[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 <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  
>              gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>                    <mailto:gmx-users at gromacs.org
>             <mailto: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!
>                    Please don't post (un)subscribe requests to the list.
>             Use the
>                    www interface or send it to
>             gmx-users-request at gromacs.org
>             <mailto:gmx-users-request at gromacs.org>
>                    <mailto:gmx-users-request at gromacs.org
>             <mailto:gmx-users-request at gromacs.org>>.
> 
>                    Can't post? Read
>             http://www.gromacs.org/Support/Mailing_Lists
> 
> 
> 
> 
>                --     Ahmet YILDIRIM
> 
> 
> 
>            --
>            gmx-users mailing list    gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>            <mailto:gmx-users at gromacs.org <mailto: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!
>            Please don't post (un)subscribe requests to the list. Use the
>            www interface or send it to gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>            <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>.
> 
>            Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 
> 
> 
>         -- 
>         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>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 
> 
> 
> -- 
> 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

========================================