[gmx-users] percentage of secondary structure

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 4 19:04:04 CET 2011



ahmet yıldırım wrote:
> Dear Justin,
> 
> I am using the commands as the following.
> do_dssp -s run.tpr -f run.xtc
> xpm2ps -f ss.xpm -o ss.eps
> 
> You said "Have a look at the other output file do_dssp gives you". which 
> one should I look?
> 

Well, there's another output file from do_dssp called "scount.xvg," which should 
  be almost exactly what you need.  See do_dssp -h for a description, then look 
at the file yourself.

-Justin

> Thanks
> 
> 04 Ocak 2011 15:51 tarihinde Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> yazdı:
> 
> 
> 
>     ahmet yıldırım wrote:
> 
>         I get the residue versus time ( secondary structure graph) using
>         do_dssp tool. I want to get the percentage value(alpha helix,
>         beta sheet, coil ...) of secondary structure. For example:
> 
>         Secondary structure percentage (%):
>         Helix:51.6
>         B-sheet:0
>         Random coil:24.0
>         Turn:24.4
> 
> 
>     Have a look at the other output file do_dssp gives you.
> 
>     -Justin
> 
> 
>         04 Ocak 2011 14:59 tarihinde Mark Abraham
>         <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
>         <mailto:Mark.Abraham at anu.edu.au
>         <mailto:Mark.Abraham at anu.edu.au>>> yazdı:
> 
> 
>            On 4/01/2011 11:38 PM, ahmet yıldırım wrote:
> 
>                Dear Mark,
> 
>                I will do by using the g_analyze tool but I do not know
>             how to use it.
> 
> 
>            There's a section in Appendix D of the manual for each tool,
>         or you
>            can use the -h argument to the tool to get the same information.
> 
>            Either way, you haven't got the right tool. Hint: it's a "protein
>            specific analysis"
> 
>            Mark
> 
> 
> 
>                Thanks
> 
>                2011/1/4 Mark Abraham <Mark.Abraham at anu.edu.au
>             <mailto:Mark.Abraham at anu.edu.au>
>                <mailto:Mark.Abraham at anu.edu.au
>             <mailto:Mark.Abraham at anu.edu.au>>>
> 
> 
>                    On 4/01/2011 8:33 PM, ahmet yıldırım wrote:
> 
>                        Hi,
> 
>                        How can I calculate the percentages (alpha helix,
>             beta
>                        sheet, coil ...) of secondary structure?
> 
> 
>                    Look in manual section 7.4 for a suitable tool.
> 
>                    Mark
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> 
> 
>                --     Ahmet YILDIRIM
> 
> 
> 
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> 
> 
>         -- 
>         Ahmet YILDIRIM
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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> 
> 
> 
> -- 
> Ahmet YILDIRIM

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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