VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Dec 11 2007 - 10:29:24 CST

Hi all,

I'm calculating the percentage of helical content of a protein (using
a NAMD-generated trajectory). I've been using the following script:

 set outfile [open protein_SS_16.txt w]
  set numframes [molinfo top get numframes]
  set sel [atomselect top "resid 16 and name CA"]
  for {set frame 0} {$frame < $numframes} {incr frame} {
    animate goto $frame
    display update ui
    vmd_calculate_structure top
    $sel frame $frame
    $sel update
    set helixlist [$sel get alpha_helix]
    set helixcount 0
    puts $outfile " Alpha helix count: $helixcount "
    }
  close $outfile

However, the script calculates the content *ONLY* for one residue at a
time, so I was wondering if you have any ideas on how to modify it so
I can get a table of residue vs count of alpha helix, or something
similar. This is basically to avoid calculating it for every residue
(which will take forever!). If you have alternative ideas, I'd be more
than happy to read them.

Thanks!
Michel