[gmx-users] percentage of secondary structure

[ahmet yıldırım]

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?

Thanks

04 Ocak 2011 15:51 tarihinde Justin A. Lemkul <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>> 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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-- 
Ahmet YILDIRIM
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