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Opened 3 months ago
Closed 3 months ago
#18477 closed defect (fixed)
Boltz: PytorchStreamReader failed reading zip archive: failed finding central directory
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.6-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show Boltz
> boltz predict protein
> MAKKNSQLPSTSEQILERSTTGATFLMMGQLFTKLVTFILNNLLIRFLSPRIFGITAFLEFIQGTVLFFSRDAIRLSTLRISDSGNGIIDDDDEEEYQETHYKSKVLQTAVNFAYIPFWIGFPLSIGLIAWQYRNINAYFITLPFFRWSIFLIWLSIIVELLSEPFFIVNQFMLNYAARSRFESIAVTTGCIVNFIVVYAVQQSRYPMGVVTSDIDKEGIAILAFALGKLAHSITLLACYYWDYLKNFKPKKLFSTRLTKIKTRENNELKKGYPKSTSYFFQNDILQHFKKVYFQLCFKHLLTEGDKLIINSLCTVEEQGIYALLSNYGSLLTRLLFAPIEESLRLFLARLLSSHNPKNLKLSIEVLVNLTRFYIYLSLMIIVFGPANSSFLLQFLIGSKWSTTSVLDTIRVYCFYIPFLSLNGIFEAFFQSVATGDQILKHSYFMMAFSGIFLLNSWLLIEKLKLSIEGLILSNIINMVLRILYCGVFLNKFHRELFTDSSFFFNFKDFKTVIIAGSTICLLDWWFIGYVKNLQQFVVNVLFAMGLLALILVKERQTIQSFINKRAVSNSKDV
> ligandSmiles
> CC(CCOP([O-])(=O)OP([O-])(=O)OC1OC(CO)C(OC2OC(CO)C(OC3OC(COC4OC(CO)C(O)C(O)C4O)C(O)C(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4O)C3O)C(O)C2NC(C)=O)C(O)C1NC(C)=O)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C
> name yeast_rft1_m5_crack
Running Boltz prediction of protein with 574 residues, 1 ligands
CC(CCOP([O-])(=O)OP([O-])(=O)OC1OC(CO)C(OC2OC(CO)C(OC3OC(COC4OC(CO)C(O)C(O)C4O)C(O)C(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4O)C3O)C(O)C2NC(C)=O)C(O)C1NC(C)=O)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C
on gpu
Using multiple sequence alignment server https://api.colabfold.com
Please cite Boltz-1 Democratizing Biomolecular Interaction Modeling. BioRxiv
https://doi.org/10.1101/2024.11.19.624167 if you use these predictions.
Running boltz prediction failed with exit code 1:
command:
/Users/n.e.xone/boltz/bin/boltz predict
/Users/n.e.xone/Desktop/boltz_yeast_rft1_m5_crack/yeast_rft1_m5_crack.yaml
--write_full_pae --use_msa_server --accelerator gpu --no_potentials
stdout:
Checking input data.
Running predictions for 1 structure
Processing input data.
WARNING: RDKit ETKDGv3 failed to generate a conformer for molecule
CC(=O)NC1C(OC2C(CO)OC(OP(=O)([O-])OP(=O)([O-])OCCC(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C)C(NC(C)=O)C2O)OC(CO)C(OC2OC(COC3OC(CO)C(O)C(O)C3O)C(O)C(OC3OC(CO)C(O)C(O)C3OC3OC(CO)C(O)C(O)C3OC3OC(CO)C(O)C(O)C3O)C2O)C1O,
so the program will start with random coordinates. Note that the performance
of the model under this behaviour was not tested.
Generating MSA for
/Users/n.e.xone/Desktop/boltz_yeast_rft1_m5_crack/yeast_rft1_m5_crack.yaml
with 1 protein entities.
