[gmx-users] SS from xpm file

[Xavier Periole]

Nguyen Hoang Phuong wrote:

>  
>
>>On Mon, 2005-10-24 at 17:01 +0200, Nguyen Hoang Phuong wrote:
>>    
>>
>>>Dear All,
>>>
>>>after performing do_dssp, I got the file like ss.xpm which looks like
>>>
>>>"SSSSSSSSSSSS~~~S~~~~~SSSSSSSSSSSS~STSSSSSSSTTTTTSTST~~~~S~~~S~~",
>>>"SSSSSSSSSSSSS~~SSSSSSSSSSSSSSSSSSSSTSSSSSSSTTTTTSTSTSSSSSSSSSSS",
>>>
>>>each line contains the information about secondary structures of one
>>>residue. I would like to compute the percentages of the structures S, T
>>>etc. for each residue. To this end I have to count how many letters S, T
>>>of each line. Do you know how to performing this counting?
>>>
>>>Many thanks in advance,
>>>      
>>>
>>look in the xvg file that is produced as well.
>>    
>>
>
>but the xvg file contains the total structures of all residues, not
>single residue.
>  
>

There is an option to generate the data per residue !


-- 
----------------------------------
 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   
 Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 
 Tel: +31-503634329
 Fax: +31-503634800
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole
----------------------------------