Opened 2 years ago
Closed 2 years ago
#9159 closed defect (duplicate)
MemoryError open mmCIF
Reported by: | Owned by: | Greg Couch | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Input/Output | Version: | |
Keywords: | Cc: | Tom Goddard | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.25375 ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 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: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show AlphaFold > alphafold predict > MKKIKIVPLILIVVVVGFGIYFYASKDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYE?RHRSKECI*KRL*SNR*RTKYF*RLYQTTNGSKVGTR*YLRST?KPLKKWMNI*VISQKNFILQLMKQKVVTIL*KKRLHIY*VMLVPLTLKN*NKKNIKAIKMMQLLVKRDSKNFTIKSSNMKMAIVSQSLTIIAIQSHIH**RKRKKMAKIFN*LLMLKFKRVFITT*KMIMAQVLLSTLKQVNY*HL*AHLHMTSIHLCMA*VTKNIIN*PKIKKNLCSTSSRLQLHQVQLKKY*QQ*LG*ITKH*TIKQVIKSMVKVGKKINLGVVTTLQDMKW*MVIST*NKQ*NHQITFSLLE*HSN*AVRNLKKA*KN*VLVKIYQVIIHFIMLKFQTKI*IMKYY*LIQVTDKVKY*LTQYRSFQSIAH*KIMAILTHLTY*KTRKTKFGRKILFPKKISIY*LMVCNKS*IKHIKKIFIDLMQT*LANPVLQNSK*NKEKLADKLGGLYHMIKIIQT**WLLMLKMYKIKEWLATMPKSQVKCMMSYMRTVIKNTI*MN Missing or invalid "sequences" argument: Sequences argument "MKKIKIVPLILIVVVVGFGIYFYASKDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYE?RHRSKECI*KRL*SNR*RTKYF*RLYQTTNGSKVGTR*YLRST?KPLKKWMNI*VISQKNFILQLMKQKVVTIL*KKRLHIY*VMLVPLTLKN*NKKNIKAIKMMQLLVKRDSKNFTIKSSNMKMAIVSQSLTIIAIQSHIH**RKRKKMAKIFN*LLMLKFKRVFITT*KMIMAQVLLSTLKQVNY*HL*AHLHMTSIHLCMA*VTKNIIN*PKIKKNLCSTSSRLQLHQVQLKKY*QQ*LG*ITKH*TIKQVIKSMVKVGKKINLGVVTTLQDMKW*MVIST*NKQ*NHQITFSLLE*HSN*AVRNLKKA*KN*VLVKIYQVIIHFIMLKFQTKI*IMKYY*LIQVTDKVKY*LTQYRSFQSIAH*KIMAILTHLTY*KTRKTKFGRKILFPKKISIY*LMVCNKS*IKHIKKIFIDLMQT*LANPVLQNSK*NKEKLADKLGGLYHMIKIIQT**WLLMLKMYKIKEWLATMPKSQVKCMMSYMRTVIKNTI*MN" is not a chain specifier, alignment id, UniProt id, or sequence characters > alphafold predict > MKKIKIVPLILIVVVVGFGIYFYASKDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQKWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQGETGRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions. Running AlphaFold prediction [Repeated 2 time(s)] > open C:/Users/alfon/AppData/Local/Temp/ChimeraX-mTuCpG/download.png Image mode RGBA is not supported (L, P, I;16, I;16B, I;16L, I;16S, F, F;32BF, I, RGB) AlphaFold prediction finished Results in C:\Users\alfon/Downloads/ChimeraX/AlphaFold/prediction_1 > open C:\Users\alfon/Downloads/ChimeraX/AlphaFold/prediction_1\best_model.pdb Chain information for best_model.pdb #1 --- Chain | Description A | No description available > open 1MWR Summary of feedback from opening 1MWR fetched from pdb --- note | Fetching compressed mmCIF 1mwr from http://files.rcsb.org/download/1mwr.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. > save "C:/Users/alfon/OneDrive - Universidad de los > andes/tesis/Resultados/Caracterizacion de aislamientos/Figuras/mecA(7) > model.bmp" width 1341 height 738 supersample 3 > open 1MWR Summary of feedback from opening 1MWR fetched from pdb --- notes | Fetching CCD CD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/CD/CD.cif Fetching CCD CL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/CL/CL.cif 1mwr title: Structure of SeMet Penicillin binding protein 2a from methicillin resistant Staphylococcus aureus strain 27r (trigonal form) at 2.45 A resolution. [more info...] Chain information for 1mwr #2 --- Chain | Description | UniProt A B | penicillin-binding protein 2a | Q93IC2_STAAU 24-668 Non-standard residues in 1mwr #2 --- CD — cadmium ion CL — chloride ion 1mwr mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > alphafold search > MKKIKIVPLILIVVVVGFGIYFYASKDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQKWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQGETGRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json