Hi Lorenzo, I just created a morph and saved all the intermediates into a file with the following example commands: open 2amy open 2fuc mm #0 #1 morph start #0 morph interpolate #1 frames 6 morph movie write trajectory 2 ~/Desktop/test.pdb It sounds like you omitted the "morph movie" step that actually calculates the intermediates. The "morph interpolate" command just sets up the parameters to use when the intermediates are calculated, but does not calculate them. The reason is that the entire morph trajectory could contain multiple segments (A -> B and then B -> C etc.) and you could have different parameters for each stage. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/morph.html> I tried this process in the 1.3 release and also the 1.4 release candidate built last night. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 20, 2009, at 11:39 AM, lorenzo wrote:

Dear all, I'm trying to write a script to interpolate between two structures and save the intermediate conformations as pdb files. I need a script since I have to repeat this procedure several times.

As far as importing the structures and interpolating is concerned I have no problem:

open A.pdb open B.pdb morph start #0 morph interpolate #1 frames 6 (I need 5 intermediates)

What I don't manage to figure out is how to save the intermediate configurations.

Figuring out that morph interpolate was generating a trajectory stored as the model #2 I tried write format pdb trajectory #2 out.pdb but it didn't write anything

I also unsuccessfully tried with perframe write format pdb out.pdb but I still got no output.

Does anybody have any suggestion? Regards Lorenzo Bongini