stderr:
0%| | 0/1 [00:00<?, ?it/s]
0%| | 0/150 [elapsed: 00:00 remaining: ?][A
SUBMIT: 0%| | 0/150 [elapsed: 00:00 remaining: ?][A
PENDING: 0%| | 0/150 [elapsed: 00:01 remaining: ?][ASleeping for 10s. Reason: PENDING
PENDING: 0%| | 0/150 [elapsed: 00:11 remaining: ?][ASleeping for 6s. Reason: PENDING
PENDING: 0%| | 0/150 [elapsed: 00:18 remaining: ?][ASleeping for 6s. Reason: PENDING
PENDING: 0%| | 0/150 [elapsed: 00:25 remaining: ?][ASleeping for 5s. Reason: PENDING
PENDING: 0%| | 0/150 [elapsed: 00:31 remaining: ?][ASleeping for 7s. Reason: PENDING
PENDING: 0%| | 0/150 [elapsed: 00:39 remaining: ?][ASleeping for 6s. Reason: PENDING
PENDING: 0%| | 0/150 [elapsed: 00:46 remaining: ?][ASleeping for 7s. Reason: PENDING
PENDING: 0%| | 0/150 [elapsed: 00:54 remaining: ?][ASleeping for 7s. Reason: PENDING
PENDING: 0%| | 0/150 [elapsed: 01:02 remaining: ?][ASleeping for 7s. Reason: PENDING
PENDING: 0%| | 0/150 [elapsed: 01:09 remaining: ?][ASleeping for 10s. Reason: PENDING
RUNNING: 0%| | 0/150 [elapsed: 01:20 remaining: ?][A
RUNNING: 7%|▋ | 10/150 [elapsed: 01:20 remaining: 18:47][ASleeping for 5s. Reason: RUNNING
RUNNING: 7%|▋ | 10/150 [elapsed: 01:27 remaining: 18:47][A
RUNNING: 10%|█ | 15/150 [elapsed: 01:27 remaining: 11:48][ASleeping for 10s. Reason: RUNNING
RUNNING: 10%|█ | 15/150 [elapsed: 01:38 remaining: 11:48][A
RUNNING: 17%|█▋ | 25/150 [elapsed: 01:38 remaining: 06:18][ASleeping for 10s. Reason: RUNNING
RUNNING: 17%|█▋ | 25/150 [elapsed: 01:49 remaining: 06:18][A
RUNNING: 23%|██▎ | 35/150 [elapsed: 01:49 remaining: 04:10][ASleeping for 9s. Reason: RUNNING
RUNNING: 23%|██▎ | 35/150 [elapsed: 01:59 remaining: 04:10][A
RUNNING: 29%|██▉ | 44/150 [elapsed: 01:59 remaining: 03:09][ASleeping for 9s. Reason: RUNNING
COMPLETE: 29%|██▉ | 44/150 [elapsed: 02:09 remaining: 03:09][A
COMPLETE: 100%|██████████| 150/150 [elapsed: 02:09 remaining: 00:00][A
COMPLETE: 100%|██████████| 150/150 [elapsed: 02:13 remaining: 00:00]
100%|██████████| 1/1 [02:18<00:00, 138.02s/it] 100%|██████████| 1/1
[02:18<00:00, 138.02s/it]
Traceback (most recent call last):
File "/Users/n.e.xone/boltz/bin/boltz", line 8, in <module>
sys.exit(cli())
^^^^^
File "/Users/n.e.xone/boltz/lib/python3.11/site-packages/click/core.py", line
1157, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/n.e.xone/boltz/lib/python3.11/site-packages/click/core.py", line
1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/Users/n.e.xone/boltz/lib/python3.11/site-packages/click/core.py", line
1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/n.e.xone/boltz/lib/python3.11/site-packages/click/core.py", line
1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/n.e.xone/boltz/lib/python3.11/site-packages/click/core.py", line
783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/n.e.xone/boltz/lib/python3.11/site-packages/boltz/main.py", line
744, in predict
model_module: Boltz1 = Boltz1.load_from_checkpoint(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/n.e.xone/boltz/lib/python3.11/site-
packages/pytorch_lightning/utilities/model_helpers.py", line 125, in wrapper
return self.method(cls, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/n.e.xone/boltz/lib/python3.11/site-
packages/pytorch_lightning/core/module.py", line 1582, in load_from_checkpoint
loaded = _load_from_checkpoint(
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/n.e.xone/boltz/lib/python3.11/site-
packages/pytorch_lightning/core/saving.py", line 63, in _load_from_checkpoint
checkpoint = pl_load(checkpoint_path, map_location=map_location)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/n.e.xone/boltz/lib/python3.11/site-
packages/lightning_fabric/utilities/cloud_io.py", line 60, in _load
return torch.load(
^^^^^^^^^^^
File "/Users/n.e.xone/boltz/lib/python3.11/site-
packages/torch/serialization.py", line 1491, in load
with _open_zipfile_reader(opened_file) as opened_zipfile:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/n.e.xone/boltz/lib/python3.11/site-
packages/torch/serialization.py", line 771, in __init__
super().__init__(torch._C.PyTorchFileReader(name_or_buffer))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: PytorchStreamReader failed reading zip archive: failed finding
central directory
> open "/Users/n.e.xone/Library/CloudStorage/Dropbox/ULB postdoc/Lab
> work/Structural Bioinformatics/Glycosylation enzymes/yeast
> rft1/omp/AF_P38206_F1_model_v4out.pdb"
AF_P38206_F1_model_v4out.pdb title:
Protein RFT1 (P38206) [more info...]
