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#9202 closed defect (duplicate)

MemoryError open mmCIF

Reported by:	chimerax-bug-report@…	Owned by:	Greg Couch
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:        Windows-10-10.0.22621
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.  

> open "D:\Promotion\Strukturen\Protein structures\IRED\IRED 246 alphafold
> dimer and 7OG3.cxs" format session

Log from Sat Feb 25 00:17:41 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold predict
> MNSASIPASVTVIGLGHMGVALADAFLKGGHPTTVWNRSADKAKGLVEKGAVLAGSVSEAIAASSLVVVCLSTYKVMQELLAPLENELSGRVIVNLTTGTPEDARKTAKWVIEHGGQYLDGAIMAIPQMIGLPETLIFYGGSKALFEAYEPTLKLLGGNAAYLGEDYGVPLIYDLSLLTMMYGAWYGSMHAHALLSTANITGTEFLPYATNWVNHLIAPLLTDPVAARARDEGNFTTDVSNLNTNKLGLEHIIHASQEQGITVEWLMPLLTLATQKVAEGYGADSFDRVIEAIRKPRVK,MNSASIPASVTVIGLGHMGVALADAFLKGGHPTTVWNRSADKAKGLVEKGAVLAGSVSEAIAASSLVVVCLSTYKVMQELLAPLENELSGRVIVNLTTGTPEDARKTAKWVIEHGGQYLDGAIMAIPQMIGLPETLIFYGGSKALFEAYEPTLKLLGGNAAYLGEDYGVPLIYDLSLLTMMYGAWYGSMHAHALLSTANITGTEFLPYATNWVNHLIAPLLTDPVAARARDEGNFTTDVSNLNTNKLGLEHIIHASQEQGITVEWLMPLLTLATQKVAEGYGADSFDRVIEAIRKPRVK

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  
AlphaFold prediction finished  
Results in C:\Users\Alex/Downloads/ChimeraX/AlphaFold/prediction_2  

> open C:\Users\Alex/Downloads/ChimeraX/AlphaFold/prediction_2\best_model.pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
B C | No description available  
  

> save "D:/Promotion/Strukturen/Protein structures/IRED/IRED 246 alphafold
> dimer.cxs"

> open 7OG3

7og3 title:  
Ired-88 [more info...]  
  
Chain information for 7og3 #2  
---  
Chain | Description | UniProt  
A B | NAD(P)-dependent oxidoreductase | A0A5P2XKZ4_STRST  
  
Non-standard residues in 7og3 #2  
---  
NA — sodium ion  
NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate  
  

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker best_model.pdb, chain B (#1) with 7og3, chain A (#2), sequence
alignment score = 810  
RMSD between 179 pruned atom pairs is 0.929 angstroms; (across all 290 pairs:
3.461)  
  

> hide #!2 models

> show #!2 models

> hide #1 models

> show #1 models

> hide #!2 models

> show #!2 models

> close #2

> open 5OCM

Summary of feedback from opening 5OCM fetched from pdb  
---  
notes | Fetching compressed mmCIF 5ocm from
http://files.rcsb.org/download/5ocm.cif  
Fetching CCD NAP from http://ligand-expo.rcsb.org/reports/N/NAP/NAP.cif  
Fetching CCD 9RH from http://ligand-expo.rcsb.org/reports/9/9RH/9RH.cif  
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif  
  
5ocm title:  
Imine Reductase from Streptosporangium roseum in complex with NADP+ and
2,2,2-trifluoroacetophenone hydrate [more info...]  
  
Chain information for 5ocm #2  
---  
Chain | Description | UniProt  
A B C D E F | NAD_Gly3P_dh, NAD-dependent glycerol-3-phosphate dehydrogenase |
D2B7Z8_STRRD  
  
Non-standard residues in 5ocm #2  
---  
9RH — 2,2,2-trifluoromethyl acetophenone hydrate  
MG — magnesium ion  
NAP — nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)  
  
5ocm mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
  

> undo

[Repeated 2 time(s)]

> show #1 models

> close #2

> open 5OCM

5ocm title:  
Imine Reductase from Streptosporangium roseum in complex with NADP+ and
2,2,2-trifluoroacetophenone hydrate [more info...]  
  
