[gmx-users] percentage of secondary structure
ahmet yıldırım
ahmedo047 at gmail.com
Tue Jan 4 19:32:54 CET 2011
Dear Justin,
Thanks for your reply. There are not percentage of secondary structure in
"scount.xvg".
The content of the "scount.xvg" file are as the following:
# This file was created Tue Jan 4 19:28:47 2011
# by the following command:
# do_dssp -s run.tpr -f run.xtc
#
# do_dssp is part of G R O M A C S:
#
# GROup of MAchos and Cynical Suckers
#
@ title "Secondary Structure"
@ xaxis label "Time (ps)"
@ yaxis label "Number of Residues"
@TYPE xy
@ subtitle "Structure = A-Helix + B-Sheet + B-Bridge + Turn"
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Structure"
@ s1 legend "Coil"
@ s2 legend "B-Sheet"
@ s3 legend "B-Bridge"
@ s4 legend "Bend"
@ s5 legend "Turn"
@ s6 legend "A-Helix"
@ s7 legend "3-Helix"
0 128 19 14 1 17 11 102 0
0.2 131 19 14 1 14 14 102 0
0.4 132 19 14 1 13 23 94 0
0.6 130 19 14 1 15 12 103 0
0.8 132 19 14 1 13 19 98 0
1 130 21 14 1 13 28 87 0
.................................................................
04 Ocak 2011 20:04 tarihinde Justin A. Lemkul <jalemkul at vt.edu> yazdı:
>
>
> 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
>> -- gmx-users mailing list
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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
>>
>> ========================================
>>
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
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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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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--
Ahmet YILDIRIM
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