MemoryError opening mmCIF

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.7.dev202306100015 (2023-06-10 00:15:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.7.dev202306100015 (2023-06-10)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show ESMFold

> esmfold match
> MKIIICLAGLLALCYGQEEHKVTAANNHFGFKLLNAIPVSPQTNLFYSPYSVSTAMAMAYVGARGETQRDLHETLGYSSVGLTPDHVPSAHAQHTHLLRAPSNSTLRVANAAVVQENYTVTDEYLGLLRQSFDAEVSVSSLHDEQSVRAINDWVKNKTEQKIEKLLSEPLPPNTRLVLLNAIYFKGVWNVPFDARGTQKRPFFNAGTEIVEVDTMYEQISAGYARDDETNADVLDLPYAGLDYSLTIILPRERTGVDALRQNLSWPIFQRLLSKLNMNSPMEVSLPKFKIEGSYKLKAPLSALGASKAFDERYADFSGISGARDLTIYDVVHKAVVEVNEEGSEAAGATAVIFYTKSAAVGIPFVVDHPFLFFIRNRHTGDVLFAGQVNHL

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\esmfold\match.py", line 35, in esmfold_match  
seq_models = _fetch_by_sequence(session, sequences,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\match.py", line 97, in _fetch_by_sequence  
match_uids = sequence_search(seq_strings, log = log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\esmfold\search.py", line 30, in esmfold_sequence_search  
seq_mgnify_ids = _search_sequences_web(useqs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\esmfold\search.py", line 52, in _search_sequences_web  
raise SearchError('ESMFold sequence search web service failed (%s) "%s"\n\n%s'  
chimerax.esmfold.search.SearchError: ESMFold sequence search web service
failed (500) "Internal Server Error"  
  
https://www.rbvi.ucsf.edu/chimerax/cgi-bin/esmfold_search_cgi.py  
  
chimerax.esmfold.search.SearchError: ESMFold sequence search web service
failed (500) "Internal Server Error"  
  
https://www.rbvi.ucsf.edu/chimerax/cgi-bin/esmfold_search_cgi.py  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\esmfold\search.py", line 52, in _search_sequences_web  
raise SearchError('ESMFold sequence search web service failed (%s) "%s"\n\n%s'  
  
See log for complete Python traceback.  
  

> esmfold search
> MKIIICLAGLLALCYGQEEHKVTAANNHFGFKLLNAIPVSPQTNLFYSPYSVSTAMAMAYVGARGETQRDLHETLGYSSVGLTPDHVPSAHAQHTHLLRAPSNSTLRVANAAVVQENYTVTDEYLGLLRQSFDAEVSVSSLHDEQSVRAINDWVKNKTEQKIEKLLSEPLPPNTRLVLLNAIYFKGVWNVPFDARGTQKRPFFNAGTEIVEVDTMYEQISAGYARDDETNADVLDLPYAGLDYSLTIILPRERTGVDALRQNLSWPIFQRLLSKLNMNSPMEVSLPKFKIEGSYKLKAPLSALGASKAFDERYADFSGISGARDLTIYDVVHKAVVEVNEEGSEAAGATAVIFYTKSAAVGIPFVVDHPFLFFIRNRHTGDVLFAGQVNHL

Fetching ESMFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/esmfold_database.json  

> esmfold predict
> MKIIICLAGLLALCYGQEEHKVTAANNHFGFKLLNAIPVSPQTNLFYSPYSVSTAMAMAYVGARGETQRDLHETLGYSSVGLTPDHVPSAHAQHTHLLRAPSNSTLRVANAAVVQENYTVTDEYLGLLRQSFDAEVSVSSLHDEQSVRAINDWVKNKTEQKIEKLLSEPLPPNTRLVLLNAIYFKGVWNVPFDARGTQKRPFFNAGTEIVEVDTMYEQISAGYARDDETNADVLDLPYAGLDYSLTIILPRERTGVDALRQNLSWPIFQRLLSKLNMNSPMEVSLPKFKIEGSYKLKAPLSALGASKAFDERYADFSGISGARDLTIYDVVHKAVVEVNEEGSEAAGATAVIFYTKSAAVGIPFVVDHPFLFFIRNRHTGDVLFAGQVNHL
> directory "C:\Users\shabir ahmad/Downloads/ChimeraX/ESMFold"

Please cite Language models of protein sequences at the scale of evolution
enable accurate structure prediction. if you use these predictions.  

> open C:\Users\shabir ahmad/Downloads/ChimeraX/ESMFold\MKIIICLAGL_391.pdb

MKIIICLAGL_391.pdb title:  
Esmfold V1 prediction for input [more info...]  
  
