Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#7336 closed defect (fixed)

AlphaFold reporting old files

Reported by: anthony.morgan@… 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-10.15.5-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Run Colabfold. Folder called "Prediction #2" appears  in the Downloads folder.
Problem: if I *move* the folder out of Downloads, the next prediction (for a different protein sequence — same session?) displays the correct structure inside CX, but the NEW 'Prediction 2' folder that appears contains the previous OLD protein files (not the ones associated new one). 

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

Populating font family aliases took 282 ms. Replace uses of missing font
family "Calibri" with one that exists to avoid this cost.  

> alphafold predict
> MAAPPGEYFSVGSQVSCRTCQEQRLQGEVVAFDYQSKMLALKCPNHADILLINLQYVSEVEIINDRTET

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in /Users/anthonymorgan/Downloads/ChimeraX/AlphaFold/prediction_2  
Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  

> show surfaces

> close

> alphafold predict
> MAAPPGEYFSVGSAVSCRTCQEQRLQGEVVAFDYQSKMLALKCPNHADILLINLQYVSEVEIINDRTET

Running AlphaFold prediction  

> open "/Users/anthonymorgan/Dropbox/Work temp/Chimera
> X_Dropbx/TPC2-GG_iTASSER/model1.pdb" format pdb

No such file/path: /Users/anthonymorgan/Dropbox/Work temp/Chimera
X_Dropbx/TPC2-GG_iTASSER/model1.pdb  
AlphaFold prediction finished  
Results in /Users/anthonymorgan/Downloads/ChimeraX/AlphaFold/prediction_2  
Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  

> close

> alphafold predict
> MAAPPGEYFSVGSQVSCRTCQEQRLQGAVVAFDYQSKMLALKCPNHADILLINLQYVSEVEIINDRTET

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in /Users/anthonymorgan/Downloads/ChimeraX/AlphaFold/prediction_2  
Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  

> alphafold predict
> MAAPPGEYFSVGSQVSCRTCQEQRLQGEVVAFDYQSKMLALKCPSSSGKPNHADILLINLQYVSEVEIINDRTET

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in /Users/anthonymorgan/Downloads/ChimeraX/AlphaFold/prediction_2  
Chain information for best_model.pdb #2  
---  
Chain | Description  
A | No description available  
  

> close

> alphafold predict
> MAAPPGEYFSVGSQVSCRTCQEQRLQGEVVAFDYQSKMLALKCPNHADILLINLQYVSEVEIINDRTETPPVGTVSKGEELIKENMRMKVVMEGSVNGHQFKCTGEGEGRPYEGVQTMRIKVIEGGPLPFAFDILATSFMYGSRTFIKYPADIPDFFKQSFPEGFTWERVTRYEDGGVVTVTQDTSLEDGELVYNVKVRGVNFPSNGPVMQKKTKGWEPNTEMMYPADGGLRGYTDIALKVDGGGHLHCNFVTTYRSKKTVGNIKMPGVHAVDHRLERIEESDNETYVVQREVAVAKYSNLGGGMDELYK
> minimize false

Running AlphaFold prediction  

> open "/Users/anthonymorgan/Dropbox/Work temp/Chimera
> X_Dropbx/LSm12/LION/LION-WT/af69_relaxed_rank_1_model_1.pdb"

Chain information for af69_relaxed_rank_1_model_1.pdb #1  
---  
Chain | Description  
A | No description available  
  

> color bfactor

1072 atoms, 69 residues, atom bfactor range 40 to 95.6  

> color bfactor #1 palette alphafold

1072 atoms, 69 residues, atom bfactor range 40 to 95.6  

> open "/Users/anthonymorgan/Dropbox/Work temp/Chimera X_Dropbx/LSm12/LION/LSm
> FL-domain/af69_relaxed_rank_1_model_1.pdb"

Chain information for af69_relaxed_rank_1_model_1.pdb #2  
---  
Chain | Description  
A | No description available  
  

