Opened 15 months ago

Closed 15 months ago

Last modified 15 months ago

#15797 closed defect (fixed)

alphafold pae file: structure is None

Reported by: pmcarlton@… 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:        Linux-6.8.0-40-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Attempting to load the attached alphafold PAE file, and received an unexpected error. This error did not occur in ChimeraX 1.7.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /run/user/1000/gvfs/google-
> drive:host=gmail.com,user=pmcarlton/0ABz9jp0Qbo8wUk9PVA/0Bxz9jp0Qbo8wfnY3SDA3SVR5V2t6TkNWeXg1X0NqM21MalUtTEpJd01FWE81NmpfYzBRVnM/18N_tuL-58EAmDuVjoKICbQlcBvtA6MtZ/1sl97SLBQK-
> RjzRim0qoF4vehoOaHKX_T

'/run/user/1000/gvfs/google-
drive:host=gmail.com,user=pmcarlton/0ABz9jp0Qbo8wUk9PVA/0Bxz9jp0Qbo8wfnY3SDA3SVR5V2t6TkNWeXg1X0NqM21MalUtTEpJd01FWE81NmpfYzBRVnM/18N_tuL-58EAmDuVjoKICbQlcBvtA6MtZ/1sl97SLBQK-
RjzRim0qoF4vehoOaHKX_T' has no suffix  

> open /home/pcarlton/Documents/fold_syp11223344562024_05_09_15_09_model_0.cif

Chain information for fold_syp11223344562024_05_09_15_09_model_0.cif #1  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
G H | .  
I | .  
J | .  
  

> hide cartoons

> hide atoms

> show cartoons

> show atoms

> hide atoms

> alphafold pae file
> /home/pcarlton/Documents/fold_syp11223344562024_05_09_15_09_full_data_0.json

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1405, in alphafold_pae  
pae = AlphaFoldPAE(file, structure)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 944, in __init__  
self._num_atoms = structure.num_atoms  
^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'num_atoms'  
  
AttributeError: 'NoneType' object has no attribute 'num_atoms'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 944, in __init__  
self._num_atoms = structure.num_atoms  
^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Alignment identifier is 1  
Alignment identifier is 2  
Alignment identifier is 3  
Alignment identifier is 4  
Alignment identifier is 1/I  
Alignment identifier is 1/J  

> rainbow

> close

> open
> /home/pcarlton/af3/syp-5s541ph_him-3_syp-1t452ph_htp-3/fold_syp_5_s541phos_him_3_syp_1t452phos_htp_3_full_data_0.json

Opening an AlphaFold PAE file requires specifying the structure to associate.
Did not find an open structure from the same directory. To specify the
structure use menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command, for example  
  
open
/home/pcarlton/af3/syp-5s541ph_him-3_syp-1t452ph_htp-3/fold_syp_5_s541phos_him_3_syp_1t452phos_htp_3_full_data_0.json
format pae structure #1  

> open
> /home/pcarlton/af3/syp-5s541ph_him-3_syp-1t452ph_htp-3/fold_syp_5_s541phos_him_3_syp_1t452phos_htp_3_model_0.cif

Chain information for
fold_syp_5_s541phos_him_3_syp_1t452phos_htp_3_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
Alignment identifier is 1/C  
Alignment identifier is 1/D  

> select /D:260

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

> select /D:260-568

2412 atoms, 2446 bonds, 309 residues, 1 model selected  

> select clear

> select /C:18

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /C:18-19

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select clear

> select /D:739

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

> select /D:242-739

3830 atoms, 3889 bonds, 498 residues, 1 model selected  

> color sel orange

> select clear

> color bychain

> select /C:452

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /C:452

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel sphere

Changed 11 atom styles  

> color sel byhetero

> select clear

> select
> /A:2-96,100-230,233-254,260-263,266-361,364-367,369-380,382-400,403-440,443-486,491-493,495-508,511-522,526-546

4139 atoms, 4175 bonds, 515 residues, 1 model selected  

> select /A:488

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

> select /A:488-489

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:544

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:541-544

36 atoms, 37 bonds, 4 residues, 1 model selected  

> select clear

> alphafold pae file
> /home/pcarlton/af3/syp-5s541ph_him-3_syp-1t452ph_htp-3/t.json

