VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 08 2008 - 11:16:37 CDT

Hi,
  Another option for structures with matching 3-D structure but
mismatched index order etc is to use the "order" option to the
"measure fit" command. Here's a trivial "identity" example using titin:

mol new 1tit
mol new 1tit
set sel1 [atomselect top "index 0 1 2 3 4"]
set sel2 [atomselect top "index 0 1 2 3 4"]
measure fit $sel1 $sel2 order { 0 1 2 3 4 }

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Sep 07, 2008 at 03:09:44PM -0400, Axel Kohlmeyer wrote:
> On Sat, 6 Sep 2008, guillaume.santini_at_free.fr wrote:
>
> GS> Hi all,
>
> hi guillaume,
>
> GS>
> GS> I have 2 proteins which share 2 domains A and B with reverse topology:
> GS>
> GS> P1: -----[ Domain A ]----------[ Domain B ]--------
> GS> P2: -----[ Domain B ]----------[ Domain A ]--------
> GS>
> 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>
> GS> mol load pdb 1.pdb
> GS> mol load pdb 2.pdb
> GS>
> 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>
> 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>
> GS> set mat [ measure fit $sel_1 $sel_0 ]
> GS> [ atomselect 1 all ] move $mat
> GS>
> GS> And of course it doesnt works... As mentioned in the documentation for RMSd
> GS> computation: "There are two atom selections needed to do an RMSD computation,
> GS> the list of atoms to compare in both molecules. The first atom of the first
> GS> selection is compared to the first atom of the second selection, fifth to fifth,
> GS> and so on. The actual order is identical to the order from the input PDB file."
> GS>
> GS> Due to the reverse topology of the 2 molecules the superimposition is not
> GS> possible through this simple process.
> GS>
> GS> Is there a way to perform such superimposition?
>
> i would try to write out the two domains from the second
> protein seperately:
>
> set domA [atomselect 1 "$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.
>
> cheers,
> axel.
>
> GS>
> GS> Thanks for your help
> GS>
> GS>
> GS> Guillaume
> GS>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> 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. 

-- 
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