Opened 2 years ago

Closed 2 years ago

#9188 closed defect (fixed)

ArtiaX: problem loading Star file

Reported by: amehrani@… Owned by: Utz Ermel
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Hi, 

I'm trying to load a star file containing particle corrdinates in ArtiaX using the Open List but I get the following error and was wondering how to resolve the issue. 

Thank you so much in advance. 

pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields in line 12, saw 10


File "pandas/_libs/parsers.pyx", line 2025, in pandas._libs.parsers.raise_parser_error

See log for complete Python traceback.


Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> artiax start

Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  
Opened tomo-20-b6.mrc_rec.mrc as #1.1.1, grid size 682,960,66, pixel
6.36,6.36,6.36, shown at level 24, step 1, values int8  

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

> artiax tomo #1.1.1 pixelSize 6.360000028638196

> artiax view xy

> artiax tomo #1.1.1 pixelSize 6.3

> artiax view xy

> artiax tomo #1.1.1 pixelSize 6.3

> artiax view xy

> artiax tomo #1.1.1 pixelSize 6.36

> artiax view xy

> artiax tomo #1.1.1 pixelSize 6.36

> artiax view xy

> artiax tomo #1.1.1 slice 35

> open "/Users/Atousa/Desktop/tomo-20-Ben
> 2/tomo-20-b6.mrc_rec_invert_map.star" format star

Traceback (most recent call last):  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 181, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 432, in collated_open  
return remember_data_format()  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/artiax/io/formats.py", line 25, in open  
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/artiax/io/io.py", line 35, in open_particle_list  
data = formats[format_name].particle_data(session, file_name, oripix=1,
trapix=1, additional_files=additional_files)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 120, in
__init__  
super().__init__(session, file_name, oripix=oripix, trapix=trapix,
additional_files=additional_files)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/artiax/io/ParticleData.py", line 441, in __init__  
self.read_file()  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 123, in
read_file  
content = starfile.read(self.file_name, always_dict=True)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/starfile/functions.py", line 24, in read  
star = StarParser(filename, read_n_blocks=read_n_blocks)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/starfile/parser.py", line 30, in __init__  
self.parse_file()  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/starfile/parser.py", line 38, in parse_file  
self._parse_data_block()  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/starfile/parser.py", line 54, in _parse_data_block  
self._parse_loop_block()  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/starfile/parser.py", line 77, in _parse_loop_block  
df = self._parse_loop_data()  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/starfile/parser.py", line 177, in _parse_loop_data  
df = pd.read_csv(  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/pandas/io/parsers/readers.py", line 912, in read_csv  
return _read(filepath_or_buffer, kwds)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/pandas/io/parsers/readers.py", line 583, in _read  
return parser.read(nrows)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/pandas/io/parsers/readers.py", line 1704, in read  
) = self._engine.read( # type: ignore[attr-defined]  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/pandas/io/parsers/c_parser_wrapper.py", line 234, in read  
chunks = self._reader.read_low_memory(nrows)  
File "pandas/_libs/parsers.pyx", line 812, in
pandas._libs.parsers.TextReader.read_low_memory  
File "pandas/_libs/parsers.pyx", line 873, in
pandas._libs.parsers.TextReader._read_rows  
File "pandas/_libs/parsers.pyx", line 848, in
pandas._libs.parsers.TextReader._tokenize_rows  
File "pandas/_libs/parsers.pyx", line 859, in
pandas._libs.parsers.TextReader._check_tokenize_status  
File "pandas/_libs/parsers.pyx", line 2025, in
pandas._libs.parsers.raise_parser_error  
pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields
in line 12, saw 10  
  
  
pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields
in line 12, saw 10  
  
  
File "pandas/_libs/parsers.pyx", line 2025, in
pandas._libs.parsers.raise_parser_error  
  
See log for complete Python traceback.  
  

