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.
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)
3. Save the image as VRML.
4. Open Blender and delete the cube object.
5. Import the VRML file.
6. Here is your molecule.
7. Check the camera view.
8. Export as COLLADA DAE file.
9. On a mac you can preview in either Preview or Quicklook.