[gmx-users] Secondary structure content
jalemkul at vt.edu
Sat Sep 9 20:08:03 CEST 2017
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
> 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.
> 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
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>> jalemkul at vt.edu | (540) 231-3129
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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