<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Nov 25, 2015, at 12:11 PM, Pande, Ajay K <<a href="mailto:apande@albany.edu" class="">apande@albany.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">I really do need it for many structures, and I am reasonable certain many other people will too. What would be nice is that the dipole vector shows as an arrow on the pdb structure. If you can change the script file, it would be very useful.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Thanks</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Ajay</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><br class=""><br class=""><div style="" class=""><hr tabindex="-1" style="display: inline-block; width: 645.8125px;" class=""><div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Wednesday, November 25, 2015 2:50 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Pande, Ajay K<br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span>chimera List<br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] calculating dipole moment of a protein in pdb</font><div class=""> </div></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Nov 23, 2015, at 10:37 AM, Pande, Ajay K <<a href="mailto:apande@albany.edu" class="">apande@albany.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" class="" style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;"><div class="" style="margin-top: 0px; margin-bottom: 0px;">Hi Eric,</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">It does give me the numerical value of the dipole moment, but how do I generate the dipole vector in the pdb structure?</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">Thanks</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">Ajay</div></div></div></blockquote><div class=""><br class=""></div>If you add the following two lines to the script it will print out the center of mass and dipole vector:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>print “center of mass:”, com.data()</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>print “dipole:”, dipole.data()</div><div class=""><br class=""></div><div class="">Make sure the lines are indented to the same level as the final print statement in the original script. With those values you can easily write a BILD format file that will draw an arrow from the center of mass to the (center of mass + dipole) and open that file to show the arrow. The BILD format is described here:</div><div class=""><br class=""></div><div class=""><a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/bild.html" class="">http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/bild.html</a></div><div class=""><br class=""></div><div class="">If you are doing this for<span class="Apple-converted-space"> </span><i class="">many</i> structures, it would be possible to modify the script itself to create/open the BILD file, but that would be significantly more work. But if you really need it let me know.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><blockquote type="cite" class=""><div class=""><div id="divtagdefaultwrapper" class="" style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;"><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><br class=""><br class=""><div class=""><hr tabindex="-1" class="" style="display: inline-block; width: 636.015625px;"><div id="divRplyFwdMsg" dir="ltr" class=""><font class="" face="Calibri, sans-serif" style="font-size: 11pt;"><b class="">From:</b><span class="Apple-converted-space"> </span>Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Thursday, November 19, 2015 7:56 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Pande, Ajay K<br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] calculating dipole moment of a protein in pdb</font><div class=""> </div></div><div class="">Hi Ajay,<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>The script referenced in this chimera-users archive message will compute it:</div><div class=""><br class=""></div><div class=""><a id="LPlnk627799" href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004780.html" class="">http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004780.html</a></div><div id="LPBorder_GT_14483037953820.4461792358501253" class="" style="margin-top: 20px; margin-bottom: 20px; overflow: auto; width: 649px;"><table id="LPContainer_14483037953810.7723616813367392" class="" style="border-top-width: 1px; border-top-style: solid; border-top-color: rgb(204, 204, 204); border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: rgb(204, 204, 204); width: 519px; background-color: rgb(255, 255, 255); overflow: auto;"><tbody class=""><tr class="" valign="top" style="border-spacing: 0px;"><td class=""><div id="LPTitle_14483037953820.6295622129413163" class="" style="top: 0px; margin-top: 8px; font-size: 21px; font-family: wf_segoe-ui_semilight, 'Segoe UI Semilight', 'Segoe WP Semilight', 'Segoe UI', 'Segoe WP', Tahoma, Arial, sans-serif; color: rgb(51, 51, 51); margin-left: 14px; margin-right: 14px;">[Chimera-users] BCC CHARGES</div><div id="LPDescription_14483037953820.8486864722593821" class="" style="margin-top: 8px; font-size: 13px; font-family: wf_segoe-ui_normal, 'Segoe UI', 'Segoe WP', Tahoma, Arial, sans-serif; color: rgb(102, 102, 102); margin-left: 14px; margin-right: 14px;">I've attached a script that if you run it (File->Open, or "open ~/ dipole.py" [if it's in your home directory]) will print the dipole moments of all open molecular ...</div><div id="LPUrlContainer_14483037953820.514023261198443" class="" style="margin: 8px 14px 10px; height: 18px; text-overflow: ellipsis; overflow: hidden; white-space: nowrap;"><a target="_blank" href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004780.html" id="LPUrlAnchor_14483037953820.4094834771546695" class="" style="font-size: 11px; font-family: wf_segoe-ui_normal, 'Segoe UI', 'Segoe WP', Tahoma, Arial, sans-serif; text-decoration: none;">Read more...</a></div></td></tr></tbody></table></div><div class=""><br class=""></div><div class="">Extracting the script from that message may be challenging, so I’m attaching it again. It’s also available from our Chimera Scripts page:</div><div class=""><br class=""></div><div class=""><a href="http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts" class="">http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts</a></div><div class=""><br class=""></div><div class="">Like it says in the original message you have to assign partial charges before running the script (Tools->Structure Editing->AddCharge, or the “addcharge” command).</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class=""><div class="" style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; word-wrap: break-word;"><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div></div></div></div></div></div><span class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; float: none; display: inline !important;">_______________________________________________</span><br class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><span class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; float: none; display: inline !important;">Chimera-users mailing list</span><br class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><a href="mailto:Chimera-users@cgl.ucsf.edu" class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;">Chimera-users@cgl.ucsf.edu</a><br class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;"><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div></div></div></div></div></blockquote></div><br class=""></div></body></html>