Blender and PyMOL

An open space where people who use Blender in an academic environment can share progress and the typical problems and needs of academic environments.

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Blender and PyMOL

Post by shiven » Wed Dec 23, 2009 4:37 pm

Hi Everyone,

PyMOL is a user-sponsored molecular visualization system on an open-source foundation. It is one of the best 3D visualization software for biological macromolecules/proteins. For more information please check the PyMOL website at

The PyMOL Wiki is one of the foremost user resources for people learning and using PyMOL. The wiki is located at

Recently, attempts have been made to document the use of Blender with PyMOL:

Your feedback and assistance is welcome to help improve the Wiki resources with tutorials, examples or scripts involving Blender+PyMOL.


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Post by rdoherty » Tue Mar 02, 2010 1:51 am

I like the Blender/Pymol tutorial.. but how do I import the protein ribbon / surface colour from Pymol into Blender?

I would like the ribbo representation in Blender to have different colours depending on the type of secondary structure.

I would like the surface to be coloured based on electrostatic potential.

When I try to load the protein from Pymol (or other protein structure programs), the colour is not transferred.



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Location: CA

Post by grahamj » Sat Aug 06, 2011 7:36 am

rdoherty wrote: When I try to load the protein from Pymol (or other protein structure programs), the colour is not transferred.
Hi Ryan,
I'm a little late, but for other people interested, you can generate molecular models with all types of proper color-coding (including ones like color-per-residue that require a plugin for PyMOL) directly in Blender using our lab's plugin ePMV (the embedded Python Molecular Viewer). Here is a link for overview, download, and install instructions.

You can also use to generate sophisticated animations for forcefields, etc.

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