VMD-L Mailing List

From: jrui_at_ci.uc.pt
Date: Mon Feb 11 2008 - 04:55:39 CST

No, I doesn't work. I should have tested it... :)
Change the for loop to:

for { set i 0 } { $i < $n } { incr i } {
  animate goto $i
  display update ui
  $sel frame $i
  mol ssrecalc top
  set secstruct [$sel get structure]
  puts $fileID "$secstruct"
}

I've tested it and it works.
Rui Rodrigues

Quoting OZGE ENGIN <OZENGIN_at_KU.EDU.TR>:

> 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
>
>