<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br></div><div>My understanding is that the solvent accessible surface is not (yet) available in Chimera. However, Elaine showed me once how to get more or less such a surface: </div><div><br></div><div>1. Before calculating the surface issue the chimera command: </div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>vdwdefine +1.4</div><div><br></div><div>which adds 1.4 A (roughly the usual radius for the water probe) to all atom radii</div><div><br></div><div>2. Show the surface</div><div><br></div><div>3. On the Model Panel, select the surface and under "attributes" change the probe radius to 0.5 It should be 0.0 but this is not possible. This means that intersections of atom spheres will be smoothed slightly. Still, the surface represents almost correctly the solvent accessible one.</div><div><br></div><div>The error on this surfaces doesn't depend directly on the quality of the electron density but on the accuracy of the atoms positions. Which of course depends on the data...</div><div><br></div><div>I hope it helps,</div><div><br></div><div><br></div><div>Miguel</div><div><br></div><div><br></div><div><div><div>Le 27 mars 09 à 16:59, David Chenoweth a écrit :</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><br><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>From: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">David Chenoweth <<a href="mailto:dchen@caltech.edu">dchen@caltech.edu</a>></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>Date: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">March 27, 2009 8:58:31 AM PDT</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>To: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>Subject: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><b>Re: [Chimera-users] accessible surface area for electron density maps</b></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> </div><div>Hi Elaine and Murali,<br><br>I have a similar problem that I've been trying to resolve. Calculating the accessible surface or solvent accessible surface is also something I've been interested in doing with Chimera but I don't think the area of the molecular surface is the same as the solvent accessible surface area. I believe that accessible surface comes from the locus of the center of a spherical probe as it rolls over the Van der Waals surface of a molecule. The molecular surface uses the locus of the inward facing spherical probe. They both depend on the spherical probe size which is set to the appropriate solvent molecule. Can you tell me which of these two methods Chimera is using when it calculates the area (if either)? Is there a way to calculate the solvent accessible surface area of a molecule with Chimera or some way to manipulate the current area calculator to give this value? I also think that depending on the quality of the electron density map one could get very different results for this calculation (especially if there is missing electron density or at different map contour values). If anyone has any advice for the best way to calculate solvent accessible surface area I would really appreciate the help.<br><br>Thanks,<br>Dave Chenoweth<br><br>**********************************************<br>David M. Chenoweth<br>California Institute of Technology<br>Division of Chemistry and Chemical Engineering<br>Mail Code: 164-30<br>1200 California Boulevard, 91125 Pasadena<br>California, USA<br><br>Phone: 626-395-6074<br>Email: <a href="mailto:dchen@caltech.edu">dchen@caltech.edu</a><br>**********************************************<br><br>On Mar 27, 2009, at 8:14 AM, Elaine Meng wrote:<br><br><blockquote type="cite">Hi Murali,<br></blockquote><blockquote type="cite">If I understand correctly, you want to get the area of a contour<br></blockquote><blockquote type="cite">surface of the density shown using the Volume Viewer tool. If you<br></blockquote><blockquote type="cite">want the total surface area, even of multiple separate blobs, use<br></blockquote><blockquote type="cite">"Measure Volume and Area." If you want to measure the area of<br></blockquote><blockquote type="cite">different blobs individually, use "Measure and Color Blobs."<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">These can be started from the Tools menu of the Volume Viewer dialog,<br></blockquote><blockquote type="cite">and also from the main Chimera Tools menu (Tools... Volume Data...<br></blockquote><blockquote type="cite">[name of tool]).<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">For more details on how to use a tool, press the Help button on the<br></blockquote><blockquote type="cite">dialog. That opens the documentation included with your download.<br></blockquote><blockquote type="cite">Our web site also has copies of the documentation:<br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/measurevol/measurevol.html">http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/measurevol/measurevol.html</a><br></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/pickblobs/pickblobs.html">http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/pickblobs/pickblobs.html</a><br></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I hope this helps,<br></blockquote><blockquote type="cite">Elaine<br></blockquote><blockquote type="cite">-----<br></blockquote><blockquote type="cite">Elaine C. Meng, Ph.D. <a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a><br></blockquote><blockquote type="cite">UCSF Computer Graphics Lab and Babbitt Lab<br></blockquote><blockquote type="cite">Department of Pharmaceutical Chemistry<br></blockquote><blockquote type="cite">University of California, San Francisco<br></blockquote><blockquote type="cite"> <a href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Mar 27, 2009, at 7:42 AM, Murali Ayaluru wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Dear Chimera users,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I want to calculate the accessible surface area for an electron<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">density map (mrc format) that I am working on. Can anyone, who<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">knows how to do this, tell me how to do this?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thanks in advance for your reply,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Regards,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Murali<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">Chimera-users mailing list<br></blockquote><blockquote type="cite"><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br></blockquote><blockquote type="cite"><a href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></blockquote><br><br><br><br><br><br></div></blockquote></div><br><br>-- <br>This message has been scanned for viruses and <br>dangerous content by <a href="http://www.mailscanner.info/"><b>MailScanner</b></a>, and is <br>believed to be clean. </div> _______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></blockquote></div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; 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