[gmx-users] Secondary structure content

[Sundari]

Thank you all..

On Saturday, September 9, 2017, Justin Lemkul <jalemkul at 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" <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
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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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