A:225@SG #3/A:282@OD2

Distance already exists; modify distance properties with 'distance style'  

> label create dist_label1 text "C225–H267" size 2 color white

Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword  

> label create dist_label2 text "H267–D282" size 2 color white

Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword  

> label create dist_label3 text "C225–D282" size 2 color white

Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword  

> label create dist_label3 text "C225–D282" size 2 color white

Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword  

> label size 2

> label color yellow

> color #3.1 yellow models

> select add #3.1

24 atoms, 22 bonds, 3 residues, 2 models selected  

> select subtract #3.1

24 atoms, 22 bonds, 3 residues, 1 model selected  

> label size default

[Repeated 1 time(s)]

> label color default

> color default target distance

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> show distances

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show distances

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> labelopt size 2 color yellow background true

Unknown command: labelopt size 2 color yellow background true  

> distance show true /A:225@SG /A:267@NE2

Missing or invalid "objects" argument: invalid objects specifier  

> distance show true /A:267@NE2 /A:282@OD2

Missing or invalid "objects" argument: invalid objects specifier  

> distance show true /A:225@SG /A:282@OD2

Missing or invalid "objects" argument: invalid objects specifier  

> style stick /A:225,267,282

Expected a keyword  

> color red /A:225

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color blue /A:267

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color orange /A:282

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> labelopt size 2 color white

Unknown command: labelopt size 2 color white  

> set silhouettes

Missing "silhouettes" keyword's argument  

> color yellow :225,267,282

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> style stick :225,267,282

Expected a keyword  

> show :225,267,282

> distance :225@SG :267@NE2

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 3 atoms and 0
measurable objects  

> distance :267@NE2 :282@OD2

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 3 atoms and 0
measurable objects  

> distance :225@SG :282@OD2

Distance already exists; modify distance properties with 'distance style'  

> distance :225@SG :282@OD2

Distance already exists; modify distance properties with 'distance style'  

> distance :225 :267

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 32 atoms and 0
measurable objects  

> distance :267 :282

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 33 atoms and 0
measurable objects  

> distance :225 :282

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 25 atoms and 0
measurable objects  

> style stick /A:225,267,282

Expected a keyword  

> color red /A:225

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color blue /A:267

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color orange /A:282

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> labelopt size 2 color white

Unknown command: labelopt size 2 color white  

> set silhouettes

Missing "silhouettes" keyword's argument  

> show distances

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> labelopt size 2 color yellow background true

Unknown command: labelopt size 2 color yellow background true  

> show distances

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> distance #3:/A:277@SG #3:/A:335@NE2

Missing or invalid "objects" argument: only initial part "#3" of atom
specifier valid  

> distance sel

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 24 atoms and 0
measurable objects  

> label size 2

> label color yellow

> distance color hotpink

Missing or invalid "objects" argument: invalid objects specifier  

> hide #3.1 models

> label size 2

> label color yellow

> distance color hotpink

Missing or invalid "objects" argument: invalid objects specifier  

> show #3.1 models

> hide #3.1 models

> show #3.1 models

> hide #3.1 models

> show #3.1 models

> hide #3.1 models

> distance #3:/A:225@SG #3:/A:267@NE2

Missing or invalid "objects" argument: only initial part "#3" of atom
specifier valid  

> distance #3:/A:267@NE2 #3:/A:282@OD2

Missing or invalid "objects" argument: only initial part "#3" of atom
specifier valid  

> distance #3:/A:225@SG #3:/A:282@OD2

Missing or invalid "objects" argument: only initial part "#3" of atom
specifier valid  

> distance color red

Missing or invalid "objects" argument: invalid objects specifier  

> label color yellow

> label size 2

> show #3.1 models

> select add #3.1

24 atoms, 22 bonds, 3 residues, 2 models selected  

> select subtract #3.1

24 atoms, 22 bonds, 3 residues, 1 model selected  

> hide #3.1 models

> info atoms #3:/A:225@SG

Expected a keyword  

> info atoms #3:/A:267@NE2

Expected a keyword  

> info atoms #3:/A:282@OD2

Expected a keyword  

> color red :225,267,282

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> label :225,267,282

> distance show true

Missing or invalid "objects" argument: invalid objects specifier  

> distance #3/A:225@SG #3/A:267@NE2

Distance already exists; modify distance properties with 'distance style'  

> distance #3/A:267@NE2 #3/A:282@OD2

Distance already exists; modify distance properties with 'distance style'  

> distance #3/A:225@SG #3/A:282@OD2

Distance already exists; modify distance properties with 'distance style'  

> distance #3/A:267@NE2 #3/A:282@OD2

Distance already exists; modify distance properties with 'distance style'  

> view #3.1 clip false

No displayed objects specified.  

