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[Bug] merged pdb structure: any protein + DNA (1BNA.pdb) breaks Molecule3D #467

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IvoLeist opened this issue Jan 20, 2020 · 1 comment
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@IvoLeist
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IvoLeist commented Jan 20, 2020

Describe the bug
If I am trying to upload a merged pdb structure (any protein + DNA (1BNA.pdb)
Molecule3D stops working. This holds true for dash-bio on localhost and
https://dash-gallery.plotly.host/dash-molecule-3d-viewer/

To Reproduce

  1. Download two pdb structures from rcsb.org (where one is a DNA duplex)
    (e.g. https://files.rcsb.org/download/1BNA.pdb and https://files.rcsb.org/download/2MRU.pdb)
  2. Upload them in pymol (https://pymol.org/2/)
  3. Save them in a new pdb file
  4. Upload this file

Or download the attached example and change the file extension to .pdb
2mru_1bna_merged.txt

Expected behavior
It should show the two molecules

Bug message if hosted on local host
(This error originated from the built-in JavaScript code that runs Dash apps. Click to see the full stack trace or open your browser's console.)
TypeError: Cannot read property 'atom' of undefined

at u (http://localhost:8050/_dash-component-suites/dash_bio/async~moleculeviewer3.js?v=0.4.6&m=1579173631:1:264066)

at Object.drawCartoon (http://localhost:8050/_dash-component-suites/dash_bio/async~moleculeviewer3.js?v=0.4.6&m=1579173631:1:265971)

at e.globj (http://localhost:8050/_dash-component-suites/dash_bio/async~moleculeviewer3.js?v=0.4.6&m=1579173631:1:293822)

at $3Dmol.GLViewer.render (http://localhost:8050/_dash-component-suites/dash_bio/async~moleculeviewer3.js?v=0.4.6&m=1579173631:1:328877)

at t.value (http://localhost:8050/_dash-component-suites/dash_bio/async~moleculeviewer3.js?v=0.4.6&m=1579173631:1:5304)

at t.value (http://localhost:8050/_dash-component-suites/dash_bio/async~moleculeviewer3.js?v=0.4.6&m=1579173631:1:3633)

at commitLifeCycles (http://localhost:8050/_dash-component-suites/dash_renderer/react-dom@16.8.6.js?v=1.1.2&m=1576595738:17484:22)

at commitAllLifeCycles (http://localhost:8050/_dash-component-suites/dash_renderer/react-dom@16.8.6.js?v=1.1.2&m=1576595738:18871:7)

at HTMLUnknownElement.callCallback (http://localhost:8050/_dash-component-suites/dash_renderer/react-dom@16.8.6.js?v=1.1.2&m=1576595738:143:14)

at Object.invokeGuardedCallbackDev (http://localhost:8050/_dash-component-suites/dash_renderer/react-dom@16.8.6.js?v=1.1.2&m=1576595738:193:16)
@IvoLeist
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Below is the error showing up on
https://dash-gallery.plotly.host/dash-molecule-3d-viewer/

The number in front of Uncaught TypeError: Cannot read property 'children' of null
is constantly increasing + the app cannot be used any longer
(e.g. selecting a new molecule from the dropdown or uploading a new one.
*Page has to be reloaded to use it again

image

@IvoLeist IvoLeist changed the title merged pdb structure: any protein + DNA (1BNA.pdb) breaks Molecule3D [BUG] merged pdb structure: any protein + DNA (1BNA.pdb) breaks Molecule3D Jan 20, 2020
@IvoLeist IvoLeist changed the title [BUG] merged pdb structure: any protein + DNA (1BNA.pdb) breaks Molecule3D [Bug] merged pdb structure: any protein + DNA (1BNA.pdb) breaks Molecule3D Jan 20, 2020
@IvoLeist IvoLeist mentioned this issue Mar 5, 2020
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@emmeb emmeb closed this as completed Oct 28, 2021
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