VMD-L Mailing List

From: h9826299_at_hkusua.hku.hk
Date: Wed Jan 18 2006 - 15:22:41 CST

Hi,

  I've used John's script (below) to calculate the ss composition of every frame
of a traj. But it's strange that the results for every frame is the same, which
is the ss composition of the last frame. Anybody, knows the reason? The the ss
assignment needed to be updated? I've try the sscache.tcl for updating the ss
but it don't work, though it works for the animation with changing ss.
Thanks!!

### The script I used ###

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
}

cheers,
Chung