I wanted to import molecules easily into iBooks format.

After googling, I found several options. One option, mentioned here, uses Blender: http://www.gravitropic.net/2012/07/pdb-to-collada/ uses a plugin for Blender (ePMV). I haven’t investigated this but it looks nice. It is downloadable from the Olsen group at Scripps. (http://epmv.scripps.edu/)

There is, however, a very simple way illustrated here using Pymol and Blender: http://vimeo.com/53674695. However, for small molecules, the small number of polygons means that they look a little blocky (you can subdivide the polygons in Blender, but this doesn’t alter the Collada output).  For most purposes, I suspect that this isn’t going to be a problem. (Instructions as per the video are shown below)

Blender can be downloaded from the Blender.org website, and free academic version of Pymol can be downloaded on Ubuntu linux using apt-get (apt-get install pymol). Similarly on mac you can use Homebrew. The steps are shown below:

1. Open (or create) your molecule in Pymol. If it’s a protein and in the PDB, you can use ‘fetch’ along with the PDB code.

Screen Shot 2014-04-11 at 16.25.39

2. I wanted ball and sticks, so in the command terminal enter

set_bond stick_radius, 0.14, (all)

set sphere_scale, 0.25, (all)

show sticks, (all)

3. Save the image as VRML.

Screen Shot 2014-04-11 at 16.25.48

4. Open Blender and delete the cube object.

Screen Shot 2014-04-11 at 16.29.02

5. Import the VRML file.

Screen Shot 2014-04-11 at 16.29.10

6. Here is your molecule.

Screen Shot 2014-04-11 at 16.29.20

7. Check the camera view.

Screen Shot 2014-04-11 at 16.29.40

8. Export as COLLADA DAE file.

Screen Shot 2014-04-11 at 16.35.20

9. On a mac you can preview in either Preview or Quicklook.

Screen Shot 2014-04-11 at 16.37.30

10. Drag-and-Drop it into your iBook Author document. Screen Shot 2014-04-11 at 16.36.53


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