Re: [PyMOL] morphing

[Thomas H. <sp...@us...>]

Hi Hasan,

if your structures are identical in sequence (same number of atoms), the 
direct way for morphing would be to load them into the same object in 
two states and then call rigimol.morph, like this:

from epymol import rigimol
cmd.extend('morph', rigimol.morph)

load conf1.pdb, inobj, 1
load conf2.pdb, inobj, 2
morph inobj, outobj, refinement=5

If the sequence is different or one of the structures have missing 
atoms, you need to match them before creating the two-state object. I 
have a script that does this, see attachment. It provides a "morpheasy" 
command.

import morpheasy
load conf1.pdb
load conf2.pdb
morpheasy conf1, conf2

Hope that helps.

Cheers,
   Thomas

Hasan Demirci wrote, On 01/25/12 22:37:
> Hi,
>  
> In the past I was using rigimol to morph my structures.
> I used to follow the path
> 
> pymol -qc prepare.pml
> 
> pymol -qc rigimol.pml
> 
> pymol domains.pml
> 
> pymol -qc refine.py
> 
> pymol view.pml
> 
>  
> 
> I lost my old pml files and in the current pymolv1.5 as far as I can see 
> rigimol (or any of the pml files) doesn't exist anymore.
> I have two structures and they are dramatically different from one 
> another due to a mutation.
> I would be grateful if you can help me with the morphing and refinement 
> scripts in pymolv1.5 (both windows 64 and/or linux 64 version is fine).
> With my very best regards.
>  
> Hasan-

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen