You can use Martz-Authored PDB Tools / MORPH2 Citation: MORPH2 generates a series of interpolated frames between two PDB files. The PDB files must match, atom by atom, in the same order. The interpolation is linear: each atom "moves" in a straight line between its start and end positions. The original pair of PDB files and the interpolations are concatenated into a single PDB file, delimited by MODEL and ENDMDL records, which is ready to play as an animation in Protein Explorer
Morph2 generates 1 pdb-file containing all frames. Once loaded to PyMOL this movie can be played by the program. You can even export "rayed" frames as single images and use them for movie creation in your favourite format. I used this method and it worked fine. Martz-Authored PDB Tools can be downloaded from www.umass.edu/microbio/rasmol/pdbtools.htm (end of the page) link: ftp://www.bio.umass.edu/pub/shareware/rasmol/distrib/heller/pdbtools.exe ---------------- Alexey Pakhomov, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian academy of sciences.
