VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Jul 02 2009 - 14:42:30 CDT

On Thu, 2009-07-02 at 19:00 +0800, John C. H. Chao wrote:
> Dear All,
>

dear john chao,
 
>
> If there is a way to assign secondary structures on residues read from
> pdb file and finally displayed by VMD in NewCartoon as what I assign.

yes. you can create a selection with atomselect and then assign
structure codes to all atoms/residues using the "structure" keyword.

example:

set sel [atomselect top "residue 0 to 5"]
$sel set structure H

this will flag the first six residues as helix.

please give it a try and let us know if this solves
your problem.

cheers,
   axel.

> VMD auto assign those features, however, I just want to illustrate why
> some secondary structures are not possible in my system.
>
> Hence, the assigned secondary structure may NOT be realistic.
>
>
>
>
>
> Thanks for any suggestion,
>
>
>
> John Chao
>
>
>
>
>
> John Ching-Hao Chao (JCH Chao)
> Email Address: f93223037_at_ntu.edu.tw
> ssNMR Lab in Dept. of Chemistry
> National Taiwan University
> No. 1, Sec. 4, Roosevelt Road, Taipei, Taiwan, R.O.C.
>
>
>
>
>
> 

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