[gmx-users] percentage of secondary structure

[ahmet yıldırım]

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

04 Ocak 2011 14:59 tarihinde Mark Abraham <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>
>
>> 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
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