VMD-L Mailing List

From: Ban Arn (ban.arn_at_gmail.com)
Date: Tue May 01 2012 - 05:55:51 CDT

Dear VMD users

I got the script from the vmd mailing list for calculating helical content
of the residues.

set outfile [open protein_SS.txt w]
set numframes [molinfo top get numframes]
set sel [atomselect top "resid 56 to 83 and name CA"]
set helcounts [list]
foreach ind [$sel get index] {
    lappend helcounts 0
}
for {set i 0} {$i < $numframes} {incr i} {
    animate goto $i
    display update ui
    mol reanalyze top
    set structs [$sel get structure]
    for {set j 0} {$j < [llength $structs]} {incr j} {
       if {[lindex $structs $j] == "H"} {
          set helcounts [lreplace $helcounts $j $j [expr [lindex $helcounts
$j] + 1] ]
       }
    }
}

The scripts runs however it doesn't gives the vmdoutput of list of frames &
the residue helical content.

Kindly advice.

Many Thanks
Balaji