[Chimera-users] script for

lorenzo bongini at fi.infn.it
Tue Oct 20 11:39:21 PDT 2009

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

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?

                   Lorenzo Bongini

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