<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Fernando,<div class=""><br class=""></div><div class=""> I don't understand what you need vertex coordinates for. But you could put a print statement into the Chimera Python code that does surface coloring to output vertex coordinates and potential values. This would be in file</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span> chimera/share/SurfaceColor/__init__.py</div><div class=""><br class=""></div><div class="">or on Mac in </div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Chimera.app/Contents/Resources/share/SurfaceColor/__init__.py</div><div class=""><br class=""></div><div class="">in the volume_values() routine change</div><div class=""><br class=""></div><div class=""><div class=""> def volume_values(self, surface_piece):</div><div class=""><br class=""></div><div class=""> p = surface_piece</div><div class=""> xf = p.model.openState.xform</div><div class=""> v = p.geometry[0]</div><div class=""> n = p.normals</div><div class=""> return self.offset_values(v, n, xf)</div><div class=""><br class=""></div><div class="">to</div><div class=""><br class=""></div><div class=""><div class=""> def volume_values(self, surface_piece):</div><div class=""><br class=""></div><div class=""> p = surface_piece</div><div class=""> xf = p.model.openState.xform</div><div class=""> v = p.geometry[0]</div><div class=""> n = p.normals</div><div class=""> values, outside = self.offset_values(v, n, xf)</div></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>print '\n'.join('%.5g %.5g %.5g %.5g' % (x, y, z, val) for (x,y,z), val in zip(v, values))</div><div class=""> return values, outside</div><div class=""><br class=""></div><div class="">Use the Surface Color tool and the vertices and values will be printed to the reply log.</div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Sep 16, 2019, at 1:20 PM, Fernando Villa <<a href="mailto:fer.vdl1928@gmail.com" class="">fer.vdl1928@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Dear Tom and Chimera users,</div><div class=""><br class=""></div>In ChimeraX or Chimera, is it possible to calculate the number of vertices and their respective total charges?<br class=""><br class="">I calculated the electrostatic potential surface (Coulombic) with another program, it gave me the following results (attached in this email) and I calculated the area in red and blue, above and below a threshold = 0.<br class=""><br class="">Unfortunately, these results do not help me, because I need to obtain an electrostatics calculations from Adaptive Poisson-Boltzmann Solver (Calculations that I have already made for study proteins with PDB2PQR and APBS, in interface with Chimera: .pqr and .dx files and emulated in Chimera X)<div class=""><br class=""></div><div class="">e.g.<div class=""><div class=""><span id="cid:ii_k0mujhlt0"><image.png></span><br class=""></div><br class="">Now my question is:<br class="">Can I obtain these results of vertices and charges in a file from Chimera or Chimera X (possibly .cvs, .txt, etc.), so that I can make the corresponding calculations?<br class=""><br class="">I would greatly appreciate your help<br class=""><br class="">best regards,<br class=""><br class="">Fer<br clear="all" class=""><div class=""><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div style="text-align:center" class=""><br class=""></div></div></div></div></div></div></div></div><br class=""></div></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El lun., 16 de sep. de 2019 a la(s) 13:03, Tom Goddard (<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>) escribió:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;" class="">Hi Fernando,<div class=""><br class=""></div><div class=""> Instead of thinking about the coloring, it would be clearer to ask how much surface area has electrostatic potential value >= 5. Chimera does not have any code to compute that, although it is something we could add to ChimeraX.</div><div class=""><br class=""></div><div class=""><span class="gmail-m_-5456589366825104533Apple-tab-span" style="white-space:pre-wrap"> </span>Tom</div><div class=""><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Sep 11, 2019, at 7:27 PM, Fernando Villa <<a href="mailto:fer.vdl1928@gmail.com" target="_blank" class="">fer.vdl1928@gmail.com</a>> wrote:</div><br class="gmail-m_-5456589366825104533Apple-interchange-newline"><div class=""><div dir="ltr" class=""><font face="Roboto, RobotoDraft, Helvetica, Arial, sans-serif" class=""><span style="font-size:14px" class="">Dear all Chimera users</span></font><div class=""><font face="Roboto, RobotoDraft, Helvetica, Arial, sans-serif" class=""><span style="font-size:14px" class=""><br class=""></span></font><div class="">In UCSF ChimeraX version 0.91 (2019-08-30)</div><div class="">I opened a .pqr file (generated with pdb2pqr in Chimera 1.14) and then I opened a .dx file
(generated with APBS in Chimera 1.14)
</div><div class=""><br class=""></div><div class="">Then I input the commands:<br class=""></div><div class=""><br class=""></div><div class=""><div class=""><div dir="ltr" class="gmail-m_-5456589366825104533gmail_signature"><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div style="text-align:center" class=""><div style="text-align:left" class="">>surface</div><div style="text-align:left" class="">>color electrostatic #1 map #2 palette -10,red:0,white:10,blue<br class=""></div><div style="text-align:left" class=""><br class=""></div><div style="text-align:left" class=""><div class=""><span id="gmail-m_-5456589366825104533cid:ii_k0g23mqj2" class=""><image.png></span><br class=""></div></div><div style="text-align:left" class="">Is it possible to calculate the red and blue area in Å2 of the molecule?</div><div style="text-align:left" class=""><br class="">Best regards,<br class=""><br class="">Fernando<br class=""></div><div style="text-align:left" class=""><br class=""></div></div><div style="text-align:center" class=""><i style="color:rgb(0,0,255);font-size:small" class=""><font face="arial narrow, sans-serif" class=""><br class=""></font></i></div><div style="text-align:center" class=""><font face="arial narrow, sans-serif" class="">ATTE</font></div><div style="text-align:center" class=""><font face="arial narrow, sans-serif" class="">Fernando Villa Díaz</font></div><div style="text-align:center" class=""><font face="monospace, monospace" class=""><br class=""><br class=""></font></div></div></div></div></div></div></div></div></div></div>
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