VMD-L Mailing List

From: Nuno Loureiro Ferreira (nunolf_at_ci.uc.pt)
Date: Mon Feb 11 2008 - 03:03:19 CST

Hi

"$sel update" should be right after "$sel frame $i".
Thus, try this:

===========================================================
set sel [atomselect top "protein and name CA"]
set n [molinfo top get numframes]
set filename "s_s.txt"
set fileID [open /home/ozengin/remd_vacuum_26/$filename w]
for { set i 0 } { $i < $n } { incr i } {
$sel frame $i
$sel update
set secstruct [$sel get structure]
puts $fileID "$i\t$secstruct"
}
close $fileID
==========================================================

Cheers,
Nuno

OZGE ENGIN wrote:
> Hi Rui,
>
> I tried to do what you suggested to me. However, I could not update the frame for secondary structure calculation. Consequently, I had the same secondary structure assignment of the first frame for other frames.
> I attach the code below. Could you look at it, please?
>
> Thank you very much!!!
> ===========================================================
> set sel [atomselect top "protein and name CA"]
> set n [molinfo top get numframes]
> set filename "s_s.txt"
> set fileID [open /home/ozengin/remd_vacuum_26/$filename w]
> for { set i 0 } { $i < $n } { incr i } {
> $sel frame $i
> set secstruct [$sel get structure]
> puts $fileID "$secstruct"
> $sel update
> }
> close $fileID
> ==========================================================
> Ozge Engin
> =================================
> Computational Science & Engineering
> Koc University
>
>
>
>