I also have same doubt. On 9 Sep 2017 11:13 p.m., "nidhi" <nidhi020...@gmail.com> wrote:
> Thank you :) > Can you please suggest me than what's the last line of scount.xvg file > indicates? > It is ss(%), what does it mean? Which kind of secondary structure > percentage is this? > > Thank you for your time and help.. > > On 9 Sep 2017 7:03 p.m., "Justin Lemkul" <jalem...@vt.edu> wrote: > >> >> >> On 9/9/17 9:30 AM, Smith, Micholas D. wrote: >> >>> If i remember correctly the DSSP plot should be something like residue # >>> on y-axis, and time on the x-axis, then it is normally a color plot of what >>> secondary structure each residue is in at that time point. Secondary >>> structure content (%) vs time sounds more like a single plot of the >>> fraction of residues (%) of residues at each time point that are not in a >>> 'coil' state. >>> >>> >> That's just the ss.xpm file. The scount.xvg has a time series of the >> number of residues in each type of secondary structure over time. To the >> OP's question, it is not a percentage, it is the number of residues, from >> which computing percentage is trivial based on the number of total residues. >> >> -Justin >> >> Hope that makes sense. >>> =================== >>> Micholas Dean Smith, PhD. >>> Post-doctoral Research Associate >>> University of Tennessee/Oak Ridge National Laboratory >>> Center for Molecular Biophysics >>> >>> ________________________________________ >>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sundari >>> <sundi6...@gmail.com> >>> Sent: Saturday, September 09, 2017 5:48 AM >>> To: gromacs.org_gmx-users@maillist.sys.kth.se >>> Subject: [gmx-users] Secondary structure content >>> >>> Dear all, >>> I am confused with 'dssp' output graph i.e "number of residues vs time". >>> Is >>> it also called "secondary structure content(%) vs time" ?? Or it is >>> different term? >>> >>> please, anyone help me to solve this confusion or send me any link >>> contained proper definition of these two. >>> >>> Thanks in advance >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/Support >>> /Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Virginia Tech Department of Biochemistry >> >> 303 Engel Hall >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalem...@vt.edu | (540) 231-3129 >> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >> >> ================================================== >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support >> /Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.