disclaimer:  i am probably not the best person to give advice about this, but you might check out the morph server.
i am assuming that you have two pdb files that differ only the helix/sheet that you are interested in trying to create the morph.  if this is the case, i think this server might help you out.  Furthermore, I think there is a version of PymoL (included with purchasing a license, i think) that includes plugins (scripts? or whatever) that is capable of doing these 'morphing' movies directly within Pymol.  You might want to email Warren or other Pymol reps to get more information on the specifics.
here is another link that uses LSQMAN to do morphing also and might be another option.
Hope some of this helps and best of luck!
----- Original Message -----
From: Ashutosh Mishra
Sent: Friday, October 20, 2006 8:26 AM
Subject: [PyMOL] Protein Movie

Can some body help me in making a movie in which only one helix/sheet in the protein is moving while rest of the molecule remain static.
Thanks a lot

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