[gmx-users] Secondary structure content

[nidhi]

I also have same doubt.

On 9 Sep 2017 11:13 p.m., "nidhi" <nidhi020191 at 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" <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.
>>
>> -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-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
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
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>