Webservices job id: 1L6T9OUDYORW1MIN > hide #!2 models > show #!2 models > select add #2 10089 atoms, 10238 bonds, 25 pseudobonds, 1269 residues, 3 models selected > select subtract #2 Nothing selected > hide #1 models > open C:/Users/alfon/Downloads/1mwr.pdb 1mwr.pdb title: Structure of semet penicillin binding protein 2A from methicillin resistant staphylococcus aureus strain 27R (trigonal form) At 2.45 A resolution. [more info...] Chain information for 1mwr.pdb #3 --- Chain | Description | UniProt A B | SAUPBP2A | Q93IC2_STAAU 24-668 Non-standard residues in 1mwr.pdb #3 --- CD — cadmium ion CL — chloride ion > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > open 1MWS Summary of feedback from opening 1MWS fetched from pdb --- notes | Fetching compressed mmCIF 1mws from http://files.rcsb.org/download/1mws.cif Fetching CCD NC1 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/NC1/NC1.cif 1mws title: Structure of nitrocefin acyl-Penicillin binding protein 2a from methicillin resistant Staphylococcus aureus strain 27r at 2.00 A resolution. [more info...] Chain information for 1mws #4 --- Chain | Description | UniProt A B | penicillin-binding protein 2a | Q93IC2_STAAU 24-668 Non-standard residues in 1mws #4 --- CD — cadmium ion CL — chloride ion 1mws mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > hide #!4 models > show #!4 models > hide #!3 models > hide #!2 models > show #1 models > hide #1 models > show #1 models > hide #!4 models > alphafold fetch D3JN96 version 4 Fetching compressed AlphaFold D3JN96 from https://alphafold.ebi.ac.uk/files/AF-D3JN96-F1-model_v4.cif Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\blastprotein\ui\results.py", line 418, in load models, chain_id = db.load_model( File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\blastprotein\data_model\databases.py", line 276, in load_model models, _ = run(chimerax_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\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 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. > hide #1 models > show #!4 models > show #!3 models > hide target m [Repeated 1 time(s)] > show #!3 models > alphafold match > MKKIKIVPLILIVVVVGFGIYFYASKDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQKWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQGETGRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE Fetching compressed AlphaFold Q93IC2 from https://alphafold.ebi.ac.uk/files/AF-Q93IC2-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 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. > alphafold match > MKKIKIVPLILIVVVVGFGIYFYASKDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQKWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQGETGRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE 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 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 - Build 31.0.101.4338 OpenGL renderer: Intel(R) Iris(R) Xe Graphics OpenGL vendor: Intel Python: 3.9.11 Locale: es_CO.cp1252 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: windows Manufacturer: ASUSTeK COMPUTER INC. Model: ZenBook UX325EA_UX325EA OS: Microsoft Windows 11 Pro (Build 25375) Memory: 8,271,470,592 MaxProcessMemory: 137,438,953,344 CPU: 8 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz OSLanguage: en-US 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 , 2 years ago
Cc: | added |
---|---|
Component: | Unassigned → Input/Output |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → MemoryError open mmCIF |
comment:2 by , 2 years ago
Resolution: | → duplicate |
---|---|
Status: | assigned → closed |
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Duplicated of #8815.