> Matchmaker #2 to #1

Unknown command: Matchmaker #2 to #1  

> Matchmaker #1 to #2

Unknown command: Matchmaker #1 to #2  

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> select #2/A:9

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select up

175 atoms, 178 bonds, 13 residues, 1 model selected  

> select up

1067 atoms, 1075 bonds, 69 residues, 1 model selected  

> select up

2139 atoms, 2155 bonds, 138 residues, 2 models selected  

> select up

2139 atoms, 2155 bonds, 138 residues, 2 models selected  

> select down

1067 atoms, 1075 bonds, 69 residues, 1 model selected  

> select up

2139 atoms, 2155 bonds, 138 residues, 2 models selected  

> lighting soft

> lighting simple

> close

> open "/Users/anthonymorgan/Dropbox/Work temp/Chimera
> X_Dropbx/LSm12/LION/LION-WT/af69_relaxed_rank_1_model_1.pdb" format pdb

Chain information for af69_relaxed_rank_1_model_1.pdb #1  
---  
Chain | Description  
A | No description available  
  

> close

> open "/Users/anthonymorgan/Dropbox/Work temp/Chimera X_Dropbx/LSm12/LION/LSm
> FL-domain/af69_relaxed_rank_1_model_1.pdb" format pdb

Chain information for af69_relaxed_rank_1_model_1.pdb #1  
---  
Chain | Description  
A | No description available  
  
Alignment identifier is 1/A  

> select /A:14-18,24-33,38-42,49-53,59-64

505 atoms, 501 bonds, 31 residues, 1 model selected  

> close

> open "/Users/anthonymorgan/Dropbox/Work temp/Chimera X_Dropbx/LSm12/LION/LSm
> FL-domain/af69_relaxed_rank_1_model_1.pdb"

Chain information for af69_relaxed_rank_1_model_1.pdb #1  
---  
Chain | Description  
A | No description available  
  
Alignment identifier is 1/A  

> select /A:14-18,24-33,38-42,49-53,59-64

505 atoms, 501 bonds, 31 residues, 1 model selected  

> select /A:69

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select /A:69

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select /A:14-18,24-33,38-42,49-53,59-64

505 atoms, 501 bonds, 31 residues, 1 model selected  

> close

AlphaFold prediction finished  
Results in /Users/anthonymorgan/Downloads/ChimeraX/AlphaFold/prediction_2  
Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  
Alignment identifier is 1/A  

> select
> /A:14-18,24-33,38-42,49-53,59-64,86-96,99-110,115-124,165-173,178-188,191-201,220-227,230-240,246-257,270-281,287-297

1209 atoms, 1211 bonds, 149 residues, 1 model selected  

> select /A:54-56,132-134,136-138,144-146,158-160,283-285,300-302

172 atoms, 168 bonds, 21 residues, 1 model selected  

> select /A:62

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select down

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select down

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

49 atoms, 48 bonds, 6 residues, 1 model selected  

> select up

2428 atoms, 2480 bonds, 310 residues, 1 model selected  

> select down

49 atoms, 48 bonds, 6 residues, 1 model selected  

> alphafold pae #1 file "/Users/anthonymorgan/Dropbox/Work temp/Chimera
> X_Dropbx/LSm12/LION/LION-WT-mRuby3/af69_predicted_aligned_error_v1.json"

Number of residues in structure "best_model.pdb #1" is 310 which does not
match PAE matrix size 69.  
  
This can happen if the AlphaFold model has been trimmed to match an
experimental structure, or if residues have been deleted. The full-length
AlphaFold model must be used to show predicted aligned error.  

> alphafold pae #1 file "/Users/anthonymorgan/Dropbox/Work temp/Chimera
> X_Dropbx/LSm12/LION/LION-WT-
> mRuby3/af69_unrelaxed_rank_1_model_1_scores.json"

Number of residues in structure "best_model.pdb #1" is 310 which does not
match PAE matrix size 69.  
  
This can happen if the AlphaFold model has been trimmed to match an
experimental structure, or if residues have been deleted. The full-length
AlphaFold model must be used to show predicted aligned error.  

> alphafold pae #1 file "/Users/anthonymorgan/Dropbox/Work temp/Chimera
> X_Dropbx/LSm12/LION/LION-WT-
> mRuby3/af69_unrelaxed_rank_1_model_1_scores.json"

Number of residues in structure "best_model.pdb #1" is 310 which does not
match PAE matrix size 69.  
  
This can happen if the AlphaFold model has been trimmed to match an
experimental structure, or if residues have been deleted. The full-length
AlphaFold model must be used to show predicted aligned error.  

