This is the way I got it to work, I exported Chimera scene to VRML (.wrl).
Next you need blender. You can download it from
Then 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
Either open empty_blender_file.blend or continue from above and read in the the .wrl file from Chimera
File -> import->X3D Extensible 3D (.x3d/.wrl)
this reads in the file
In Blender you need to delete the three lights that came in from Chimera called TOPO, TOPO.001 and TOPO.002
In the upper right corner in the Scene section
right click on TOPO and delete it
right click on TOPO.001 and delete it
right click on TOPO.002 and delete it
Now you need to move around the viewport to get it centered
In the upper right corner in the Scene section
click on the Viewport
then press number pad 0
Press the cube icon below the Scene section
Now in the transform section move the location x,y,z. When you have it the way you want it is ready for export.
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.
Here is a link to a .dae file of 1crn that you can import into iBooks Author or 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/or X3D to collada converter that will work with PyMol and Chimera etc.
Have fun!