From: OZGE ENGIN (OZENGIN_at_KU.EDU.TR)
Date: Sat Feb 09 2008 - 07:22:59 CST

Ok, I think the script will work for only one frame. If I want to write all the strings obtained during the trajectory, then ?
-----Original Message-----
From: jrui_at_ci.uc.pt
To: OZGE ENGIN <OZENGIN_at_KU.EDU.TR>
Date: Sat, 9 Feb 2008 13:03:45 +0000
Subject: Re: Re: vmd-l: output of the ssrecalc command

Yes:

set sel [atomselect top "protein and name CA"]
set secstruct [$sel get structure]

set filename "your_output_file.txt"
set fileID [open ./$filename w]
puts $fileID "$secstruct"
close $fileID
$sel delete

This should work. Don't forget to close the file and delete the
selection if you
don't need it anymore (last two lines).

Rui

Quoting OZGE ENGIN <OZENGIN_at_KU.EDU.TR>:

> Hi,
>
> Thank you Rui, it works. Is there any way of writing these strings
> that describe the secondary structure of each residue within a
> peptide into an output file? Is there any script?
>
> Thanks in advance
>
> -----Original Message-----
> From: jrui_at_ci.uc.pt
> To: OZGE ENGIN <OZENGIN_at_KU.EDU.TR>
> Date: Sat, 9 Feb 2008 10:50:46 +0000
> Subject: Re: vmd-l: output of the ssrecalc command
>
> Hi,
>
> After ssrecalc, you could make an atom selection and then get the secondary
> structure for that selection:
>
> set sel [atomselect top "protein and name CA"]
> $sel get structure
>
> This will give you a list of the secondary structure of each residue.
>
> Hope this helps,
> Rui Rodrigues
>
>
> Quoting OZGE ENGIN <OZENGIN_at_KU.EDU.TR>:
>
>> Hi all,
>>
>> I have a question about ssrecalc command. I want to calculate the
>> secondary structures of each of the residue of my protein. This
>> command gives any output file? Wnen I write it in the command line,
>> it gives nothing.
>>
>> Thanks in advance
>> Ozge Engin
>> =================================
>> Computational Science & Engineering
>> Koc University
>>
>>
>
>
>
>
>
>
> Ozge Engin
> =================================
> Computational Science & Engineering
> Koc University
>
>

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