VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 11 2005 - 14:33:06 CDT

Hi,
  You could actually do this without even writing the secondary structure
to a file. This can be done with atom selections very easily with a
script like this one. Feel free to hack this to do whatever you need.
Enjoy,
  John

proc calcsscounts {} {
  set numframes [molinfo top get numframes]
  set sel [atomselect top "name CA"]
  for {set frame 0} {$frame < $numframes} {incr frame} {
    animate goto $frame
    vmd_calculate_structure top
    $sel frame $frame
    $sel update
    set helixlist [$sel get alpha_helix]
    set sheetlist [$sel get sheet]
    set helixcount 0
    foreach i $helixlist { incr helixcount $i }
    set sheetcount 0
    foreach i $sheetlist { incr sheetcount $i }
    puts "Frame: $frame"
    puts " Alpha helix count: $helixcount"
    puts " Beta sheet count: $sheetcount"
  }
  $sel delete
}

On Tue, Aug 09, 2005 at 10:50:11AM +0200, Ting Wang wrote:
> Is it possible to output the secondary structure assignment of each
> frame in a trajectory into a file so that we can calculate the number of
> residues in alpha-helical or beta-strand conformations? I am using
> sscache.txt to update secondary structure assignment.
>
> Thanks in advance!
>
> Ting
>
> --
> Dr. Ting Wang
>
> Molecular & Cellular Modelling
> EML Research gGmbH
>
> Villa Bosch
> Schloss-Wolfsbrunnenweg 31c
> 69118 Heidelberg
> Germany
> Tel: +49 6221 533 262
> Fax: +49 6221 533 298
> Email: ting.wang_at_eml-r.villa-bosch.de
> Web: http://www.embl-heidelberg.de/~twang 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078