<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Trent,<div><span class="Apple-tab-span" style="white-space:pre"> </span>Elaine's tool seems like a good start since it helps you visualize the various sphere clusters. You are right that it would be nice to have a tool more closely integrated with Chimera that would also allow you to delete spheres and rewrite your sphere file. I will open an enhancement-request ticket in our bug-tracking database with you and the other cc recipients on it so that you all will be notified when it gets implemented.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>I hope Elaine's program will be helpful enough until I have time to get to it.</div><div><br></div><div>--Eric</div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div><div><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "><br></font></div><div><div>On Nov 2, 2011, at 10:09 AM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear Trent,<br>If I remember correctly there was a utility program included with DOCK, "showsphere" to convert sphere format to PDB. It was pretty decent for display in Midas, but not so great in Chimera, so in 2008 I wrote a fortran program (yeah, yeah stop laughing) to convert sphere format for better display in Chimera.<br><br>This is not to say your suggestion isn't valid (or has been taken care of), but in the meanwhile this program I wrote might be helpful.<br><br>I will dig up that 2008 email with the program attached and more detailed information and forward it momentarily. Best,<br>Elaine<br>-----<br>Elaine C. Meng, Ph.D. <br>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br><br>On Nov 2, 2011, at 9:09 AM, Trent E. Balius wrote:<br><br><blockquote type="cite">Dear Chimera-user list,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I believe, currently, Chimera can not visualize docking spheres (<a href="http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#OrientingtheLigand">http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#OrientingtheLigand</a>) files directly, in order to do so, we need to create a pdb file of the spheres and then visualize them. <br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">It would be vary helpful for DOCK users if we could visualizes spheres directly from the .sph files produced by sphgen (<a href="http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Sphgen">http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Sphgen</a>) or sphgen_cpp. Radius and color information could then also be displayed. <br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">This might be a helpful new feature to be included in a future release of Chimera. <br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thank you,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Trent E. Balius<br></blockquote><blockquote type="cite">Graduate Student, Rizzo Group,<br></blockquote><blockquote type="cite">Department of Applied Mathematics and Statistics,<br></blockquote><blockquote type="cite">Stony Brook University.<br></blockquote><blockquote type="cite">Office: Math Tower 3-129, Phone: (631) 632-8519<br></blockquote><blockquote type="cite">URL: <a href="http://www.ams.sunysb.edu/~tbalius/">http://www.ams.sunysb.edu/~tbalius/</a><br></blockquote><br><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><br></div><br><br><div apple-content-edited="true"> </div><br></body></html>