Re: [gmx-users] percentage of secondary structure

[Justin A. Lemkul]

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 <jalem...@vt.edu 
<mailto:jalem...@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.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
        <mailto:mark.abra...@anu.edu.au
        <mailto:mark.abra...@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.abra...@anu.edu.au
            <mailto:mark.abra...@anu.edu.au>
               <mailto:mark.abra...@anu.edu.au
            <mailto:mark.abra...@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 <http://vt.edu> | (540) 231-9080
    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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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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