Hi Dave, The Morph Conformations tool (under Tools... Structure Comparison) generates interpolated intermediate structures and then opens the result as a trajectory in the MD Movie tool. With MD Movie you can interactively play the trajectory but also save a movie file. These are not in command form, however. Take a look and see if these tools allow you to do what you want... Morph Conformations: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html
MD Movie: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.ht...
Tutorials with morphing examples: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html
Tutorial that includes saving a movie with MD Movie: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#pa...
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 19, 2008, at 11:11 AM, David Chenoweth wrote:
Dear Chimera team,
Is there a movie command that can easily depict the interconversion between two alternate conformations in a nucleic acid or protein residue (designated conformation a and b) within a pdb file. I am really trying to illustrate with a movie how the phosphates flip between two well defined states in an ultra-high resolution DNA crystal structure using a chimera movie.
Thanks in advance, Dave Chenoweth