Chain information for MKIIICLAGL_391.pdb #1  
---  
Chain | Description  
A | No description available  
  
Webservices job id: C7LQ3WSJ56O11WDD  

> ui tool show AlphaFold

> alphafold match
> MKIIICLAGLLALCYGQEEHKVTAANNHFGFKLLNAIPVSPQTNLFYSPYSVSTAMAMAYVGARGETQRDLHETLGYSSVGLTPDHVPSAHAQHTHLLRAPSNSTLRVANAAVVQENYTVTDEYLGLLRQSFDAEVSVSSLHDEQSVRAINDWVKNKTEQKIEKLLSEPLPPNTRLVLLNAIYFKGVWNVPFDARGTQKRPFFNAGTEIVEVDTMYEQISAGYARDDETNADVLDLPYAGLDYSLTIILPRERTGVDALRQNLSWPIFQRLLSKLNMNSPMEVSLPKFKIEGSYKLKAPLSALGASKAFDERYADFSGISGARDLTIYDVVHKAVVEVNEEGSEAAGATAVIFYTKSAAVGIPFVVDHPFLFFIRNRHTGDVLFAGQVNHL

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold V9VLN6 from
https://alphafold.ebi.ac.uk/files/AF-V9VLN6-F1-model_v4.cif  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\match.py", line 40, in alphafold_match  
search_seq_models = _fetch_by_sequence(session, search_seqs,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\match.py", line 109, in _fetch_by_sequence  
_database_models(session, seq_uids,  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\match.py", line 139, in _database_models  
models, status = fetch(session, db_id.id,  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\fetch.py", line 35, in alphafold_fetch  
models, status = session.open_command.open_data(filename, format = 'mmCIF',  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\manager.py", line 197, in open_data  
return provider_open(self.session, [path], _return_status=True,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 195, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 484, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 454, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\mmcif\\__init__.py", line 43, in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "src\mmcif.pyx", line 89, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory!  
  
MemoryError: not enough memory!  
  
File "src\mmcif.pyx", line 89, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  

> set bgColor white

> lighting simple

> lighting soft

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting flat

> lighting full

> lighting soft

> lighting depthCue false

> cartoon style modeHelix tube sides 20

> cartoon style coil xsection oval

> cartoon style xsection barbell modeHelix default

> alphafold match
> MKIIICLAGLLALCYGQEEHKVTAANNHFGFKLLNAIPVSPQTNLFYSPYSVSTAMAMAYVGARGETQRDLHETLGYSSVGLTPDHVPSAHAQHTHLLRAPSNSTLRVANAAVVQENYTVTDEYLGLLRQSFDAEVSVSSLHDEQSVRAINDWVKNKTEQKIEKLLSEPLPPNTRLVLLNAIYFKGVWNVPFDARGTQKRPFFNAGTEIVEVDTMYEQISAGYARDDETNADVLDLPYAGLDYSLTIILPRERTGVDALRQNLSWPIFQRLLSKLNMNSPMEVSLPKFKIEGSYKLKAPLSALGASKAFDERYADFSGISGARDLTIYDVVHKAVVEVNEEGSEAAGATAVIFYTKSAAVGIPFVVDHPFLFFIRNRHTGDVLFAGQVNHL

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\panel.py", line 197, in _fetch  
self._run_command('match', options = options)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\panel.py", line 303, in _run_command  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\match.py", line 40, in alphafold_match  
search_seq_models = _fetch_by_sequence(session, search_seqs,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\match.py", line 109, in _fetch_by_sequence  
_database_models(session, seq_uids,  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\match.py", line 139, in _database_models  
models, status = fetch(session, db_id.id,  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\fetch.py", line 35, in alphafold_fetch  
models, status = session.open_command.open_data(filename, format = 'mmCIF',  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\manager.py", line 197, in open_data  
return provider_open(self.session, [path], _return_status=True,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 195, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 484, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 454, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\mmcif\\__init__.py", line 43, in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "src\mmcif.pyx", line 89, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory!  
  
MemoryError: not enough memory!  
  
File "src\mmcif.pyx", line 89, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 10.18.10.5161
OpenGL renderer: Intel(R) HD Graphics 4000
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_GB.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: Sony Corporation
Model: SVF14215CBB
OS: Microsoft Windows 10 Home Single Language (Build 19045)
Memory: 6,315,364,352
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-3337U CPU @ 1.80GHz
OSLanguage: en-US

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
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    blosc2: 2.0.0
    build: 0.10.0
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    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
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    ChimeraX-Contacts: 1.0.1
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    ChimeraX-CoreFormats: 1.1
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    psutil: 5.9.4
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.6
    PyOpenGL-accelerate: 3.1.6
    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
    pywin32: 305
    pyzmq: 25.1.0
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.31.0
    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
    tables: 3.8.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.2
    traitlets: 5.9.0
    typing-extensions: 4.6.3
    tzdata: 2023.3
    urllib3: 2.0.3
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1

[Greg Couch]

Duplicated of #8815.