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>
<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 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></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 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><font color="#888888">
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</font></blockquote></div><br><br clear="all"><br></div></div><div><div></div><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 href="tel:608-265-3644" value="+16082653644" target="_blank">608-265-3644</a><br>
Email: <a href="mailto:korkmaz@wisc.edu" target="_blank">korkmaz@wisc.edu</a><br><br><br>
</div></div></blockquote></div><br><br clear="all"><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 href="mailto:korkmaz@wisc.edu" target="_blank">korkmaz@wisc.edu</a><br><br><br>