How to create Protein or Chemical structures in .pdb or .mol format for use with iBooks Author. Please help.

Question

Dear Community,
       There are a large variety of software packages used by Chemists and Biologists to view and manipulate Protein and Chemical structures in 3D. They typically have formats such as .pdb, or .mol. I have looked around and none of the software packages that I currently use allow me to export to the COLLADA (.dae) format.
        Does anyone have any idea where to begin to allow me to do this. I would like to try and put in some of the 3D objects into the iBook Author program.
Thank you. Chase

Answer 1

I believe that Apple should have provided an easily way to get Pymol images into iBooks Author as VRML has been the de facto standard.  After a number of days, I have a method which works, but this much effort should not be necessary.  Anyway here it is.
1)  Set the viewport in Pymol to 512,384 to do this in the command window type
viewport 512,384
Note, I'm not totally sure you need to do this.
2) Draw you image in Pymol and output the image in VRML format, to do that
File -> Save Image As -> VRML 2 ...
I'll assume that you have given the file the name "pymol_output", you actual get pymol_output.wrl
3) In a terminal window go to the folder where the above file is located and issue the following command.  This removes some stuff that messes up the lightening
sed '9,15d' pymol_output.wrl > bender_in.wrl
4) Next you need blender.  You can download it from
http://www.blender.org/download/get-blender/
5)  Open Blender.  In the upper right corner in the Scene section
right click on Lamp and delete it
right click on Cube and delete it
right click on Camera and delete it
Save this file so you don't have to do this every time.  I called mine empty_blender_file.blend
6) Either open empty_blender_file.blend or continue from #5 and read in the file from #3
File -> import->X3D Extensible 3D (.x3d/.wrl)
this reads in the file
7) Write out the file in collada .dae format
File->export->collada (.dae)
Done.  This file will read into iBooks Author and have somewhat uniform lighting.  By the way, .dae files can be opened an checked in Preview.  Its easier than going back and forth into the iPad, since you can rotate the image in Preview.
Hope this helps, let me know if it works for you and if you have any suggestions.
Finally someone needs to write a one step VRML and X3D to collada converter that will work with PyMol and Chimera etc.
Have fun!