[Chimera-users] Electrostatics potential of amino acid residues

[Ankush Sharma]

file attached for better understanding.

On Fri, Jan 13, 2012 at 6:48 PM, Ankush Sharma <ankush.sak at gmail.com> wrote:

> Regards Elaine ,
>
> Thank s Elaine for your reply  i'm aware of these facts . what I wanted to
> say if we considered the protein divided into grid boxes , i need to
> calculate electrostatic potential of one particular area( in attached  fig
> box e) . Plot can be plotted on X axis as the distance acquired by
> electrostatic potential surface from the centre of the protein (for whole
> protein). For One grid or one box, distance acquired by the electrostatic
> potential surface from the centre of that part of protein to the distance
> of the  one grid( off course protein will be divided into many grids while
> performing these kinds of analysis.) and Y axis Will the electrostatic
> potential.
>
> Thanks
> Ankush Sharma
>
>
>
>
>
>
> Hi Ankush,
>> If you want to show the electrostatic potential by coloring the molecular
>> surface in Chimera, please see this recent post for two possible ways:
>> <
>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-January/007058.html
>> >
>>
>> See also this tutorial:
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
>>
>> For plotting, you would need to use some other program.  Also, it is
>> unclear what would be on the X-axis and Y-axis of this plot, since the
>> potential varies in 3D space.  There is not a single potential value per
>> residue or anything like that.
>>
>> For comparing electrostatics of proteins, you might be interested in this
>> web server:
>> <http://pipsa.eml.org/pipsa/>
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>> On Jan 13, 2012, at 9:05 AM, Ankush Sharma wrote:
>>
>> > Regards all,
>> > i wanted to calculate the calculate the Electrostatics potential
>> associated with a specific part of the protein and differentiate from the
>> other part of protein. How can it Possible . is there any method apart from
>> MD to plot a graph of both to diffrentiate Quantitatively the The Potential
>> > Thanks in advance
>> > Ankush Sharma
>>
>>
>
>
> --
> Regards
> Ankush Sharma
> Doctoral student in Computational Biology
> Second University of Naples & Centro Ricerche Oncologiche
> di Mercogliano
> Email ID : ankush.sharma at unina2.it
> Phone: +39 331 831 6370
>
>
>
>  *P** Please do not print this email unless it is absolutely necessary.
> Spread environmental awareness.*
>
>
>


-- 
Regards
Ankush Sharma
Doctoral student in Computational Biology
Second University of Naples & Centro Ricerche Oncologiche
di Mercogliano
Email ID : ankush.sharma at unina2.it
Phone: +39 331 831 6370



 *P** Please do not print this email unless it is absolutely necessary.
Spread environmental awareness.*
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