VMD-L Mailing List

From: Eduard Schreiner (eduard.schreiner_at_theochem.ruhr-uni-bochum.de)
Date: Fri Feb 11 2005 - 04:42:24 CST

matteo.pennestri_at_virgilio.it wrote:
> HI VMD user, I have some problem with the alignment,
>
> I am not able to align to protein which have not the same number of residue.
>
> For exaple I want to align the first (with only 25 aminoacids) and the secondo
> with 150 aminoacids. But I want to align only 25 of the first with 25 of
> the second.
>
> I hope someone could help me
>
> best wishes
>
> Matteo
>
>
>
>
Hello Matteo,
You can also align selections. Therefore You have just to select
the first 25 aminoacids of the first protein (supposed it is
molecule 0):

set sel1 [atomselect 0 "residue < 26"]

these of the second protein:

set sel2 [atomselect 1 "residue < 26"]

calculate the trafo-matrix:

set transformation_matrix [measure fit $sel1 $sel2]

and use this matrix to align the molecules (in this case the first is
aligned to the second):

set move_sel [atomselect 0 "all"]
$move_sel move $transformation_matrix

This should do it.

Please check section 11.4.2 of the VMD-UG: RMS and scripting,
there is also an example.

Eddi 

-- 
--
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Eduard Schreiner                        e-mail: eduard.schreiner_at_rub.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-22121
Ruhr-Universitaet Bochum - NC 03/52         Fax:   ++49 (0)234/32-14045
D-44780 Bochum                               http://www.theochem.rub.de
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