> label create dist_label1 text "C225–H267" size 2 color white

Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword  

> label create dist_label2 text "H267–D282" size 2 color white

Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword  

> label create dist_label3 text "C225–D282" size 2 color white

Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword  

> label create dist_label3 text "C225–D282" size 2 color white

Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword  

> distance style stick

Expected a keyword  

> label size 2

> label color yellow

> color hotpink target distance

Invalid "target" argument: Character 'd' is not an allowed target, must be one
of acrsbmpfl  

> show distances

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #3.1 models

> hide #3.1 models

> select add #3.1

24 atoms, 22 bonds, 3 residues, 2 models selected  

> select subtract #3.1

24 atoms, 22 bonds, 3 residues, 1 model selected  

> label size 2

> show

> style stick

Changed 10812 atom styles  

> ~style stick

Unknown command: ~style stick  

> style sel stick

Changed 24 atom styles  

> style sel stick

Changed 24 atom styles  

> style sel sphere

Changed 24 atom styles  

> style sel sphere

Changed 24 atom styles  

> style sel ball

Changed 24 atom styles  

> style sel ball

Changed 24 atom styles  

> hide sel cartoons

[Repeated 2 time(s)]

> hide sel atoms

[Repeated 1 time(s)]

> show sel atoms

> show sel cartoons

> ui mousemode right "delete markers"

Hide dust shortcut requires a displayed map surface  

> transparency 50

> set bgColor white

[Repeated 1 time(s)]

> set bgColor black

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> style sel stick

Changed 24 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> style sel stick

Changed 24 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> color sel byhetero

[Repeated 1 time(s)]

> color sel bychain

> color sel bynucleotide

> lighting soft

> lighting simple

> undo

> hide #!3 models

> show #!3 models

> show #3.1 models

> hide #3.1 models

> surface hidePatches

> ribbon hide

> ui tool show Matchmaker

No reference and/or match structure/chain chosen  

> matchmaker #!1 to #3

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 AF-Q8C8H8-F1-model_v4.pdb, chain A (#3) with pdb2q3z.ent, chain A
(#1), sequence alignment score = 77.4  
RMSD between 51 pruned atom pairs is 0.980 angstroms; (across all 498 pairs:
44.075)  
  

> matchmaker #!1 to #3

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 AF-Q8C8H8-F1-model_v4.pdb, chain A (#3) with pdb2q3z.ent, chain A
(#1), sequence alignment score = 77.4  
RMSD between 51 pruned atom pairs is 0.980 angstroms; (across all 498 pairs:
44.075)  
  

> close session

> open C:\Users\Ahmed\Downloads\pdb2q3z.ent format pdb

pdb2q3z.ent title:  
Transglutaminase 2 undergoes large conformational change upon activation [more
info...]  
  
Chain information for pdb2q3z.ent #1  
---  
Chain | Description | UniProt  
A | transglutaminase 2 | TGM2_HUMAN 1-687  
X | polypeptide |   
  
Non-standard residues in pdb2q3z.ent #1  
---  
ACE — acetyl group  
NH2 — amino group  
ONL — 5-oxo-L-norleucine  
SO4 — sulfate ion  
  

> 282

Unknown command: 282  

> select ::name="ASP"

280 atoms, 246 bonds, 35 residues, 1 model selected  

> close session

> open "D:/download/after change.pdb"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\gui.py", line 768, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\gui.py", line 2154, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX 1.10\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 1.10\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\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 1.10\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 0xa0 in position 139:
invalid start byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 139:
invalid start byte  
  
File "", line 322, in decode  
  
See log for complete Python traceback.  
  

> open "D:/download/after change.pdb"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 339, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX 1.10\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 1.10\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\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 1.10\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 0xa0 in position 139:
invalid start byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 139:
invalid start byte  
  
File "", line 322, in decode  
  
See log for complete Python traceback.  
  

> open "D:/download/AHMED STRUCTURE.pdb"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 339, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX 1.10\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 1.10\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\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 1.10\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 0xb4 in position 5280:
invalid start byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb4 in position 5280:
invalid start byte  
  
File "", line 322, in decode  
  
See log for complete Python traceback.  
  

> open "D:/download/mutunt wt.pdb"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 339, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX 1.10\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 1.10\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\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 1.10\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 0xa0 in position 124:
invalid start byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 124:
invalid start byte  
  
File "", line 322, in decode  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 32.0.101.6647
OpenGL renderer: Intel(R) Arc(TM) 140V GPU (8GB)
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_GB.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: SAMSUNG ELECTRONICS CO., LTD.
Model: 960QHA
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 16,688,824,320
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) Ultra 7 256V
OSLanguage: en-GB

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: 3.5.0
    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: 1.10
    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: 1.45.2
    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
    nvidia-cuda-cupti-cu12: 12.9.79
    nvidia-cuda-nvcc-cu12: 12.9.86
    nvidia-cuda-nvrtc-cu12: 12.9.86
    nvidia-cuda-runtime-cu12: 12.9.79
    nvidia-cufft-cu12: 11.4.1.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 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: 2.5.0
    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