> open "/Users/Atousa/Desktop/tomo-20-Ben
> 2/tomo-20-b6.mrc_rec_invert_map.star" format star

Traceback (most recent call last):  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 181, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 432, in collated_open  
return remember_data_format()  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/artiax/io/formats.py", line 25, in open  
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/artiax/io/io.py", line 35, in open_particle_list  
data = formats[format_name].particle_data(session, file_name, oripix=1,
trapix=1, additional_files=additional_files)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 120, in
__init__  
super().__init__(session, file_name, oripix=oripix, trapix=trapix,
additional_files=additional_files)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/artiax/io/ParticleData.py", line 441, in __init__  
self.read_file()  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 123, in
read_file  
content = starfile.read(self.file_name, always_dict=True)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/starfile/functions.py", line 24, in read  
star = StarParser(filename, read_n_blocks=read_n_blocks)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/starfile/parser.py", line 30, in __init__  
self.parse_file()  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/starfile/parser.py", line 38, in parse_file  
self._parse_data_block()  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/starfile/parser.py", line 54, in _parse_data_block  
self._parse_loop_block()  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/starfile/parser.py", line 77, in _parse_loop_block  
df = self._parse_loop_data()  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/starfile/parser.py", line 177, in _parse_loop_data  
df = pd.read_csv(  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/pandas/io/parsers/readers.py", line 912, in read_csv  
return _read(filepath_or_buffer, kwds)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/pandas/io/parsers/readers.py", line 583, in _read  
return parser.read(nrows)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/pandas/io/parsers/readers.py", line 1704, in read  
) = self._engine.read( # type: ignore[attr-defined]  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/pandas/io/parsers/c_parser_wrapper.py", line 234, in read  
chunks = self._reader.read_low_memory(nrows)  
File "pandas/_libs/parsers.pyx", line 812, in
pandas._libs.parsers.TextReader.read_low_memory  
File "pandas/_libs/parsers.pyx", line 873, in
pandas._libs.parsers.TextReader._read_rows  
File "pandas/_libs/parsers.pyx", line 848, in
pandas._libs.parsers.TextReader._tokenize_rows  
File "pandas/_libs/parsers.pyx", line 859, in
pandas._libs.parsers.TextReader._check_tokenize_status  
File "pandas/_libs/parsers.pyx", line 2025, in
pandas._libs.parsers.raise_parser_error  
pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields
in line 12, saw 10  
  
  
pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields
in line 12, saw 10  
  
  
File "pandas/_libs/parsers.pyx", line 2025, in
pandas._libs.parsers.raise_parser_error  
  
See log for complete Python traceback.  
  

> open "/Users/Atousa/Desktop/tomo-20-Ben
> 2/tomo-20-b6.mrc_rec_invert_map.star" format star

