[gmx-users] percentage of secondary structure

[Justin A. Lemkul]

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>> 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>>
>>
>>         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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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