PyMOL2Jmol Translator

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The translator has not yet been released for public use

The Proteopedia PyMOL2Jmol Translator (beta) by User:Roni Gordon

Watch a demo of the Proteopedia PyMOL2Jmol Translator, developed by Roni Gordon and the Proteopedia Team. You can also read more about the Proteopedia PyMOL2Jmol Translator (beta). To use it you may need to request a Proteopedia user account if you don't yet have one.



The PyMOL2Jmol Translator allows you to choose a PyMOL session file (.pse file) that you have saved on your computer and have it converted directly into a Jmol scene to be saved and displayed in Proteopedia. To access the translator, edit any page and scroll down to the Proteopedia Scene Authoring Tools (if you want a general introduction to Proteopedia see the Proteopedia Video Guide). Open the Scene Authoring Tools by clicking on "show" and then click on the "load molecule" tab. You'll see an option to load "From PyMOL Session File (.pse)" and then a button right next to that text for choosing your file. Choose your file and the PyMOL2Jmol Translator should automatically convert it from PyMOL to Jmol and display the result in the Jmol applet of the Scene Authoring Tools (be patient if your file is over 1MB, it may take a few minutes). At that point you may edit the scene using the Scene Authoring Tools as you have done in the past, and you may save the scene to Proteopedia using the "save scene" tab, allowing you to drop the wiki-text for that scene directly into the text of the Proteopedia page that you are editing, thereby creating a green scene link from your PyMOL session file!

The translator is still in beta, so expect some bugs. Please send feedback and bug reports to Image:Contact-email.png.

More Information

View the abstract of the poster being presented at the 2009 ACA meeting here.

Details coming soon! Stay tuned...

Features Not Implemented Yet

These features in a PyMOL session file have not yet been implemented in the conversion -- please take note.

    • scenes & views
    • movies
    • multiple models per file (i.e. for NMR files)
    • electron density maps
    • CGOs
    • unit cells
    • PyMOL settings that are (a) less common and/or (b) currently have no Jmol equivalent
    • slab/depth settings
    • object transparency
    • atom labels (no z-axis offset)
    • measurement lines (width cannot be changed)
    • measurement labels (line always rendered)
    • tube & putty cartoon representations (not dumbbell, arrow, oval, loop, rectangle modifications)
    • nucleic acid backbones & end-caps cannot be coloured
    • shading & lighting, particularly in cavities
    • accuracy of cartoon/ribbon traces is limited, as is the ability to control arrowheads
    • fidelity of surface & mesh colouring for multi-coloured representations
    • dot representation (density of dots cannot be changed)

The translator is still in beta, so expect some bugs. Please send feedback and bug reports to Image:Contact-email.png.

See Also

Pymol2Jmol Translator Images

Proteopedia Page Contributors and Editors (what is this?)

Eran Hodis, Roni Gordon, Adithya Sagar, Eric Martz

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