Traceback (most recent call last):  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 181, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 432, in collated_open  
return remember_data_format()  
File
"/private/var/folders/h3/nzdnmv017yd13y_p8yfcq36h0000gq/T/AppTranslocation/F12573D5-C62C-4CD6-80E6-48141B57D208/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/artiax/io/formats.py", line 25, in open  
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/artiax/io/io.py", line 35, in open_particle_list  
data = formats[format_name].particle_data(session, file_name, oripix=1,
trapix=1, additional_files=additional_files)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 120, in
__init__  
super().__init__(session, file_name, oripix=oripix, trapix=trapix,
additional_files=additional_files)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/artiax/io/ParticleData.py", line 441, in __init__  
self.read_file()  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 123, in
read_file  
content = starfile.read(self.file_name, always_dict=True)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/starfile/functions.py", line 24, in read  
star = StarParser(filename, read_n_blocks=read_n_blocks)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/starfile/parser.py", line 30, in __init__  
self.parse_file()  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/starfile/parser.py", line 38, in parse_file  
self._parse_data_block()  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/starfile/parser.py", line 54, in _parse_data_block  
self._parse_loop_block()  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/starfile/parser.py", line 77, in _parse_loop_block  
df = self._parse_loop_data()  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/starfile/parser.py", line 177, in _parse_loop_data  
df = pd.read_csv(  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/pandas/io/parsers/readers.py", line 912, in read_csv  
return _read(filepath_or_buffer, kwds)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/pandas/io/parsers/readers.py", line 583, in _read  
return parser.read(nrows)  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/pandas/io/parsers/readers.py", line 1704, in read  
) = self._engine.read( # type: ignore[attr-defined]  
File "/Users/Atousa/Library/Application Support/ChimeraX/1.3/site-
packages/pandas/io/parsers/c_parser_wrapper.py", line 234, in read  
chunks = self._reader.read_low_memory(nrows)  
File "pandas/_libs/parsers.pyx", line 812, in
pandas._libs.parsers.TextReader.read_low_memory  
File "pandas/_libs/parsers.pyx", line 873, in
pandas._libs.parsers.TextReader._read_rows  
File "pandas/_libs/parsers.pyx", line 848, in
pandas._libs.parsers.TextReader._tokenize_rows  
File "pandas/_libs/parsers.pyx", line 859, in
pandas._libs.parsers.TextReader._check_tokenize_status  
File "pandas/_libs/parsers.pyx", line 2025, in
pandas._libs.parsers.raise_parser_error  
pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields
in line 12, saw 10  
  
  
pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields
in line 12, saw 10  
  
  
File "pandas/_libs/parsers.pyx", line 2025, in
pandas._libs.parsers.raise_parser_error  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-18.4.6
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1715.81.2.0.0 (iBridge: 19.16.10744.0.0,0)
      OS Loader Version: 540.80.2~11

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 5 days 19:36

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-ArtiaX: 0.3
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    geomdl: 5.3.1
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    pandas: 2.0.1
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    starfile: 0.4.12
    suds-jurko: 0.6
    superqt: 0.4.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (3)

comment:1 by amehrani@…, 2 years ago 

Hi there,


I realized that the error was because of extra spaces in the star file I was importing. The bug was resolved after removing the spaces.


Thank you so much and best,


Atousa Mehrani, PhD

Postdoctoral Fellow|Laboratory of Genetics-Lyumkis

Salk Institute for Biological Studies

10010 N Torrey Pines Rd, La Jolla, CA 92037<https://www.salk.edu/>

amehrani@salk.edu

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, June 14, 2023 8:15 PM
To: Atousa Mehrani
Subject: Re: [ChimeraX] #9188: ChimeraX bug report submission

#9188: ChimeraX bug report submission
------------------------+-----------------------------
 Reporter:  amehrani@…  |                Type:  defect
   Status:  new         |            Priority:  normal
Component:  Unassigned  |          Blocked By:
 Blocking:              |  Notify when closed:
------------------------+-----------------------------
--
Ticket URL: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/9188__;!!GX6Nv3_Pjr8b-17qtCok029Ok438DqXQ!2mNTgVy2x395_0EItZMm-G3Aas49GDd6C0RI7vVisVQp4xS2fMR4jTIxYzJ7QdJv5I6J0lVM-ZzphOwy0vARzY4q5DE8lJsA$ >
ChimeraX <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/__;!!GX6Nv3_Pjr8b-17qtCok029Ok438DqXQ!2mNTgVy2x395_0EItZMm-G3Aas49GDd6C0RI7vVisVQp4xS2fMR4jTIxYzJ7QdJv5I6J0lVM-ZzphOwy0vARzY4q5NujzFAV$ >
ChimeraX Issue Tracker

comment:2 by Eric Pettersen, 2 years ago

Component: Unassigned → Third Party
Owner: set to Utz Ermel
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ArtiaX: problem loading Star file

Reported by Atousa Mehrani

comment:3 by Eric Pettersen, 2 years ago

Resolution: → fixed
Status: assigned → closed

Removing spaces from file resolved the issue.

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