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#14913 closed defect (can't reproduce)

AlphaFold: File is not a zip file

Reported by:	chimerax-bug-report@…	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:        Windows-10-10.0.22631
ChimeraX Version: 1.8.dev202404020138 (2024-04-02 01:38:30 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.8.dev202404020138 (2024-04-02)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> C:/Users/Wcsob/OneDrive/Desktop/ChimeraX/AlphaFold/nnLuz_V4/bestmodel1.cxs

Log from Wed Apr 3 15:23:29 2024UCSF ChimeraX version: 1.8.dev202404020138
(2024-04-02)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\Wcsob\Downloads\ChimeraX\AlphaFold\prediction_3\best_model.pdb
> format pdb

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

> save
> C:/Users/Wcsob/OneDrive/Desktop/ChimeraX/AlphaFold/nnLuz_V4/bestmodel1.cxs

——— End of log from Wed Apr 3 15:23:29 2024 ———

opened ChimeraX session  

> open C:/Users/Wcsob/Downloads/ChimeraX/AlphaFold/prediction_3/best_model.pdb

Chain information for best_model.pdb #2  
---  
Chain | Description  
A | No description available  
  

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

Chain information for best_model.pdb #3  
---  
Chain | Description  
A | No description available  
  

> select #3/A:1-134

1078 atoms, 1099 bonds, 134 residues, 1 model selected  

> select #2/A:1-267

2137 atoms, 2189 bonds, 267 residues, 1 model selected  

> hide #3 models

> show #3 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #1 models

> hide #2 models

> hide #3 models

> close #3

> close #1

> close

> open C:/Users/Wcsob/Downloads/ChimeraX/AlphaFold/prediction_1/best_model.pdb

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

> cd C:/Users/Wcsob/OneDrive/Desktop/ChimeraX/AlphaFold/Luxsit-eppcr

Current working directory is:
C:\Users\Wcsob\OneDrive\Desktop\ChimeraX\AlphaFold\Luxsit-eppcr  

> alphafold predict
> MGSGSAEAQRRFVDRFYAALDAGDADTASALFPDGTEIHLWDGRTFRTRAEFRAWFRELRARSDNARREVVAFEVDGDTAHVEVVLRASIDGEERVVRLRHTFYFEGDRLVRVEVEIEPL

Running AlphaFold prediction  

> close

AlphaFold prediction finished  
Results in C:\Users\Wcsob/Downloads/ChimeraX/AlphaFold/prediction_2  

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

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

> alphafold predict
> MGSGSAEQQREFVKRFYEALDAGDADTASALFPDGTEIHLWDGTTFRTRAEFRAWFEELYSTSENASREVTSFSVDGDVADVEVVLRANLGGEDRTVSLRHVFHFAGDRLVRVEVSIRPL
> outputDir C:\Users\Wcsob\OneDrive\Desktop\ChimeraX\AlphaFold\Luxsit-
> eppcr\03-383

Expected a keyword  

> alphafold predict
> MGSGSAEQQREFVKRFYEALDAGDADTASALFPDGTEIHLWDGTTFRTRAEFRAWFEELYSTSENASREVTSFSVDGDVADVEVVLRANLGGEDRTVSLRHVFHFAGDRLVRVEVSIRPL
> outputDir C:\Users\Wcsob\OneDrive\Desktop\ChimeraX\AlphaFold\Luxsit-eppcr\

Expected a keyword  

> alphafold predict
> MGSGSAEQQREFVKRFYEALDAGDADTASALFPDGTEIHLWDGTTFRTRAEFRAWFEELYSTSENASREVTSFSVDGDVADVEVVLRANLGGEDRTVSLRHVFHFAGDRLVRVEVSIRPL
> outputDir C:/Users/Wcsob/OneDrive/Desktop/ChimeraX/AlphaFold/Luxsit-eppcr/

Expected a keyword  

> alphafold predict
> MGSGSAEQQREFVKRFYEALDAGDADTASALFPDGTEIHLWDGTTFRTRAEFRAWFEELYSTSENASREVTSFSVDGDVADVEVVLRANLGGEDRTVSLRHVFHFAGDRLVRVEVSIRPL
> outputDir C:\Users\Wcsob\OneDrive\Desktop\ChimeraX\AlphaFold\Luxsit-eppcr

Expected a keyword  

> alphafold predict
> MGSGSAEQQREFVKRFYEALDAGDADTASALFPDGTEIHLWDGTTFRTRAEFRAWFEELYSTSENASREVTSFSVDGDVADVEVVLRANLGGEDRTVSLRHVFHFAGDRLVRVEVSIRPL
> outputDir r"C:\Users\Wcsob\OneDrive\Desktop\ChimeraX\AlphaFold\Luxsit-eppcr"

