Dear Tom,

If I'm not mistaken, it is always the camera that is moving when you rotate a molecule.  That is how Pymol is so fast - only one point is actually moving.

Have you investigated the mset command to set waypoints for the camera?
After you set a number of waypoints you can play the animation and PyMol interpolates camera positions between your waypoints.  I would suggest you keep a text file (or .pml script) open when you work with mset so that you can keep a record of all of your waypoints (use get_view) and what they correspond to.

You might have better luck working with surfaces if you want to export a protein into a 3D modeller.  I have done some work with meshlab where I import .x3d files corresponding to the mesh vertices from electron density contours.

Good luck!  I'd love to hear the solution you decide on.


On Tue, May 11, 2010 at 7:27 PM, Tom Dupree <> wrote:
Hello everyone,

I am trying to do something that seems a little uncommon. I wish to have a moveable camera. So instead of rotating/translating the protein/molecule/DNA I move the camera point/location and the vector that the camera points in. I wish to be able to move into the molecule and view binding pockets from the perspective of the molecule. I have tried a few web searches on this and thought I would ask everyone here if they have heard of something similar?

I am currently trying to find some 3d modelling software that will load a .PDB file so that I can export it to a game engine (Unreal development kit) as a back up method if all else fails.

Thanks for your time,


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Michael Zimmermann
Ph.D. student in Bioinformatics and Computational Biology
Department of Biochemistry, Biophysics and Molecular Biology
Iowa State University