On Tue, Jan 12, 2010 at 11:13 AM, Schubert, Carsten [PRDUS] <CSCHUBER@its.jnj.com> wrote:

I am trying to make a movie form a set of morphed pdb files. Currently the individual files are loaded into the same object with increasing states, all pdb files contain the SHEET and HELIX record created by dssp.  The object is then displayed as a cartoon. When I loop over the states I noticed that Pymol only seems to take secondary structure information from the first pdb file into account. For instance I have a helix which is split into 2 during the morph, but only displayed as one helix during the animation, albeit a bit stretched. Loading the individual files produces the right sec. structure. Any idea how I can convince Pymol to update the cartoon representation with each frame?

I don't think there's any way to do this that doesn't involve some scripting.  My experience may be out of date, since I last tried this around 2002, but I don't think the movie API has changed much since then.  I ultimately rendered each frame separately (i.e. different object for each PDB file) using the same view matrix.  However, depending on how finely you want to show the changes in secondary structure, something like the following should work:

load frame1.pdb, morph
. . .
load frame20.pdb, morph
mset 1 -10
mpng movie, first=1
alter morph and resi 100:120, ss='H'
mset 11 -20
mpng movie, first=11

This is just off the top of my head - I can't guarantee that it will work exactly as written, but it's pretty close to what you need.  In theory, it will produce 20 frames, movie0001.png through movie0020.png, which should appear continuous.