Expected a keyword  

> alphafold predict
> MGSGSAEQQREFVKRFYEALDAGDADTASALFPDGTEIHLWDGTTFRTRAEFRAWFEELYSTSENASREVTSFSVDGDVADVEVVLRANLGGEDRTVSLRHVFHFAGDRLVRVEVSIRPL
> outputDir
> C:\\\Users\\\Wcsob\\\OneDrive\\\Desktop\\\ChimeraX\\\AlphaFold\\\Luxsit-
> eppcr

Expected a keyword  

> alphafold predict
> MGSGSAEQQREFVKRFYEALDAGDADTASALFPDGTEIHLWDGTTFRTRAEFRAWFEELYSTSENASREVTSFSVDGDVADVEVVLRANLGGEDRTVSLRHVFHFAGDRLVRVEVSIRPL
> outputDir
> "C:\\\Users\\\Wcsob\\\OneDrive\\\Desktop\\\ChimeraX\\\AlphaFold\\\Luxsit-
> eppcr"

Expected a keyword  

> alphafold predict
> MGSGSAEQQREFVKRFYEALDAGDADTASALFPDGTEIHLWDGTTFRTRAEFRAWFEELYSTSENASREVTSFSVDGDVADVEVVLRANLGGEDRTVSLRHVFHFAGDRLVRVEVSIRPL
> outputDir "C:/Users/Wcsob/OneDrive/Desktop/ChimeraX/AlphaFold/Luxsit-eppcr"

Expected a keyword  

> alphafold predict
> MGSGSAEQQREFVKRFYEALDAGDADTASALFPDGTEIHLWDGTTFRTRAEFRAWFEELYSTSENASREVTSFSVDGDVADVEVVLRANLGGEDRTVSLRHVFHFAGDRLVRVEVSIRPL
> directory C:/Users/Wcsob/OneDrive/Desktop/ChimeraX/AlphaFold/Luxsit-eppcr

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in C:/Users/Wcsob/OneDrive/Desktop/ChimeraX/AlphaFold/Luxsit-eppcr  

> open C:/Users/Wcsob/OneDrive/Desktop/ChimeraX/AlphaFold/Luxsit-
> eppcr\best_model.pdb

Chain information for best_model.pdb #2  
---  
Chain | Description  
A | No description available  
  

> alphafold predict
> MGSGTDEEIAEFVKAFYEALDAGDAETAADLLFGAGCKEIHLWDGTVFTSKEGFETWFKKLQSAVTGAKRKIESVEIKDGEAVVKVTLTATYKATGKKFVVELEHTFTFDRERNELVEVKVTATPL
> directory C:/Users/Wcsob/OneDrive/Desktop/ChimeraX/AlphaFold/Luxsit-
> eppcr/1C1_prediction

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in C:/Users/Wcsob/OneDrive/Desktop/ChimeraX/AlphaFold/Luxsit-
eppcr/1C1_prediction  

> open C:/Users/Wcsob/OneDrive/Desktop/ChimeraX/AlphaFold/Luxsit-
> eppcr/1C1_prediction\best_model.pdb

Chain information for best_model.pdb #3  
---  
Chain | Description  
A | No description available  
  

> hide #1 models

> hide #2 models

> close #1

> close #2

> close

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 1 time(s)]

> fetch1DNA

Unknown command: fetch1DNA  

> fetch 1dna

Unknown command: fetch 1dna  

> fetch 1DNA

Unknown command: fetch 1DNA  

> open 1DNA

Summary of feedback from opening 1DNA fetched from pdb  
---  
notes | Fetching compressed mmCIF 1dna from http://files.rcsb.org/download/1dna.cif  
Fetching CCD CXM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/CXM/CXM.cif  
Fetching CCD UMP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/UMP/UMP.cif  
Fetching CCD CB3 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/3/CB3/CB3.cif  
  
1dna title:  
D221(169)N mutant does not promote opening of the cofactor imidazolidine ring
[more info...]  
  
Chain information for 1dna #1  
---  
Chain | Description | UniProt  
A B | THYMIDYLATE SYNTHASE | TYSY_ECOLI 2-264  
  
Non-standard residues in 1dna #1  
---  
CB3 — 10-propargyl-5,8-dideazafolic acid  
UMP — 2'-deoxyuridine 5'-monophosphate (DUMP)  
  

> open 1DNA

1dna title:  
D221(169)N mutant does not promote opening of the cofactor imidazolidine ring
[more info...]  
  
