[Chimera-users] script for

Elaine Meng meng at cgl.ucsf.edu
Tue Oct 20 13:30:59 PDT 2009

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.

I tried this process in the 1.3 release and also the 1.4 release  
candidate built last night.

I hope this helps,
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

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