[gmx-users] Secondary structure content

Justin Lemkul jalemkul at vt.edu
Sat Sep 9 15:33:30 CEST 2017

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.


> 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-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Sundari <sundi6170 at gmail.com>
> Sent: Saturday, September 09, 2017 5:48 AM
> To: gromacs.org_gmx-users at 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
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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