Re: [gmx-users] Secondary structure content
Thank you all.. On Saturday, September 9, 2017, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/9/17 1:43 PM, nidhi 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? >> > > It should be the fraction of residues of each type of structure. > > -Justin > > 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. >>> >>> > -- > == > > 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.
Re: [gmx-users] Secondary structure content
On 9/9/17 1:43 PM, nidhi 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? It should be the fraction of residues of each type of structure. -Justin 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. -- == 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.
Re: [gmx-users] Secondary structure content
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.
Re: [gmx-users] Secondary structure content
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.
Re: [gmx-users] Secondary structure content
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.
Re: [gmx-users] Secondary structure content
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. 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. -- 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.
[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.