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1405, in alphafold_pae  
pae = AlphaFoldPAE(file, structure)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 944, in __init__  
self._num_atoms = structure.num_atoms  
^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'num_atoms'  
  
AttributeError: 'NoneType' object has no attribute 'num_atoms'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 944, in __init__  
self._num_atoms = structure.num_atoms  
^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> alphafold pae file
> /home/pcarlton/af3/syp-5s541ph_him-3_syp-1t452ph_htp-3/fold_syp_5_s541phos_him_3_syp_1t452phos_htp_3_full_data_0.json

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1405, in alphafold_pae  
pae = AlphaFoldPAE(file, structure)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 944, in __init__  
self._num_atoms = structure.num_atoms  
^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'num_atoms'  
  
AttributeError: 'NoneType' object has no attribute 'num_atoms'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 944, in __init__  
self._num_atoms = structure.num_atoms  
^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: Mesa Intel(R) Graphics (RPL-S)
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: Gigabyte Technology Co., Ltd.
Model: Z690 UD AX DDR4
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 13th Gen Intel(R) Core(TM) i5-13600K
Cache Size: 24576 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           125Gi        12Gi        93Gi       5.6Gi        19Gi       106Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Raptor Lake-S GT1 [UHD Graphics 770] [8086:a780] (rev 04)	
	DeviceName: Onboard - Video	
	Subsystem: Gigabyte Technology Co., Ltd Device [1458:d000]

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    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: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    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: 1.2.4
    ChimeraX-DiffPlot: 1.0
    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: 1.1.10
    ChimeraX-LinuxSupport: 1.0.1
    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: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    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: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    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: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    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: 3.0.15
    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: 1.16.5
    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
    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: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
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    line-profiler: 4.1.2
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    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
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    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    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: 2.0.1
    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: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
File attachment: fold_syp_5_s541phos_him_3_syp_1t452phos_htp_3_full_data_0.json

fold_syp_5_s541phos_him_3_syp_1t452phos_htp_3_full_data_0.json​

Attachments (1)

fold_syp_5_s541phos_him_3_syp_1t452phos_htp_3_full_data_0.json​ (45.6 MB ) - added by pmcarlton@… 15 months ago.
Added by email2trac

Change History (5)

by pmcarlton@…, 15 months ago

Attachment: fold_syp_5_s541phos_him_3_syp_1t452phos_htp_3_full_data_0.json​ added

Added by email2trac

comment:1 by Eric Pettersen, 15 months ago

Component: Unassigned → Structure Prediction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → alphafold pae file: structure is None

Reported by Peter Carlton

comment:2 by Tom Goddard, 15 months ago

Thanks for reporting the problem. ChimeraX expects to associate the atomic model with the PAE so you need to open the structure first then use

alphafold pae file /home/pcarlton/af3/syp-5s541ph_him-3_syp-1t452ph_htp-3/fold_syp_5_s541phos_him_3_syp_1t452phos_htp_3_full_data_0.json structure #1

where the open atomic model has id #1.

I thought I made it so the "structure #1" was not needed and it would either find the already opened structure or would work with no structure open, although not much you can do with the PAE data without a structure. Apparently I did not do that but I'll look into improving it now.

The usual way I open the PAE data is to open the predicted structure and then use menu Tools / Structure Prediction / AlphaFold Error Plot. That is working in my tests.

comment:3 by Tom Goddard, 15 months ago

Resolution: → fixed
Status: assigned → closed

Fixed.

I improved the code so it will tell you that you have to open the predicted atomic model before opening the PAE json file.

I considered allowing you to open the PAE json file without first opening atomic model. But then the PAE plot is almost useless because ChimeraX does not know any of the residue or atom names associated with the rows and columns of the plot, and most of the methods to visualize the PAE data require the structure.

comment:4 by pmcarlton@…, 15 months ago 

Thanks very much! I had omitted the model number (#1) before from the command as well; when I added it back everything works well with no error. It's a really great feature.

On 2024-08-22 at 08:29, ChimeraX-bugs-admin@cgl.ucsf.edu wrote:
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