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<p class="MsoNormal" style="text-align:justify;margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;line-height:107%;font-family:"Verdana",sans-serif" lang="EN-US">Hi all Chimera users,<span></span></span></p>
<p class="MsoNormal" style="text-align:justify;margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;line-height:107%;font-family:"Verdana",sans-serif" lang="EN-US"><span> </span></span></p>
<p class="MsoNormal" style="text-align:justify;margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;line-height:107%;font-family:"Verdana",sans-serif" lang="EN-US">I would like to know how to calculate the values of
Coulombic ESP on the interface between two proteins:<span></span></span></p>
<p class="MsoNormal" style="text-align:justify;margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;line-height:107%;font-family:"Verdana",sans-serif" lang="EN-US"><span> </span></span></p>
<p class="MsoNormal" style="text-align:justify;margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;line-height:107%;font-family:"Verdana",sans-serif" lang="EN-US">At the moment I have done the following:<span></span></span></p>
<p class="MsoNormal" style="text-align:justify;margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;line-height:107%;font-family:"Verdana",sans-serif" lang="EN-US">*UCSF Chimera version 1.14<span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;line-height:107%;font-family:"Verdana",sans-serif;color:black" lang="EN-US">Commands:</span><span style="font-size:12pt;line-height:107%;font-family:"Verdana",sans-serif" lang="EN-US"><span></span></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif"><span style="font-family:"Verdana",sans-serif" lang="EN-US"><span> </span><span> </span></span><span style="font-family:"Verdana",sans-serif"><a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/open.html" style="color:blue;text-decoration:underline"><span style="color:windowtext;text-decoration:none" lang="EN-US">open</span></a></span><span style="font-family:"Verdana",sans-serif" lang="EN-US"> 1avx<span></span></span></p>
<p style="margin:0cm 0cm 0.0001pt 18pt;font-size:12pt;font-family:"Times New Roman",serif"><span style="font-family:"Verdana",sans-serif" lang="EN-US">display</span><span style="font-family:"Verdana",sans-serif" lang="EN-US"><span></span></span></p>
<p style="margin:0cm 0cm 0.0001pt 18pt;font-size:12pt;font-family:"Times New Roman",serif"><span style="font-family:"Verdana",sans-serif"><a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/longbond.html" style="color:blue;text-decoration:underline"><span style="color:windowtext;text-decoration:none" lang="EN-US">~longbond</span></a></span><span style="font-family:"Verdana",sans-serif" lang="EN-US"> <span><span></span></span></span></p>
<p style="margin:0cm 0cm 0.0001pt 18pt;font-size:12pt;font-family:"Times New Roman",serif"><span style="font-family:"Verdana",sans-serif"><a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/split.html" style="color:blue;text-decoration:underline"><span style="color:windowtext;text-decoration:none" lang="EN-US">split</span></a></span><span class="gmail-MsoHyperlink" style="color:blue;text-decoration:underline"><span style="font-family:"Verdana",sans-serif;color:windowtext;text-decoration:none" lang="EN-US"><span></span></span></span></p>
<p style="margin:0cm 0cm 0.0001pt 18pt;font-size:12pt;font-family:"Times New Roman",serif"><span style="font-family:"Verdana",sans-serif"><a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html" style="color:blue;text-decoration:underline"><span style="color:windowtext;text-decoration:none" lang="EN-US">delete</span></a></span><span style="font-family:"Verdana",sans-serif" lang="EN-US"> solvent</span><span style="font-family:"Verdana",sans-serif" lang="EN-US"> <span><span></span></span></span></p>
<p style="margin:0cm 0cm 0.0001pt 18pt;font-size:12pt;font-family:"Times New Roman",serif"><span style="font-family:"Verdana",sans-serif" lang="EN-US">surf #0.1<span></span></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif"><span style="font-family:"Verdana",sans-serif;color:black" lang="EN-US"><span> </span></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif"><span style="font-family:"Verdana",sans-serif;color:black" lang="EN-US">Tools>Surface/Binding analysis>Coulombic
surface coloring<span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:normal;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;font-family:"Verdana",sans-serif;color:black" lang="EN-US">>Check the
box compute grid<span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:normal;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;font-family:"Verdana",sans-serif;color:black" lang="EN-US">>Apply<span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:normal;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;font-family:"Verdana",sans-serif;color:black" lang="EN-US">>Surface
color>Options<span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:normal;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;font-family:"Verdana",sans-serif;color:black" lang="EN-US"><span> </span><span> </span>>Check the box Report value at mouse
position<span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:normal;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;font-family:"Verdana",sans-serif;color:black" lang="EN-US"><span> </span><span> </span>>Click color:<span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:normal;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;font-family:"Verdana",sans-serif;color:black" lang="EN-US"><span> </span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:normal;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;font-family:"Verdana",sans-serif;color:black" lang="EN-US">All the
electrostatic potential values appear by Coulombic Kcal/(Mol.e) at the mouse
