Opened 2 years ago

Closed 2 years ago

#9948 closed defect (can't reproduce)

UnicodeDecodeError opening PDB file

Reported by: chimerax-bug-report@… Owned by: pett
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:        Linux-5.15.0-86-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> artiax start

Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  

> open
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/particles/backplot/41K_matrix__unbin_fa_stack_101_test.star
> format star

Summary of feedback from opening
/camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/particles/backplot/41K_matrix__unbin_fa_stack_101_test.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list 41K_matrix__unbin_fa_stack_101_test.star with 549
particles.  
set axis size 20.7  
20.7  
['.arrow', '0', '0', '0', '20.7', '0', '0', '1.38', '5.52']  

> artiax particles #1.2.1 originScaleFactor 1.38

> artiax view xy

> open
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/particles/backplot/23K_HA_sel_job225_stack_101.star
> format star

Summary of feedback from opening
/camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/particles/backplot/23K_HA_sel_job225_stack_101.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list 23K_HA_sel_job225_stack_101.star with 287 particles.  
set axis size 20.7  
20.7  
['.arrow', '0', '0', '0', '20.7', '0', '0', '1.38', '5.52']  

> artiax particles #1.2.2 originScaleFactor 1.38

> artiax view xy

> artiax hide axes

> open
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_77.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_76.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_75.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_74.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_73.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_72.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_71.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_70.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_69.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_68.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_67.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_66.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_65.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_64.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_63.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_62.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_61.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_60.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_59.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_58.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_57.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_56.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_55.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_54.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_53.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_52.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_51.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_50.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_49.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_48.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_47.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_46.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_45.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_44.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_43.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_42.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_41.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_40.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_39.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_38.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_37.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_36.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_35.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_34.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_33.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_32.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_31.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_30.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_29.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_28.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_27.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_26.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_25.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_24.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_23.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_22.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_21.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_20.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_19.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_18.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_17.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_16.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_15.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_14.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_13.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_12.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_11.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_10.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_9.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_8.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_7.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_6.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_5.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_4.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_3.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_2.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_1.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_0.pdb

Summary of feedback from opening
/camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_75.pdb  
---  
warning | Ignored bad PDB record found on line 3  
CRYST11.000 1.000 1.000 90.00 90.00 90.00 P 1 ??1  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open  
return remember_data_format()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/pdb/__init__.py", line 34, in open  
return pdb.open_pdb(session, data, file_name, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/pdb/pdb.py",
line 78, in open_pdb  
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,  
File "/usr/bin/../../usr/lib/ucsf-chimerax/lib/python3.9/codecs.py", line 322,
in decode  
(result, consumed) = self._buffer_decode(data, self.errors, final)  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xda in position 581:
invalid continuation byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xda in position 581:
invalid continuation byte  
  
File "/usr/bin/../../usr/lib/ucsf-chimerax/lib/python3.9/codecs.py", line 322,
in decode  
(result, consumed) = self._buffer_decode(data, self.errors, final)  
  
See log for complete Python traceback.  
  

> open
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_77.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_76.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_75.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_74.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_73.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_72.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_71.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_70.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_69.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_68.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_67.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_66.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_65.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_64.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_63.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_62.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_61.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_60.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_59.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_58.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_57.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_56.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_55.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_54.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_53.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_52.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_51.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_50.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_49.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_48.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_47.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_46.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_45.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_44.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_43.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_42.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_41.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_40.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_39.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_38.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_37.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_36.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_35.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_34.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_33.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_32.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_31.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_30.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_29.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_28.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_27.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_26.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_25.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_24.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_23.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_22.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_21.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_20.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_19.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_18.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_17.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_16.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_15.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_14.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_13.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_12.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_11.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_10.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_9.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_8.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_7.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_6.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_5.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_4.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_3.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_2.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_1.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_0.pdb

Summary of feedback from opening
/camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_75.pdb  
---  
warning | Ignored bad PDB record found on line 3  
CRYST11.000 1.000 1.000 90.00 90.00 90.00 P 1 ??1  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open  
return remember_data_format()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/pdb/__init__.py", line 34, in open  
return pdb.open_pdb(session, data, file_name, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/pdb/pdb.py",
line 78, in open_pdb  
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,  
File "/usr/bin/../../usr/lib/ucsf-chimerax/lib/python3.9/codecs.py", line 322,
in decode  
(result, consumed) = self._buffer_decode(data, self.errors, final)  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xda in position 581:
invalid continuation byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xda in position 581:
invalid continuation byte  
  
File "/usr/bin/../../usr/lib/ucsf-chimerax/lib/python3.9/codecs.py", line 322,
in decode  
(result, consumed) = self._buffer_decode(data, self.errors, final)  
  
See log for complete Python traceback.  
  

> open
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_77.pdb

Stack_101_77.pdb title:  
bmol -parameter /home/barry/Software/bsoft/parameters/atom_prop.star -Place
3267.4980479399997,2756.7576760999996,1181.29791368 -origin 0,0,0 -limits
0,0,0,5122.5599999999995,5299.2,2208.0
/camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/model/Stack_101/tmp_Stack_101_77.pdb
/camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/model/Stack_101/Stack_101_77.pdb
[more info...]  
  