> close

> open "/Users/anthonymorgan/Dropbox/Work temp/Chimera
> X_Dropbx/LSm12/LION/LION-WT-mRuby3/af69_relaxed_rank_1_model_1.pdb"

Chain information for af69_relaxed_rank_1_model_1.pdb #1  
---  
Chain | Description  
A | No description available  
  




OpenGL version: 4.1 INTEL-14.6.18
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine (1x6x8 (fused) LP
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir9,1
      Processor Name: Dual-Core Intel Core i3
      Processor Speed: 1.1 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 512 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      Boot ROM Version: 1037.120.87.0.0 (iBridge: 17.16.15300.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.5 (19F101)
      Kernel Version: Darwin 19.5.0
      Time since boot: 8 days 6:54

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a5c
      Revision ID: 0x0007
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (7)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Structure Prediction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → AlphaFold reporting old files

comment:2 by Tom Goddard, 3 years ago

I don't see how that can happen. If ChimeraX displays the new AlphaFold prediction, the only way it can do that is by downloading the AlphaFold results as result.zip, unzipping it, and opening the best_model.pdb file that the zip file contains into some prediction_N directory.

I suggest you check carefully. After you get an AlphaFold model in ChimeraX the Log will say

Results in /Users/anthonymorgan/Downloads/ChimeraX/AlphaFold/prediction_2

I think the model that it then opens and displays has to be the best_model.pdb from that directory. That directory cannot have an older best_model.pdb that is different from what is displayed.

in reply to:  3 ; comment:3 by anthony.morgan@…, 3 years ago 

Dear Tom,

Thanks for getting back to me, I’ve dug a little deeper.

Actually, there really is a confusion (but possibly the way I am using the interface). You’re right, it’s got nothing to do with dragging out the folders.


  *   The Prediction #N folders are accumulating all the models and files from the entire current session.
  *   Say I model proteins 1-5, then Pred 1 folder contains just the models for #1.
     *   I run the 2nd protein, and Pred 2 folder contains all the files from 1 and 2.
     *   By the time I’ve run 5 proteins, there are 5 predictions mixed up.
     *   Each folder size keeps increasing, commensurately.
  *   It’s hard to keep tabs on which files are for which protein.

The way I am running AF is:


  *   I launch the first AF prediction and enter Colab.
  *   For the next protein(s), I do NOT close the Colab window (because it speeds up the process; doesn’t need to re-load AF).

Question: am I running this incorrectly, or have I simply got to keep an eye on the order I feed the proteins into the AF?

Thanks,

Ant




On 27 Jul 2022, at 23:46, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:

#7336: AlphaFold reporting old files
-------------------------------------------+-------------------------
         Reporter:  anthony.morgan@…      |      Owner:  Tom Goddard
             Type:  defect                |     Status:  assigned
         Priority:  normal                |  Milestone:
        Component:  Structure Prediction  |    Version:
       Resolution:                        |   Keywords:
       Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
          Project:  ChimeraX              |
-------------------------------------------+-------------------------

Comment (by Tom Goddard):

I don't see how that can happen.  If ChimeraX displays the new AlphaFold
prediction, the only way it can do that is by downloading the AlphaFold
results as result.zip, unzipping it, and opening the best_model.pdb file
that the zip file contains into some prediction_N directory.

I suggest you check carefully.  After you get an AlphaFold model in
ChimeraX the Log will say

Results in /Users/anthonymorgan/Downloads/ChimeraX/AlphaFold/prediction_2

I think the model that it then opens and displays has to be the
best_model.pdb from that directory.  That directory cannot have an older
best_model.pdb that is different from what is displayed.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7336#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:4 by Tom Goddard, 3 years ago

I see the zip file made by AlphaFold does not get replaced, it just gets new files added. I will fix this today. It will not require a new ChimeraX -- it will be fixed on the colab script which is fetched each time a prediction is made.

in reply to:  5 ; comment:5 by anthony.morgan@…, 3 years ago 

Dear Tom,

Many thanks, it will be a great help.

Kind regards,

Ant

comment:6 by Tom Goddard, 3 years ago

Resolution: → fixed
Status: assigned → closed

Fixed. Does not require new ChimeraX since fix was in script fetched for each prediction.

The AlphaFold results.zip file was not removed between runs causing old prediction PDB files to be mixed with newer ones.

Thanks for reporting the problem. This will help lots of people.

in reply to:  7 ; comment:7 by anthony.morgan@…, 3 years ago 

You’re very welcome, you’re the one doing all the hard graft.

Thanks for doing it so swiftly.

BW,

Anthony
Note: See TracTickets for help on using tickets.