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.

Moderators: jesterKing, stiv

shiven
Posts: 1
Joined: Wed Dec 23, 2009 4:27 pm
Location: Central Massachusetts

Blender and PyMOL

Postby 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 http://www.pymol.org/

The PyMOL Wiki is one of the foremost user resources for people learning and using PyMOL. The wiki is located at http://www.pymolwiki.org/


Recently, attempts have been made to document the use of Blender with PyMOL: http://www.pymolwiki.org/index.php/Blender


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

Thanks!

rdoherty
Posts: 3
Joined: Fri Jan 15, 2010 8:18 pm

Postby 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.

Thanks,

Ryan

grahamj
Posts: 7
Joined: Sat Aug 06, 2011 7:07 am
Location: CA

Postby 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.
http://epmv.scripps.edu

You can also use http://bioblender.eu to generate sophisticated animations for forcefields, etc.


Return to “Academic & Research”

Who is online

Users browsing this forum: No registered users and 2 guests