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On 13/09/2011 9:47 AM, E. Nihal Korkmaz wrote:
<blockquote
cite="mid:CAK7hcuf4wHFKQB8v_zvN9BALdQF4zZSqbjC02Z2sFpVp8pNmuA@mail.gmail.com"
type="cite">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.<br>
</blockquote>
<br>
So do two calculations with different probe radii.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAK7hcuf4wHFKQB8v_zvN9BALdQF4zZSqbjC02Z2sFpVp8pNmuA@mail.gmail.com"
type="cite">
<br>
<br>
Nihal<br>
<br>
<div class="gmail_quote">On Mon, Sep 12, 2011 at 6:42 PM, E. Nihal
Korkmaz <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:enihalkorkmaz@gmail.com">enihalkorkmaz@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
R is any distance from the surface of the protein.
<div>
<div class="h5"><br>
<br>
<div class="gmail_quote">On Mon, Sep 12, 2011 at 6:31 PM,
Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt
0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div>On 13/09/2011 9:29 AM, E. Nihal Korkmaz wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt
0pt 0pt 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
Dear all,<br>
<br>
Is there any function to get the Volume around a
peptide/protein as a function of R?<br>
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.<br>
</blockquote>
<br>
</div>
You haven't said what R is, but g_sas will calculate
some volumes.<br>
<br>
Mark<br>
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<div class="h5">-- <br>
Elif Nihal Korkmaz<br>
<br>
Research Assistant <br>
University of Wisconsin - Biophysics <br>
Member of Qiang Cui & Thomas Record Labs<br>
1101 University Ave, Rm. 8359<br>
Madison, WI 53706<br>
Phone: <a moz-do-not-send="true" href="tel:608-265-3644"
value="+16082653644" target="_blank">608-265-3644</a><br>
Email: <a moz-do-not-send="true"
href="mailto:korkmaz@wisc.edu" target="_blank">korkmaz@wisc.edu</a><br>
<br>
<br>
</div>
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<br>
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<br>
-- <br>
Elif Nihal Korkmaz<br>
<br>
Research Assistant <br>
University of Wisconsin - Biophysics <br>
Member of Qiang Cui & Thomas Record Labs<br>
1101 University Ave, Rm. 8359<br>
Madison, WI 53706<br>
Phone: 608-265-3644<br>
Email: <a moz-do-not-send="true" href="mailto:korkmaz@wisc.edu"
target="_blank">korkmaz@wisc.edu</a><br>
<br>
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