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#10373 closed defect (duplicate)

read_json_pae_matrix: KeyError: 0

Reported by:	nandita.bodra@…	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-10-10.0.19045
ChimeraX Version: 1.4.dev202204010229 (2022-04-01 02:29:39 UTC)
Description
Hi, I am keep on getting this bug. Please find the enclosed attachement.

Log:
UCSF ChimeraX version: 1.4.dev202204010229 (2022-04-01)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "C:\Users\nabo0034\Desktop\Chimeraresults\Binding prediction MakD and C
> ny alphafold\ALPHAFOLD BINDING PREDICTION RESULT .cxs" format session

Log from Tue Dec 19 16:47:41 2023UCSF ChimeraX version: 1.4.dev202204010229
(2022-04-01)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold predict
> MKKVEILMVVDAAAALASRDLQSNIYLIDTNKYMGSGNEGQAELKTACKDGQLLCWRVVAISPDNEVDIVEFNGQMINDRVCIPTKQGLSGDEFWEGRVEAQGQASTQQYNATLSIDGSRLTFDPFLVISL,MKKIEILIVVDCAGALATTSLISNVYLIDSNQWLGSWDEGTCQLHTVSEDGQFICWRSCAISPDDEVNITGFYGDMIDQKACLPSPVNDAWEGRVQTRGDTGRYLYTISLSINGITMNFSPYLEVQ

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in C:\Users\nabo0034/Downloads\ChimeraX\AlphaFold\prediction_4  
Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> set bgColor white

> set bgColor #ffffff00

> select /A

2002 atoms, 2015 bonds, 131 residues, 1 model selected  

> color sel cornflower blue

> select /B

1924 atoms, 1944 bonds, 126 residues, 1 model selected  

> color sel gray

> select clear

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.1: minimum, -17.32, mean
-2.47, maximum 9.91  
Coulombic values for best_model.pdb_B SES surface #1.2: minimum, -15.33, mean
-3.26, maximum 8.31  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency 70

> contacts A/ B

Unknown command: alphafold contacts A/ B  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> C:\\\Users\\\nabo0034/Downloads\\\ChimeraX\\\AlphaFold\\\prediction_4\\\best_model_pae.json

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 158, in _open_pae  
self._open_pae_from_file(s)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 182, in _open_pae_from_file  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\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 1.4.dev202204010229\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 674, in alphafold_pae  
pae = AlphaFoldPAE(file, structure)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 477, in __init__  
self._pae_matrix = read_pae_matrix(pae_path)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 531, in read_pae_matrix  
return read_json_pae_matrix(path)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 546, in read_json_pae_matrix  
d = j[0]  
KeyError: 0  
  
KeyError: 0  
  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 546, in read_json_pae_matrix  
d = j[0]  
  
See log for complete Python traceback.  
  

> save "C:/Users/nabo0034/Desktop/Chimeraresults/Binding prediction MakD and C
> ny alphafold/ALPHAFOLD BINDING PREDICTION RESULT .cxs"

——— End of log from Tue Dec 19 16:47:41 2023 ———

opened ChimeraX session  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> C:\\\Users\\\nabo0034/Downloads\\\ChimeraX\\\AlphaFold\\\prediction_4\\\best_model_pae.json

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 158, in _open_pae  
self._open_pae_from_file(s)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 182, in _open_pae_from_file  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\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 1.4.dev202204010229\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 674, in alphafold_pae  
pae = AlphaFoldPAE(file, structure)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 477, in __init__  
self._pae_matrix = read_pae_matrix(pae_path)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 531, in read_pae_matrix  
return read_json_pae_matrix(path)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 546, in read_json_pae_matrix  
d = j[0]  
KeyError: 0  
  
KeyError: 0  
  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 546, in read_json_pae_matrix  
d = j[0]  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.9664
OpenGL renderer: Intel(R) HD Graphics 630
OpenGL vendor: Intel