Chain information for AF_P38206_F1_model_v4out.pdb #1
---
Chain | Description | UniProt
A | No description available | RFT1_YEAST 1-574
Non-standard residues in AF_P38206_F1_model_v4out.pdb #1
---
DUM — (DUM)
Computing secondary structure
> lighting soft
> color bfactor palette alphafold
8097 atoms, 3983 residues, atom bfactor range 0 to 98.1
> set bgColor white
> select ::name="DUM"
3409 atoms, 3409 residues, 1 model selected
> surface sel
> transparency (#!1 & sel) 70
> color (#!1 & sel) dim gray
> transparency (#!1 & sel) 70
> color (#!1 & sel) dark gray
> color (#!1 & sel) light gray
> transparency (#!1 & sel) 70
> select clear
> boltz predict protein
> MAKKNSQLPSTSEQILERSTTGATFLMMGQLFTKLVTFILNNLLIRFLSPRIFGITAFLEFIQGTVLFFSRDAIRLSTLRISDSGNGIIDDDDEEEYQETHYKSKVLQTAVNFAYIPFWIGFPLSIGLIAWQYRNINAYFITLPFFRWSIFLIWLSIIVELLSEPFFIVNQFMLNYAARSRFESIAVTTGCIVNFIVVYAVQQSRYPMGVVTSDIDKEGIAILAFALGKLAHSITLLACYYWDYLKNFKPKKLFSTRLTKIKTRENNELKKGYPKSTSYFFQNDILQHFKKVYFQLCFKHLLTEGDKLIINSLCTVEEQGIYALLSNYGSLLTRLLFAPIEESLRLFLARLLSSHNPKNLKLSIEVLVNLTRFYIYLSLMIIVFGPANSSFLLQFLIGSKWSTTSVLDTIRVYCFYIPFLSLNGIFEAFFQSVATGDQILKHSYFMMAFSGIFLLNSWLLIEKLKLSIEGLILSNIINMVLRILYCGVFLNKFHRELFTDSSFFFNFKDFKTVIIAGSTICLLDWWFIGYVKNLQQFVVNVLFAMGLLALILVKERQTIQSFINKRAVSNSKDV
> ligandSmiles
> CC(CCOP([O-])(=O)OP([O-])(=O)OC1OC(CO)C(OC2OC(CO)C(OC3OC(COC4OC(CO)C(O)C(O)C4O)C(O)C(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4O)C3O)C(O)C2NC(C)=O)C(O)C1NC(C)=O)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C
> name yeast_rft1_m5_crack
Running Boltz prediction of protein with 574 residues, 1 ligands
CC(CCOP([O-])(=O)OP([O-])(=O)OC1OC(CO)C(OC2OC(CO)C(OC3OC(COC4OC(CO)C(O)C(O)C4O)C(O)C(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4O)C3O)C(O)C2NC(C)=O)C(O)C1NC(C)=O)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C
on gpu
Using multiple sequence alignment server https://api.colabfold.com
> ui tool show "Side View"
> select /A
4688 atoms, 4803 bonds, 574 residues, 1 model selected
> show sel surfaces
> select clear
Boltz prediction completed in 1639 seconds
The Boltz prediction ran out of memory. The memory use depends on the number
of protein and nucleic acid residues plus the number of ligand atoms. You can
reduce the size of your molecular assembly to stay within the memory limits.
> close session
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 572, in _report_progress
if not self.tool_window.shown:
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2343, in shown
return self.__toolkit.shown
^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'shown'
Error processing trigger "new frame":
AttributeError: 'NoneType' object has no attribute 'shown'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2343, in shown
return self.__toolkit.shown
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: MLY33B/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6 (24G84)
Kernel Version: Darwin 24.6.0
Time since boot: 7 days, 22 hours, 33 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
PHL 242B1:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Main Display: Yes
Mirror: On
Mirror Status: Master Mirror
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Mirror: On
Mirror Status: Hardware Mirror
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (3)
comment:1 by , 3 months ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Boltz: PytorchStreamReader failed reading zip archive: failed finding central directory |
comment:2 by , 3 months ago
comment:3 by , 3 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed error where session is closed and Boltz panel tries to report progress.
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There are two errors in this bug report. In the first error Boltz fails trying to read the neural network weights from file ~/.boltz/boltz1_conf.ckpt. That is probably because that file failed to completely download when installing Boltz. The fix for that is to remove the ~/.boltz directory. Then when you run a Boltz prediction it will download the weights. That will take a while on the first prediction because the weights are about 3 Gbytes.
Then you ran a second boltz prediction with 1639 residues that says it ran out of memory. Your computer has only 8 GB of memory and that is probably not enough to run any Boltz prediction. Take a look at the ChimeraX Boltz run times table where you will see 16 GB of memory on a Mac can only handle predictions up to about 600 amino acids. I don't have an 8 GB Mac to test if it can run any predictions.
After that you typed "close session" and there was an error because the Boltz panel tried to show a progress message even though it had been closed. I'll fix that.