Chain information for 5ocm #2  
---  
Chain | Description | UniProt  
A B C D E F | NAD_Gly3P_dh, NAD-dependent glycerol-3-phosphate dehydrogenase |
D2B7Z8_STRRD  
  
Non-standard residues in 5ocm #2  
---  
9RH — 2,2,2-trifluoromethyl acetophenone hydrate  
MG — magnesium ion  
NAP — nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)  
  
5ocm mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
  

> style sphere

Changed 18457 atom styles  

> style sphere

Changed 18457 atom styles  

> style sphere

Changed 18457 atom styles  

> undo

[Repeated 3 time(s)]

> show #1 models

> show cartoons

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker best_model.pdb, chain B (#1) with 5ocm, chain A (#2), sequence
alignment score = 810.4  
RMSD between 158 pruned atom pairs is 0.757 angstroms; (across all 290 pairs:
4.259)  
  

> hide #1 models

> style #!2 sphere

Changed 13955 atom styles  

> style #!2 sphere

Changed 13955 atom styles  

> undo

[Repeated 1 time(s)]

> hide #!2 cartoons

> show #!2 cartoons

> hide #!2 atoms

> show #1 models

> hide #1 models

> close #2

> show #1 models

> open "D:/Promotion/Strukturen/Protein structures/IRED/5ocm.cif.gz"

File reader requires uncompressed file; 'D:/Promotion/Strukturen/Protein
structures/IRED/5ocm.cif.gz' is compressed  

> open "D:/Promotion/Strukturen/Protein structures/IRED/5ocm.cif"

5ocm.cif title:  
Imine Reductase from Streptosporangium roseum in complex with NADP+ and
2,2,2-trifluoroacetophenone hydrate [more info...]  
  
Chain information for 5ocm.cif #2  
---  
Chain | Description | UniProt  
A B C D E F | NAD_Gly3P_dh, NAD-dependent glycerol-3-phosphate dehydrogenase |
D2B7Z8_STRRD  
  
Non-standard residues in 5ocm.cif #2  
---  
9RH — 2,2,2-trifluoromethyl acetophenone hydrate  
MG — magnesium ion  
NAP — nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)  
  
5ocm.cif mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
  

> close #2

> open 7OG3

7og3 title:  
Ired-88 [more info...]  
  
Chain information for 7og3 #2  
---  
Chain | Description | UniProt  
A B | NAD(P)-dependent oxidoreductase | A0A5P2XKZ4_STRST  
  
Non-standard residues in 7og3 #2  
---  
NA — sodium ion  
NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate  
  

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker best_model.pdb, chain B (#1) with 7og3, chain A (#2), sequence
alignment score = 810  
RMSD between 179 pruned atom pairs is 0.929 angstroms; (across all 290 pairs:
3.461)  
  

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #!2 models

> show #!2 models

> hide #1 models

> ui tool show "Blast Protein"

> hide #!2 models

> show #1 models

> ui tool show "Blast Protein"

> show #!2 models

> view #1 clip false

> log metadata #1

The model has no metadata

> log chains #1

Chain information for best_model.pdb #1  
---  
Chain | Description  
B C | No description available  
  

> show #1 target m

> hide #!2 models

> blastprotein #1/B database pdb cutoff 1e-5 matrix BLOSUM62 maxSeqs 100 name
> bp1

Webservices job id: 85PNHOPZSC9MVKFL  
Alignment identifier is bp1 [1]  
Associated best_model.pdb chain B to #1/B with 0 mismatches  
Associated best_model.pdb chain C to #1/B with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp1 [1]  

> open pdb:7OSN

Summary of feedback from opening 7OSN fetched from pdb  
---  
note | Fetching compressed mmCIF 7osn from
http://files.rcsb.org/download/7osn.cif  
  
7osn title:  
IRED361 from Micromonospora sp. in complex with NADP+ [more info...]  
  
