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>
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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
Email: kork...@wisc.edu <mailto:kork...@wisc.edu>
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