Chain information for Stack_101_77.pdb #2  
---  
Chain | Description  
C D E F G H | No description available  
  

> open
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_76.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_75.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_74.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_73.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_72.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_71.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_70.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_69.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_68.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_67.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_66.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_65.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_64.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_63.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_62.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_61.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_60.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_59.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_58.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_57.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_56.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_55.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_54.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_53.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_52.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_51.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_50.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_49.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_48.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_47.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_46.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_45.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_44.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_43.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_42.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_41.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_40.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_39.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_38.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_37.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_36.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_35.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_34.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_33.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_32.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_31.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_30.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_29.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_28.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_27.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_26.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_25.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_24.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_23.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_22.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_21.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_20.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_19.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_18.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_17.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_16.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_15.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_14.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_13.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_12.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_11.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_10.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_9.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_8.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_7.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_6.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_5.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_4.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_3.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_2.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_1.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_0.pdb

Summary of feedback from opening
/camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_75.pdb  
---  
warning | Ignored bad PDB record found on line 3  
CRYST11.000 1.000 1.000 90.00 90.00 90.00 P 1 ??1  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open  
return remember_data_format()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/pdb/__init__.py", line 34, in open  
return pdb.open_pdb(session, data, file_name, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/pdb/pdb.py",
line 78, in open_pdb  
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,  
File "/usr/bin/../../usr/lib/ucsf-chimerax/lib/python3.9/codecs.py", line 322,
in decode  
(result, consumed) = self._buffer_decode(data, self.errors, final)  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xda in position 581:
invalid continuation byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xda in position 581:
invalid continuation byte  
  
File "/usr/bin/../../usr/lib/ucsf-chimerax/lib/python3.9/codecs.py", line 322,
in decode  
(result, consumed) = self._buffer_decode(data, self.errors, final)  
  
See log for complete Python traceback.  
  

> open
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_0.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_1.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_2.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_3.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_4.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_5.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_6.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_7.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_8.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_9.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_10.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_11.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_12.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_13.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_14.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_15.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_16.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_17.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_18.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_19.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_20.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_21.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_22.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_23.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_24.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_25.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_26.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_27.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_28.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_29.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_30.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_31.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_32.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_33.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_34.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_35.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_36.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_37.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_38.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_39.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_40.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_41.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_42.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_43.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_44.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_45.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_46.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_47.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_48.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_49.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_50.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_51.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_52.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_53.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_54.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_55.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_56.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_57.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_58.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_59.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_60.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_61.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_62.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_63.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_64.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_65.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_66.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_67.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_68.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_69.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_70.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_71.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_72.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_73.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_74.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_76.pdb

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open  
return remember_data_format()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/pdb/__init__.py", line 34, in open  
return pdb.open_pdb(session, data, file_name, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/pdb/pdb.py",
line 78, in open_pdb  
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,  
File "/usr/bin/../../usr/lib/ucsf-chimerax/lib/python3.9/codecs.py", line 322,
in decode  
(result, consumed) = self._buffer_decode(data, self.errors, final)  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xcd in position 584:
invalid continuation byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xcd in position 584:
invalid continuation byte  
  
File "/usr/bin/../../usr/lib/ucsf-chimerax/lib/python3.9/codecs.py", line 322,
in decode  
(result, consumed) = self._buffer_decode(data, self.errors, final)  
  
See log for complete Python traceback.  
  

> open
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_0.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_1.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_2.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_3.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_4.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_5.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_6.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_7.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_8.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_9.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_10.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_11.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_12.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_13.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_14.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_15.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_16.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_17.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_18.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_19.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_20.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_21.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_22.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_23.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_24.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_25.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_26.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_27.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_28.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_29.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_30.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_31.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_32.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_33.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_34.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_35.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_36.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_37.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_38.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_39.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_40.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_41.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_42.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_43.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_44.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_45.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_46.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_47.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_48.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_49.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_50.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_51.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_52.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_53.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_54.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_55.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_56.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_57.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_58.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_59.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_60.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_61.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_62.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_63.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_64.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_65.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_66.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_67.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_68.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_69.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_70.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_71.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_72.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_73.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_74.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_75.pdb
> /camp/lab/rosenthalp/working/liuz/FluA/FluA_neutral_pH_28_07_2023_krios_tomo/new_relion4/backplot/matrix_model/Stack_101/Stack_101_76.pdb

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open  
return remember_data_format()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/pdb/__init__.py", line 34, in open  
return pdb.open_pdb(session, data, file_name, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/pdb/pdb.py",
line 78, in open_pdb  
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,  
File "/usr/bin/../../usr/lib/ucsf-chimerax/lib/python3.9/codecs.py", line 322,
in decode  
(result, consumed) = self._buffer_decode(data, self.errors, final)  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xcd in position 584:
invalid continuation byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xcd in position 584:
invalid continuation byte  
  
File "/usr/bin/../../usr/lib/ucsf-chimerax/lib/python3.9/codecs.py", line 322,
in decode  
(result, consumed) = self._buffer_decode(data, self.errors, final)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 495.29.05
OpenGL renderer: NVIDIA GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_GB.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 Intel(R) Core(TM) i9-10920X CPU @ 3.50GHz
Cache Size: 19712 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          125Gi       6.5Gi       112Gi       211Mi       6.2Gi       117Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	17:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2204] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. Device [1043:87d5]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.3
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    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: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    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: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    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: 1.1.1
    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: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-QScore: 1.0
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    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: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    geomdl: 5.3.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    pandas: 2.0.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    starfile: 0.4.12
    superqt: 0.4.1
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by pett, 2 years ago

Component: Unassigned → Input/Output
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → UnicodeDecodeError opening PDB file

comment:2 by pett, 2 years ago

Resolution: → can't reproduce
Status: accepted → closed

1.6.1 also tries UTF-16 and UTF-32, so what encoding is this file?

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