On 13/09/2011 9:47 AM, E. Nihal Korkmaz wrote:
And I don't think g_sas would do what i want. It calculates the volume of the protein itself. I am interested in the V of space at a distance R from the surface of the protein, excluding the volume of the protein. In other words, i need the surface accessible volume as a function of distance from the surface of the protein.

So do two calculations with different probe radii.

Mark



Nihal

On Mon, Sep 12, 2011 at 6:42 PM, E. Nihal Korkmaz <enihalkork...@gmail.com <mailto:enihalkork...@gmail.com>> wrote:

    R is any distance from the surface of the protein.


    On Mon, Sep 12, 2011 at 6:31 PM, Mark Abraham
    <mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> wrote:

        On 13/09/2011 9:29 AM, E. Nihal Korkmaz wrote:

            Dear all,

            Is there any function to get the Volume around a
            peptide/protein as a function of R?
            The problem is g_rdf -surf doesn't have a volume
            correction factor, so my aim is to apply a volume
            correction factor manually by having V(R) around the protein.


        You haven't said what R is, but g_sas will calculate some volumes.

        Mark
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-- Elif Nihal Korkmaz

    Research Assistant
    University of Wisconsin - Biophysics
    Member of Qiang Cui & Thomas Record Labs
    1101 University Ave, Rm. 8359
    Madison, WI 53706
    Phone: 608-265-3644 <tel:608-265-3644>
    Email: kork...@wisc.edu <mailto:kork...@wisc.edu>





--
Elif Nihal Korkmaz

Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone:  608-265-3644
Email: kork...@wisc.edu <mailto:kork...@wisc.edu>





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