VMD-L Mailing List

From: OZGE ENGIN (OZENGIN_at_KU.EDU.TR)
Date: Mon Feb 11 2008 - 04:01:15 CST

Thank you for your feedbacks. You are right, Rui and Nuno. The script works well for your case, Rui?
Although I changed the script according to the feedbacks you gave, I can not still update the frames and got the same secondary structure assignment for each frame.
Before loading the trajectory file, I use the start_sscache command. It could be reason?

Thank you.

-----Original Message-----
From: jrui_at_ci.uc.pt
To: OZGE ENGIN <OZENGIN_at_KU.EDU.TR>
Date: Mon, 11 Feb 2008 09:10:25 +0000
Subject: Re: vmd-l: the script do not update the frame number for secondary structure analysis

Hi,
You're missing the ssrecalc, and retrieving secondary scructure _before_
updating the selection!
Try changing the for loop to:
for { set i 0 } { $i < $n } { incr i } {
  $sel frame $i
  $sel update
  mol ssrecalc top
  set secstruct [$sel get structure]
  puts $fileID "$secstruct"
}

Rui Rodrigues

Quoting OZGE ENGIN <OZENGIN_at_KU.EDU.TR>:

> 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
>
>

Ozge Engin
=================================
Computational Science & Engineering
Koc University