<div dir="ltr"><div>Dear Tom and Chimera users,</div><div><br></div>In ChimeraX or Chimera, is it possible to calculate the number of vertices and their respective total charges?<br><br>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><br>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><br></div><div>e.g.<div><div><img src="cid:ii_k0mujhlt0" alt="image.png" width="208" height="188" style="margin-right: 0px;"><br></div><br>Now my question is:<br>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><br>I would greatly appreciate your help<br><br>best regards,<br><br>Fer<br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div style="text-align:center"><br></div></div></div></div></div></div></div></div><br></div></div></div><br><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">goddard@sonic.net</a>) escribió:<br></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;">Hi Fernando,<div><br></div><div> 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><br></div><div><span class="gmail-m_-5456589366825104533Apple-tab-span" style="white-space:pre-wrap"> </span>Tom</div><div><br><div><br><blockquote type="cite"><div>On Sep 11, 2019, at 7:27 PM, Fernando Villa <<a href="mailto:fer.vdl1928@gmail.com" target="_blank">fer.vdl1928@gmail.com</a>> wrote:</div><br class="gmail-m_-5456589366825104533Apple-interchange-newline"><div><div dir="ltr"><font face="Roboto, RobotoDraft, Helvetica, Arial, sans-serif"><span style="font-size:14px">Dear all Chimera users</span></font><div><font face="Roboto, RobotoDraft, Helvetica, Arial, sans-serif"><span style="font-size:14px"><br></span></font><div>In UCSF ChimeraX version 0.91 (2019-08-30)</div><div>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><br></div><div>Then I input the commands:<br></div><div><br></div><div><div><div dir="ltr" class="gmail-m_-5456589366825104533gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div style="text-align:center"><div style="text-align:left">>surface</div><div style="text-align:left">>color electrostatic #1 map #2 palette -10,red:0,white:10,blue<br></div><div style="text-align:left"><br></div><div style="text-align:left"><div><span id="gmail-m_-5456589366825104533cid:ii_k0g23mqj2"><image.png></span><br></div></div><div style="text-align:left">Is it possible to calculate the red and blue area in Å2 of the molecule?</div><div style="text-align:left"><br>Best regards,<br><br>Fernando<br></div><div style="text-align:left"><br></div></div><div style="text-align:center"><i style="color:rgb(0,0,255);font-size:small"><font face="arial narrow, sans-serif"><br></font></i></div><div style="text-align:center"><font face="arial narrow, sans-serif">ATTE</font></div><div style="text-align:center"><font face="arial narrow, sans-serif">Fernando Villa Díaz</font></div><div style="text-align:center"><font face="monospace, monospace"><br><br></font></div></div></div></div></div></div></div></div></div></div>
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