VMD-L Mailing List

From: jrui_at_ci.uc.pt
Date: Sat Feb 09 2008 - 08:53:39 CST

Loop over all frames in the trajectory. Take a look at the manual:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node184.html
It should easy to combine what you've got so far with the first example.
Remember to keep "atomselect" and "open" outside the "for" loop and "ssrecalc"
inside.
You will also find several examples in the mailing list

Rui Rodrigues

Quoting OZGE ENGIN <OZENGIN_at_KU.EDU.TR>:

> 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
>
>