[gmx-users] Secondary structure content
nidhi020191 at gmail.com
Sat Sep 9 19:43:10 CEST 2017
Thank you :)
Can you please suggest me than what's the last line of scount.xvg file
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" <jalemkul at 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.
> 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".
>> 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
> 303 Engel Hall
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> jalemkul at vt.edu | (540) 231-3129
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