position:<span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:normal;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;font-family:"Verdana",sans-serif;color:black" lang="EN-US"><span> </span></span></p><div><img src="cid:ii_k4spuhgb0" alt="imagen.png" width="371" height="23"><br><br></div>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;line-height:107%;font-family:"Verdana",sans-serif"></span><span style="font-size:12pt;line-height:107%;font-family:"Verdana",sans-serif" lang="EN-US"><span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:normal;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;font-family:"Verdana",sans-serif;color:black" lang="EN-US">Commands:<span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt 14.2pt;line-height:normal;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;font-family:"Verdana",sans-serif;color:black" lang="EN-US">~surface #0.1<span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt 14.2pt;line-height:normal;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;font-family:"Verdana",sans-serif" lang="EN-US">measure buriedArea <span style="color:black">#0.1 #0.2<span></span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt 14.2pt;line-height:normal;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;font-family:"Verdana",sans-serif;color:black" lang="EN-US">select #0.1@/buriedSASArea> 1<span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt 14.2pt;line-height:normal;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;font-family:"Verdana",sans-serif;color:black" lang="EN-US">surf sel<span><span></span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;line-height:107%;font-family:"Verdana",sans-serif;color:black" lang="EN-US"><span> </span></span></p><p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;line-height:107%;font-family:"Verdana",sans-serif;color:black" lang="EN-US"><span>
</span></span></p><p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-family:"Arial",sans-serif" lang="EN-US">Volume
viewer>Tools>Values at atom position>Click Histogram <span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;line-height:107%;font-family:"Verdana",sans-serif" lang="EN-US"><span> </span></span></p><div><img src="cid:ii_k4spuyof1" alt="imagen.png" width="478" height="260"><br><br></div>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;line-height:107%;font-family:"Verdana",sans-serif"><br></span><span style="font-size:12pt;line-height:107%;font-family:"Verdana",sans-serif" lang="EN-US"><span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;line-height:107%;font-family:"Verdana",sans-serif" lang="EN-US">Is there a way to
save all the ESP Coulombic values in the selected interface surface in a file?<span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;line-height:107%;font-family:"Verdana",sans-serif" lang="EN-US">Is it possible to
calculate the polar and non-polar surface area in the interface?<span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;line-height:107%;font-family:"Verdana",sans-serif" lang="EN-US">Regards,<span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:12pt;line-height:107%;font-family:"Verdana",sans-serif" lang="EN-US">Fer.<span></span></span></p>
<div><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"><font face="monospace, monospace"><br></font></div><br><div style="text-align:center"><font face="monospace, monospace"><br></font></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El lun., 16 de sep. de 2019 a la(s) 17:39, 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> 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><br></div><div><span style="white-space:pre-wrap"> </span> chimera/share/SurfaceColor/__init__.py</div><div><br></div><div>or on Mac in </div><div><br></div><div><span style="white-space:pre-wrap"> </span>Chimera.app/Contents/Resources/share/SurfaceColor/__init__.py</div><div><br></div><div>in the volume_values() routine change</div><div><br></div><div><div> def volume_values(self, surface_piece):</div><div><br></div><div> p = surface_piece</div><div> xf = p.model.openState.xform</div><div> v = p.geometry[0]</div><div> n = p.normals</div><div> return self.offset_values(v, n, xf)</div><div><br></div><div>to</div><div><br></div><div><div> def volume_values(self, surface_piece):</div><div><br></div><div> p = surface_piece</div><div> xf = p.model.openState.xform</div><div> v = p.geometry[0]</div><div> n = p.normals</div><div> values, outside = self.offset_values(v, n, xf)</div></div><div><span style="white-space:pre-wrap"> </span>print '\n'.join('%.5g %.5g %.5g %.5g' % (x, y, z, val) for (x,y,z), val in zip(v, values))</div><div> return values, outside</div><div><br></div><div>Use the Surface Color tool and the vertices and values will be printed to the reply log.</div><div><br></div><div> Tom</div><div><br></div><div><br><blockquote type="cite"><div>On Sep 16, 2019, at 1:20 PM, Fernando Villa <<a href="mailto:fer.vdl1928@gmail.com" target="_blank">fer.vdl1928@gmail.com</a>> wrote:</div><br><div><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><span id="gmail-m_-3926910059143073374cid:ii_k0mujhlt0"><image.png></span><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"><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" target="_blank">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>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 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><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"><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_-3926910059143073374gmail-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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<span id="gmail-m_-3926910059143073374cid:f_k0mupes81"><Test_MEP_Protein.xlsx></span>_______________________________________________<br>Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank">Chimera-users@cgl.ucsf.edu</a><br>Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></div></blockquote></div><br></div></div></blockquote></div>