[gmx-users] percentage of secondary structure
ahmet yıldırım
ahmedo047 at gmail.com
Tue Jan 4 19:50:47 CET 2011
Dear Justin,
I understand. Thank you very much.
04 Ocak 2011 20:36 tarihinde Justin A. Lemkul <jalemkul at vt.edu> yazdı:
>
>
> ahmet yıldırım wrote:
>
>> Dear Justin,
>>
>> Thanks for your reply. There are not percentage of secondary structure in
>> "scount.xvg".
>>
>
> I know that. But this is all the information you need. If you have a
> count of how many residues are in a particular conformation over time, all
> you have to do is divide by the number of total residues and you have your
> percentage.
>
> Gromacs isn't going to do everything for you, but it quite often has the
> capability to give you whatever raw data you need to properly manipulate.
>
> -Justin
>
> 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 <mailto:
>> 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> <mailto: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>>
>> <mailto: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>>
>> <mailto: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>>
>> <mailto: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>>
>> <mailto: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
>> >>
>> <mailto: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/Searchbefore
>> 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>>
>> <mailto: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> <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>
>> <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
>
> ========================================
> --
> 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!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
Ahmet YILDIRIM
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110104/98482953/attachment.html>
More information about the gromacs.org_gmx-users
mailing list