Dear Justin, I understand. Thank you very much.
04 Ocak 2011 20:36 tarihinde Justin A. Lemkul <[email protected]> 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 <[email protected] <mailto: >> [email protected]>> 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 <[email protected] >> <mailto:[email protected]> <mailto:[email protected] >> >> <mailto:[email protected]>>> 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 >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>>> 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 <[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>>> >> >> >> 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 >> [email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>> >> >> >> 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 >> [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>>. >> >> Can't post? Read >> http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- Ahmet YILDIRIM >> >> >> >> -- >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected] >> >> >> <mailto:[email protected] >> <mailto:[email protected]> <mailto:[email protected] >> <mailto:[email protected]>>> >> >> >> 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 >> [email protected] <mailto: >> [email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>>. >> >> 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 [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> 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 [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>. >> 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 [email protected] >> <mailto:[email protected]> >> 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 [email protected] >> <mailto:[email protected]>. >> 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet YILDIRIM
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