<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><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="5" color="#000000" style="font: 16.0px Helvetica; color: #000000"><b>From: </b></font><font face="Helvetica" size="5" style="font: 16.0px Helvetica">Nikolay Igorovich Rodionov <<a href="mailto:nirodion@syr.edu">nirodion@syr.edu</a>></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" color="#000000" style="font: 16.0px Helvetica; color: #000000"><b>Date: </b></font><font face="Helvetica" size="5" style="font: 16.0px Helvetica">May 21, 2012 12:43:34 PM PDT</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" color="#000000" style="font: 16.0px Helvetica; color: #000000"><b>To: </b></font><font face="Helvetica" size="5" style="font: 16.0px Helvetica">Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" color="#000000" style="font: 16.0px Helvetica; color: #000000"><b>Subject: </b></font><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><b>RE: [Chimera-users] ESP calculations</b></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> </div><div>Thank you both,<br><br>Can either of you tell me how the information in a volume data set is organized? I am looking at a .dx file that I created using APBS which I would assume to be very similar to the volumetric data sets created by Chimera. What does each column of data represent? Is there any way for me to sort the ESP data based on position using Excel or Matlab? I am only concerned with ESP data for one region of molecule. If you could point me in the direction of some good documentation on this file type it would be great.<br></div></blockquote><div><br></div>I don't know, so I'm forwarding this out to chimera-users land, where someone might have an answer...</div><div><br></div><div>--Eric</div><div><br><blockquote type="cite"><div><br>Thanks again,<br>Nikolay Rodionov<br><br>-----Original Message-----<br>From: Eric Pettersen [<a href="mailto:pett@cgl.ucsf.edu">mailto:pett@cgl.ucsf.edu</a>] <br>Sent: Monday, May 21, 2012 2:57 PM<br>To: <a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a> BB<br>Cc: Nikolay Igorovich Rodionov<br>Subject: Re: [Chimera-users] ESP calculations<br><br>Also, if you compute a volume, you can use the "Values at Atom Positions" tool to, um, get the values at atom positions (say, a ligand), if that's relevant to what you're doing.<br><br>--Eric<br><br>On May 21, 2012, at 9:09 AM, Elaine Meng wrote:<br><br><blockquote type="cite">Hi Nikolay,<br></blockquote><blockquote type="cite">You can generate a grid of values with the "Compute grid" option of <br></blockquote><blockquote type="cite">Coulombic Surface Coloring (or corresponding option of the "coulombic" <br></blockquote><blockquote type="cite">command). The grid is a volume data set, and when it is generated the <br></blockquote><blockquote type="cite">Volume Viewer and Surface Color dialogs will automatically appear.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/co">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/co</a><br></blockquote><blockquote type="cite">ulombic.html<br></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/co">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/co</a><br></blockquote><blockquote type="cite">ulombic.html#volume<br></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">You can save the grid to a file with the FIle menu of Volume Viewer.<br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer</a><br></blockquote><blockquote type="cite">/framevolumeviewer.html<br></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">As for the values at each point of the surface, I don't know of a way <br></blockquote><blockquote type="cite">to write these all to a file, but in Surface Color if you click the <br></blockquote><blockquote type="cite">Options button and then turn on the option to "Report value at mouse <br></blockquote><blockquote type="cite">position" it will report the values in the status line at the bottom <br></blockquote><blockquote type="cite">of the Chimera window when you click into the graphics window and then <br></blockquote><blockquote type="cite">mouse over the surface. I just noticed that to make this work it is <br></blockquote><blockquote type="cite">necessary to recolor the surface first by clicking the Color button on <br></blockquote><blockquote type="cite">this dialog, which may be a bug, but that's the workaround!<br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/su">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/su</a><br></blockquote><blockquote type="cite">rfcolor.html<br></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">If you have the grid file saved you can reopen it in Chimera later and <br></blockquote><blockquote type="cite">use it in Surface Color without rerunning the ESP calculation.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">However, keep in mind that Coulombic ESP is more for qualitative <br></blockquote><blockquote type="cite">purposes of visualization or making comparisons between related <br></blockquote><blockquote type="cite">structures than for absolute quantitative accuracy. For example, you <br></blockquote><blockquote type="cite">could easily make all the ESP values half as large simply by doubling <br></blockquote><blockquote type="cite">the dielectric constant used in their calculation, as shown in the <br></blockquote><blockquote type="cite">equation in the Coulombic Surface Coloring manual page.<br></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.<br></blockquote><blockquote type="cite">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department <br></blockquote><blockquote type="cite">of Pharmaceutical Chemistry University of California, San Francisco<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On May 21, 2012, at 8:05 AM, Nikolay Igorovich Rodionov wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Hi all,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I was wondering if there was a way to get an output data file <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">regarding ESP coloring and calculations based on Coulomb's law. The <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">visualization is great but I would also like to quantify the data.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thank you,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Nikolay Rodionov<br></blockquote></blockquote><blockquote type="cite"><br></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://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></blockquote><blockquote type="cite"><br></blockquote><br><br><br><br></div></blockquote></div><br></body></html>