VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 01 2012 - 07:28:05 CDT

On Tue, May 1, 2012 at 6:55 AM, Ban Arn <ban.arn_at_gmail.com> wrote:
> 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.

why should it? there is no "puts" command anywhere.
you cannot have output without writing.

> Kindly advice.

please spend some time learning basic Tcl.

axel.

> Many Thanks
> Balaji
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.