On Mon, Dec 15, 2008 at 11:41 AM, Buz Barstow <buzb@mac.com> wrote:
I'm making a gallery of protein molecules for my PhD thesis. I'd like
to find an automatic way to ensure that all of the ray traced images
have the same scale. Is there an easy way to do this?

Translate every model so that the center is at the origin, then use the set_view command to apply the same viewing matrix for each model.  (You can still rotate the models, just don't zoom.)  I'm not sure if there's already a simple way to do the translation from within PyMOL, but it should be quite straightforward using cctbx or CNS or something similar.

-Nat