Chain information for 1dna #2  
---  
Chain | Description | UniProt  
A B | THYMIDYLATE SYNTHASE | TYSY_ECOLI 2-264  
  
Non-standard residues in 1dna #2  
---  
CB3 — 10-propargyl-5,8-dideazafolic acid  
UMP — 2'-deoxyuridine 5'-monophosphate (DUMP)  
  

> select :CB3

140 atoms, 148 bonds, 4 residues, 2 models selected  

> select #2/A:1-264

2153 atoms, 2213 bonds, 264 residues, 1 model selected  

> select clear

> find asp221

Unknown command: find asp221  

> select 221

Expected an objects specifier or a keyword  

> select ASP221

Expected an objects specifier or a keyword  

> selection +ASP 221

Unknown command: selection +ASP 221  

> selection

Unknown command: selection  

> select

9264 atoms, 9088 bonds, 1496 residues, 2 models selected  

> select +ASP

Expected an objects specifier or a keyword  

> select +ASP221

Expected an objects specifier or a keyword  

> select ASP221

Expected an objects specifier or a keyword  

> select

9264 atoms, 9088 bonds, 1496 residues, 2 models selected  

> select

9264 atoms, 9088 bonds, 1496 residues, 2 models selected  

> select help

Expected an objects specifier or a keyword  

> help

> ui dockable false "Model Panel"

> close #1

> close

> alphafold predict
> MSSGSEEEIREFVRRFYEVLDAGDAATASALFPDGTEIHLWDGTTFRTQAQFRAWFERRCAQSANARREIVDLKVEGDRAKVEVILRASFDGEEKVVNLTHEFLFEGDRLVRVSVTITPL
> directory "C:/Users/Wcsob/OneDrive/Desktop/ChimeraX/AlphaFold/Luxsit-
> eppcr/round_4-04042024/04-844.3 "

QWindowsWindow::setGeometry: Unable to set geometry 800x501+368+211 (frame:
816x540+360+180) on QWidgetWindow/"QDockWidgetClassWindow" on "2470W".
Resulting geometry: 816x550+360+170 (frame: 832x589+352+139) margins: 8, 31,
8, 8 minimum size: 82x1 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=524303, y=524326), mintrack=POINT(x=98, y=40)))  

Running AlphaFold prediction  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_V8\bin\Lib\site-
packages\chimerax\alphafold\predict.py", line 248, in _unzip_results  
with zipfile.ZipFile(path, 'r') as z:  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX_V8\bin\Lib\zipfile.py", line 1302, in __init__  
self._RealGetContents()  
File "C:\Program Files\ChimeraX_V8\bin\Lib\zipfile.py", line 1369, in
_RealGetContents  
raise BadZipFile("File is not a zip file")  
zipfile.BadZipFile: File is not a zip file  
  
zipfile.BadZipFile: File is not a zip file  
  
File "C:\Program Files\ChimeraX_V8\bin\Lib\zipfile.py", line 1369, in
_RealGetContents  
raise BadZipFile("File is not a zip file")  
  
See log for complete Python traceback.  
  
Compositor returned null texture  
[Repeated 4 time(s)]

> open C:/Users/Wcsob/OneDrive/Desktop/ChimeraX/AlphaFold/Luxsit-
> eppcr/round_4-04042024/04-844.3/04-844.3.pdb

Chain information for 04-844.3.pdb #1  
---  
Chain | Description  
A | No description available  
  

> alphafold predict
> MGLGTDEEITEFVKAFYEALDAGDAETAADLLFGAGCKEIHLWDGTVFTSKEGFETWFKKLQSAVTGAKRKIESVEIKDGEAMVKVTLTATYKATGKKFVVELEHTFTFDRERNELVEVKVTATPL
> directory "C:/Users/Wcsob/OneDrive/Desktop/ChimeraX/AlphaFold/Luxsit-
> eppcr/round_4-04042024/1C1_(04_1172.1) "

Running AlphaFold prediction  

> alphafold predict
> MGLGTDEEITEFVKAFYEALDAGDAETAADLLFGAGCKEIHLWDGTVFTSKEGFETWFKKLQSAVTGAKRKIESVEIKDGEAMVKVTLTATYKATGKKFVVELEHTFTFDRERNELVEVKVTATPL
> directory "C:/Users/Wcsob/OneDrive/Desktop/ChimeraX/AlphaFold/Luxsit-
> eppcr/round_4-04042024/1C1_(04_1172.1) "

Running AlphaFold prediction  

> alphafold predict
> MGLGTDEEITEFVKAFYEALDAGDAETAADLLFGAGCKEIHLWDGTVFTSKEGFETWFKKLQSAVTGAKRKIESVEIKDGEAMVKVTLTATYKATGKKFVVELEHTFTFDRERNELVEVKVTATPL
> directory "C:/Users/Wcsob/OneDrive/Desktop/ChimeraX/AlphaFold/Luxsit-
> eppcr/round_4-04042024/1C1_(04_1172.1) "

