VMD-L Mailing List

From: guillaume.santini_at_free.fr
Date: Sat Sep 06 2008 - 09:34:52 CDT

Hi all,

I have 2 proteins which share 2 domains A and B with reverse topology:

P1: -----[ Domain A ]----------[ Domain B ]--------
P2: -----[ Domain B ]----------[ Domain A ]--------

I want to superimpose P2 over P1 with ( DomainA of P1 over DomainA of P2 ) AND (
DomainB of P1 over DomainB of P2).
Here is my code:

mol load pdb 1.pdb
mol load pdb 2.pdb

set bl_0_A " resid > 10 and resid < 20"
set bl_0_B " resid > 40 and resid < 60"
set bl_0 " $bl_0_A or $bl_0_B and name CA"
set sel_0 [ atomselect 0 $bl_0 ]

set bl_1_B " resid > 10 and resid < 20"
set bl_1_A " resid > 40 and resid < 60"
set bl_1 " $bl_1_A or $bl_1_B and name CA"
set sel_1 [ atomselect 1 $bl_1 ]

set mat [ measure fit $sel_1 $sel_0 ]
[ atomselect 1 all ] move $mat

And of course it doesnt works... As mentioned in the documentation for RMSd
computation: "There are two atom selections needed to do an RMSD computation,
the list of atoms to compare in both molecules. The first atom of the first
selection is compared to the first atom of the second selection, fifth to fifth,
and so on. The actual order is identical to the order from the input PDB file."

Due to the reverse topology of the 2 molecules the superimposition is not
possible through this simple process.

Is there a way to perform such superimposition?

Thanks for your help

Guillaume