From: Axel Kohlmeyer (
Date: Sun Sep 07 2008 - 14:09:44 CDT

On Sat, 6 Sep 2008, wrote:

GS> Hi all,

hi guillaume,

GS> I have 2 proteins which share 2 domains A and B with reverse topology:
GS> P1: -----[ Domain A ]----------[ Domain B ]--------
GS> P2: -----[ Domain B ]----------[ Domain A ]--------
GS> I want to superimpose P2 over P1 with ( DomainA of P1 over DomainA of P2 ) AND (
GS> DomainB of P1 over DomainB of P2).
GS> Here is my code:
GS> mol load pdb 1.pdb
GS> mol load pdb 2.pdb
GS> set bl_0_A " resid > 10 and resid < 20"
GS> set bl_0_B " resid > 40 and resid < 60"
GS> set bl_0 " $bl_0_A or $bl_0_B and name CA"
GS> set sel_0 [ atomselect 0 $bl_0 ]
GS> set bl_1_B " resid > 10 and resid < 20"
GS> set bl_1_A " resid > 40 and resid < 60"
GS> set bl_1 " $bl_1_A or $bl_1_B and name CA"
GS> set sel_1 [ atomselect 1 $bl_1 ]
GS> set mat [ measure fit $sel_1 $sel_0 ]
GS> [ atomselect 1 all ] move $mat
GS> And of course it doesnt works... As mentioned in the documentation for RMSd
GS> computation: "There are two atom selections needed to do an RMSD computation,
GS> the list of atoms to compare in both molecules. The first atom of the first
GS> selection is compared to the first atom of the second selection, fifth to fifth,
GS> and so on. The actual order is identical to the order from the input PDB file."
GS> Due to the reverse topology of the 2 molecules the superimposition is not
GS> possible through this simple process.
GS> Is there a way to perform such superimposition?

i would try to write out the two domains from the second
protein seperately:

set domA [atomselect 1 "$bl_1_A and name CA"]
set domB [atomselect 1 "$bl_1_B and name CA"]
$domA writepdb domA.pdb
$domB writepdb domB.pdb

and then combine the pdb files with the A-domain first
in a text editor (removing the CRYST and END records should do)
and load this fragment as a third molecule and use this to
generate the transformation matrix.


GS> Thanks for your help
GS> Guillaume

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.