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.