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? Thanks 04 Ocak 2011 15:51 tarihinde Justin A. Lemkul <[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]>> 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]>> >>> >>> >>> 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]> >>> >>> 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 >>> >> >> >> -- >> 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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