VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Jul 01 2009 - 17:13:25 CDT

On Wed, 2009-07-01 at 10:59 -1000, Irene Newhouse wrote:

hi irene,

> In Russo & al, Structure, (2006) 14, 1449-1458, the active site of an
> encephalitis
> virus protease ( pdb 2hwk) with no closely analogous structures
> available, was modeled on
> a hydrolase (pdb 1euv) with bound inhibitor by 'superimposing' the
> residues that form
> the catalytic triad. When they did this, they found that the inhibitor
> made analogous
> contacts on 2hwk that appear sensible. There is nothing in the
> experimental on how
> they did this.
 
> Can something like this be done with VMD?

you could use "measure fit" on selected atoms of the equivalent
amino acids and then use the transformation matrix on the whole
system. measure fit just needs the same number of atoms in both
selections. if the order of the atoms doesn't match, you can use
the (still) undocumented "order" flag which takes an index list
similar to catdcd as argument.

cheers,
   axel.

>
> Thanks!
> Irene
>
>
> ______________________________________________________________________
> Lauren found her dream laptop. Find the PC that’s right for you. 

-- 
=======================================================================
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.