Running AlphaFold prediction  

> alphafold predict
> MGLGTDEEITEFVKAFYEALDAGDAETAADLLFGAGCKEIHLWDGTVFTSKEGFETWFKKLQSAVTGAKRKIESVEIKDGEAMVKVTLTATYKATGKKFVVELEHTFTFDRERNELVEVKVTATPL
> directory "C:/Users/Wcsob/OneDrive/Desktop/ChimeraX/AlphaFold/Luxsit-
> eppcr/round_4-04042024/1C1_(04_1172.1) "

Running AlphaFold prediction  

> alphafold predict
> MGLGTDEEITEFVKAFYEALDAGDAETAADLLFGAGCKEIHLWDGTVFTSKEGFETWFKKLQSAVTGAKRKIESVEIKDGEAMVKVTLTATYKATGKKFVVELEHTFTFDRERNELVEVKVTATPL
> directory "C:/Users/Wcsob/OneDrive/Desktop/ChimeraX/AlphaFold/Luxsit-
> eppcr/round_4-04042024/1C1_(04_1172.1) "

Running AlphaFold prediction  

> alphafold predict
> MGLGTDEEITEFVKAFYEALDAGDAETAADLLFGAGCKEIHLWDGTVFTSKEGFETWFKKLQSAVTGAKRKIESVEIKDGEAMVKVTLTATYKATGKKFVVELEHTFTFDRERNELVEVKVTATPL
> directory "C:/Users/Wcsob/OneDrive/Desktop/ChimeraX/AlphaFold/Luxsit-
> eppcr/round_4-04042024/1C1_(04_1172.1) "

Running AlphaFold prediction  

> alphafold predict
> MGLGTDEEITEFVKAFYEALDAGDAETAADLLFGAGCKEIHLWDGTVFTSKEGFETWFKKLQSAVTGAKRKIESVEIKDGEAMVKVTLTATYKATGKKFVVELEHTFTFDRERNELVEVKVTATPL
> directory "C:/Users/Wcsob/OneDrive/Desktop/ChimeraX/AlphaFold/Luxsit-
> eppcr/round_4-04042024/1C1_(04_1172.1) "

Running AlphaFold prediction  

> ui windowfill toggle

[Repeated 1 time(s)]Compositor returned null texture  
[Repeated 1 time(s)]Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_V8\bin\Lib\site-
packages\chimerax\alphafold\predict.py", line 248, in _unzip_results  
with zipfile.ZipFile(path, 'r') as z:  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX_V8\bin\Lib\zipfile.py", line 1302, in __init__  
self._RealGetContents()  
File "C:\Program Files\ChimeraX_V8\bin\Lib\zipfile.py", line 1369, in
_RealGetContents  
raise BadZipFile("File is not a zip file")  
zipfile.BadZipFile: File is not a zip file  
  
zipfile.BadZipFile: File is not a zip file  
  
File "C:\Program Files\ChimeraX_V8\bin\Lib\zipfile.py", line 1369, in
_RealGetContents  
raise BadZipFile("File is not a zip file")  
  
See log for complete Python traceback.  
  

QWindowsWindow::setGeometry: Unable to set geometry 600x479+468+222 (frame:
616x518+460+191) on QWidgetWindow/"QDockWidgetClassWindow" on "2470W".
Resulting geometry: 616x528+460+181 (frame: 632x567+452+150) margins: 8, 31,
8, 8 minimum size: 600x325 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=524303, y=524326), mintrack=POINT(x=616, y=364)))  




OpenGL version: 3.3.0 NVIDIA 546.26
OpenGL renderer: NVIDIA GeForce MX330/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: windows

Manufacturer: HP
Model: HP Spectre x360 Convertible 15-eb0xxx
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 16,867,721,216
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-10510U CPU @ 1.80GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.6.0
    build: 1.1.1
    certifi: 2024.2.2
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.56.1
    ChimeraX-AtomicLibrary: 14.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    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: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8.dev202404020138
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.9
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    ChimeraX-ModelPanel: 1.5
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.3
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.37.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.3.1
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.9
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.1
    fonttools: 4.50.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2024.2.26
    idna: 3.6
    ihm: 0.43
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    Jinja2: 3.1.3
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.1.0
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.8
    ndindex: 1.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.2.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.0
    ParmEd: 4.2.2
    parso: 0.8.3
    pep517: 0.13.1
    pillow: 10.2.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.3.0
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3302
    pyparsing: 3.1.2
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.2
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.2
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 25.1.2
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.12.0
    setuptools: 69.2.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.0
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.1
    tables: 3.9.2
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.1
    typing-extensions: 4.10.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 19 months ago

Component:	Unassigned → Structure Prediction
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → AlphaFold: File is not a zip file

comment:2 by Tom Goddard, 19 months ago

Resolution:	→ can't reproduce
Status:	assigned → closed

Appears that the downloaded results.zip file may have been truncated. It appears the user ran the prediction 5 times before letting it complete -- that might cause a problem, not sure. They also specified a directory to save the result and the directory name ended in a space character -- I tried that and it did not cause any problem.

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