Blender

HELP! : Fellow Blenderheads please help improve this page!!!

Introduction

This is an attempt at using Blender, an open-source, free, 3D modeling software to render, pose and animate objects exported from Pymol.

Blender may be downloaded freely for all major platforms (Win/Mac/Linux), from: http://www.blender.org/download/get-blender/

A great starting place for getting comfortable with Blender is the Blender Wiki: http://wiki.blender.org/

These tutorials are for Windows.

Tutorials

Representative examples. Please change/improve.

2. Translucent Surfaces

High quality translucent surfaces, better than PyMOL's internal renderer/ray-tracer.

3. Joining Atoms

• Step 1

When a molecule is imported into Blender from a PyMOL export (see the first tutorial), it will look like this:

(2,3-BPG from 1B86.pdb)

• Step 2

The problem is that this molecule is actually an assembly of spheres and cylinders. When the individual parts are selected using the Shift+right-click method (for scaling, rotating, moving, etc.), some parts are unable to be selected and are left behind. This ruins the molecule:

• Step 3

This problem is solved by grouping the individual pieces. Press b to launch the Blender bounding box tool:

Left-click and drag over the entire molecule. This will select all the pieces:

(selecting)

(all molecule parts selected)

• Step 4

Press Ctrl + j to join all the parts. The final product should look like this:

And there you go! Now the molecule can be moved, rotated, scaled, colored etc. as a whole entity, and selected with a single right-click.

• Step 5

If you are dealing with more than one molecule, you may want to import them into different layers, group them there, and then move them to the main layer.

Why Blender?

• Blender is FREE (as in beer)
• Blender is Open Source and therefore FREE (as in freedom)
• Blender is an extremely capable 3D graphics program and perhaps the only FOSS program capable of taking on similar commercial software head-to-head (Maya/Max/Modo etc.)
• To see some examples of what Blender can do check out:
  • http://www.elephantsdream.org/
  • http://www.bigbuckbunny.org/
  • http://www.yofrankie.org/

Blender Help

Blender is a perfect complement to PyMOL for creating high quality images and animation, but has a pretty steep learning curve. The following are a few resources that may be of help along the way:

• http://www.blender.org/education-help/
• http://en.wikibooks.org/wiki/Blender_3D:_Noob_to_Pro/Beginner_Tutorials
• http://forums.cgsociety.org/forumdisplay.php?f=91
• http://blenderartists.org/forum/

References

• Blender : http://www.blender.org/