Python: 3.9.11
Locale: sv_SE.cp1252
Qt version: PyQt6 6.2.3, Qt 6.2.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 7050
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 17,036,312,576
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700 CPU @ 3.60GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    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
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.37
    ChimeraX-AtomicLibrary: 6.1.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    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: 2.2.2
    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.dev202204010229
    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: 1.0
    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: 1.1
    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
    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: 1.8
    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
    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
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16.4
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    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: 4.31.2
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    h5py: 3.6.0
    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: 4.9.2
    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: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.28
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.7
    PyQt6-commercial: 6.2.3
    PyQt6-sip: 13.2.0
    PyQt6-WebEngine-commercial: 6.2.1
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 22.3.0
    qtconsole: 5.3.0
    QtPy: 2.0.1
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.1
    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
    WMI: 1.5.1
File attachment: ALPHAFOLD BINDING PREDICTION RESULT .cxs

ALPHAFOLD BINDING PREDICTION RESULT .cxs

Attachments (1)

ALPHAFOLD BINDING PREDICTION RESULT .cxs (9.7 MB ) - added by nandita.bodra@… 22 months ago.: Added by email2trac

Change History (5)

by nandita.bodra@…, 22 months ago

Attachment:	ALPHAFOLD BINDING PREDICTION RESULT .cxs added

Added by email2trac

comment:1 by Eric Pettersen, 22 months ago

Component:	Unassigned → Structure Prediction
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → read_json_pae_matrix: KeyError: 0

comment:2 by Tom Goddard, 22 months ago

Resolution:	→ duplicate
Status:	assigned → closed

This bug is because you are using an old ChimeraX version 1.4 prerelease. You have to update to a current ChimeraX. I responded to your same report (#10358) 2 days ago and you should have received email explaining this.

comment:3 by nandita.bodra@…, 22 months ago

Hi Tom,
Thanks a lot for fixing it. I didn't realize this as I was working on two different computers and one had the latest version of ChimeraX and I just mixed it up.
I am very sorry for this stupid issue.

Thanks again!

Regards
Nandita


________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 19 December 2023 22:24
To: Nandita Bodra <nandita.bodra@umu.se>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #10373: read_json_pae_matrix: KeyError: 0

#10373: read_json_pae_matrix: KeyError: 0
-------------------------------------------+-------------------------
          Reporter:  nandita.bodra@…       |      Owner:  Tom Goddard
              Type:  defect                |     Status:  closed
          Priority:  normal                |  Milestone:
         Component:  Structure Prediction  |    Version:
        Resolution:  duplicate             |   Keywords:
        Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
           Project:  ChimeraX              |
-------------------------------------------+-------------------------
Changes (by Tom Goddard):

 * resolution:   => duplicate
 * status:  assigned => closed

Comment:

 This bug is because you are using an old ChimeraX version 1.4 prerelease.
 You have to update to a current ChimeraX.  I responded to your same report
 (#10358) 2 days ago and you should have received email explaining this.
--
Ticket URL: <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F10373%23comment%3A2&data=05%7C02%7Cnandita.bodra%40umu.se%7C14a2857c8b444ee6e3d608dc00d8edd1%7C5a4ba6f9f5314f329467398f19e69de4%7C0%7C0%7C638386178924860934%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=HXZqda2Fxf2njioOfGFAo5s3K34UzeJchWTcy6fNqeA%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10373#comment:2>>
ChimeraX <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=05%7C02%7Cnandita.bodra%40umu.se%7C14a2857c8b444ee6e3d608dc00d8edd1%7C5a4ba6f9f5314f329467398f19e69de4%7C0%7C0%7C638386178924860934%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=bDyRDB2%2BWToCj25coc5%2B8RaUCpFyXC%2F%2FjW%2F2Z8sq2xo%3D&reserved=0<https://www.rbvi.ucsf.edu/chimerax/>>
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comment:4 by goddard@…, 22 months ago

No trouble.

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