[Chimera-users] Electrostatics potential of amino acid residues

[Ankush Sharma]

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.*
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120113/8186ddb8/attachment.html>