[gmx-users] percentage of secondary structure

[Thomas Evangelidis]

This is the way to do it with Pymol for one frame:

http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg08154.html

I guess with a little bit of python scripting you could read through all the
frames of your trajectory.

Thomas


2011/1/4 ahmet yıldırım <ahmedo047 at gmail.com>

> 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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