Chain information for 7osn #3  
---  
Chain | Description | UniProt  
A B C D E F | 6-phosphogluconate dehydrogenase | A0A1S8Y2S4_9ACTN  
  
Non-standard residues in 7osn #3  
---  
NAP — nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)  
  
7osn mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
  
Associated 7osn chain A to 7OSN_A with 0 mismatches  
Associated 7osn chain B to 7OSN_A with 0 mismatches  
Associated 7osn chain C to 7OSN_A with 0 mismatches  
Associated 7osn chain D to 7OSN_A with 0 mismatches  
Associated 7osn chain E to 7OSN_A with 0 mismatches  
Associated 7osn chain F to 7OSN_A with 0 mismatches  

> matchmaker #3/A to #1/B

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker best_model.pdb, chain B (#1) with 7osn, chain A (#3), sequence
alignment score = 847  
RMSD between 153 pruned atom pairs is 0.823 angstroms; (across all 289 pairs:
3.160)  
  

> hide #1,3 atoms

> show #1,3 atoms

> hide #1,3 cartoons

> show #1,3 cartoons

> style #1,3 stick

Changed 17465 atom styles  

> undo

[Repeated 3 time(s)]

> style #1,3 stick

Changed 17465 atom styles  

> hide #3 models

> close #3

> style #1 stick

Changed 4502 atom styles  

> show #1 cartoons

> hide #1 cartoons

> show #1 cartoons

> style #1 stick

Changed 4502 atom styles  

> show #1 atoms

> show #!2 models

> hide #!2 models

> color #1 byhetero

> show #!2 models

> hide #!2 models

> view #1 clip false

> undo

[Repeated 6 time(s)]

> ui tool show "Show Sequence Viewer"

> show #!2 models

> sequence chain #2/A #2/B

Alignment identifier is 1  

> select
> #2/A-B:21-34,44-54,61-68,78-87,89-94,105-120,131-135,147-160,172-201,205-237,245-264,267-283,289-298

2856 atoms, 2888 bonds, 388 residues, 1 model selected  

> undo

> save "D:/Promotion/Strukturen/Protein structures/IRED/IRED 246 alphafold
> dimer and 7OG3.cxs"

——— End of log from Sat Feb 25 00:17:41 2023 ———

opened ChimeraX session  

> close session

> open 1K7D format mmcif fromDatabase pdb

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 368, in thread_safe  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd  
run(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\open_command\cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, 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 97, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\manager.py", line 198, 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 194, 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 465, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, 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 88, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  

> open 1GKF

Summary of feedback from opening 1GKF fetched from pdb  
---  
note | Fetching compressed mmCIF 1gkf from
http://files.rcsb.org/download/1gkf.cif  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
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\open_command\cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, 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 97, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\manager.py", line 198, 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 194, 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 465, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, 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 88, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 471.68
OpenGL renderer: NVIDIA GeForce GTX 1050/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: de_DE.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: LENOVO
Model: 81FL
OS: Microsoft Windows 11 Home (Build 22621)
Memory: 8,458,129,408
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8300H CPU @ 2.30GHz
OSLanguage: de-DE

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-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-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-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    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-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
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    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
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    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
    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
    pywin32: 305
    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
    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
    WMI: 1.5.1
    zipp: 3.15.0

Change History (2)

comment:1 by pett, 2 years ago

Component:	Unassigned → Input/Output
Owner:	set to Greg Couch
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → MemoryError open mmCIF

comment:2 by Greg Couch, 2 years ago

Resolution:	→ duplicate
Status:	assigned → closed

Duplicated of #8815.

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