VMD-L Mailing List

From: alexandra.marques_at_fc.up.pt
Date: Wed Apr 18 2007 - 11:28:43 CDT

Hi

I am using a script found in the mailing list to calculate the secondary
structure. However the secondary structure calculation is not updated so that I
obtain the same number of the secondary structure elements in all the frames. I
don’t see any error in the script…Could someone please help me? Here is the
script:

 set outfile [open secondary.txt w]
  set numframes [molinfo top get numframes]
  set sel [atomselect top "resid 1 to 200 and 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 [$sel get sheet]
    set coillist [$sel get coil]
    set turnlist [$sel get turn]
    set pihelixlist [$sel get pi_helix]
    set helixcount 0
    foreach i $helixlist {incr helixcount $i}
    set sheetcount 0
    foreach i $sheetlist {incr sheetcount $i}
    set coilcount 0
    foreach i $coillist {incr coilcount $i}
    set turncount 0
    foreach i $turnlist {incr turncount $i}
    set pihelixcount 0
    foreach i $pihelixlist {incr pihelixcount $i}
    puts $outfile "Alpha helix count: $helixcount"
    puts $outfile "Beta sheet count: $sheetcount"
    puts $outfile "turn count: $turncount"
    puts $outfile "coil count: $coilcount"
    puts $outfile "pihelix count: $pihelixcount"
  }
  $sel delete
  close $outfile

Thanks
Alexandra

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