<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252" class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 14px; font-family: Calibri, sans-serif;" class="">
<div class="">Hi Tom, </div>
<div class="">So if you align the pdb files of the rotated proteins, they have an exact match. But when you make the PQR files, it adds hydrogens differently to the rotated proteins, resulting in a charge difference in the said histidine. Should the program be adding
hydrogens differently to the rotated proteins, and is there a way to remedy this></div>
<div class="">Thanks a lot,</div>
<div class="">Vatsala Sagar</div>
<div class=""><br class="">
</div>
<span id="OLK_SRC_BODY_SECTION" class="">
<div style="font-family: Calibri; font-size: 11pt; text-align: left; border-width: 1pt medium medium; border-style: solid none none; padding: 3pt 0in 0in; border-top-color: rgb(181, 196, 223);" class="">
<span style="font-weight:bold" class="">From: </span>"Sagar, Vatsala (NIH/NEI) [F]" <<a href="mailto:vatsala.sagar@nih.gov" class="">vatsala.sagar@nih.gov</a>><br class="">
<span style="font-weight:bold" class="">Date: </span>Friday, January 6, 2017 at 10:27 AM<br class="">
<span style="font-weight:bold" class="">To: </span>"<a href="mailto:chimera-bugs@cgl.ucsf.edu" class="">chimera-bugs@cgl.ucsf.edu</a>" <<a href="mailto:chimera-bugs@cgl.ucsf.edu" class="">chimera-bugs@cgl.ucsf.edu</a>><br class="">
<span style="font-weight:bold" class="">Subject: </span>FW: [Chimera-users] dipoles<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 14px; font-family: Calibri, sans-serif;" class="">
<div class="">
<div class="">Hi Tom, </div>
<div class="">I am attaching the PQR files and raw PDB files of the crystal structure of human gamma D with two monomers rotated 90 degrees to one another. Please take a look at it and tell me what you think,</div>
<div class="">Thanks,</div>
<div class="">Vatsala</div>
</div>
<div class=""><br class="">
</div>
<span id="OLK_SRC_BODY_SECTION" class="">
<div style="font-family: Calibri; font-size: 11pt; text-align: left; border-width: 1pt medium medium; border-style: solid none none; padding: 3pt 0in 0in; border-top-color: rgb(181, 196, 223);" class="">
<span style="font-weight:bold" class="">From: </span>Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>><br class="">
<span style="font-weight:bold" class="">Date: </span>Thursday, January 5, 2017 at 7:07 PM<br class="">
<span style="font-weight:bold" class="">To: </span>"<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a> BB" <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>>, "Sagar, Vatsala (NIH/NEI) [F]" <<a href="mailto:vatsala.sagar@nih.gov" class="">vatsala.sagar@nih.gov</a>><br class="">
<span style="font-weight:bold" class="">Subject: </span>Re: [Chimera-users] dipoles<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi Vatsala,
<div class=""><br class="">
</div>
<div class=""> I guess you are refering to the dipole.py script on the Chimera Python scripts web page:</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span><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="">Yes it should give the same answer for a molecule and a copy of that molecule rotated by 90 degrees. Without have the structure and rotated PQR files I don’t know what is going wrong.</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Tom</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On Jan 4, 2017, at 11:17 AM, Sagar, Vatsala (NIH/NEI) [F] wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 14px; font-family: Calibri, sans-serif;" class="">
<div class="">Hi,</div>
<div class="">Do you know if there is a method to calculate dipoles in Chimera? I have generated a PQR structure in predicted protonation state and uploaded it onto Chimera. I then used a downloaded app called dimer.py to calculate the dipole moments of two
of the same monomers rotated 90degrees. Technically they should both give the same dipole as the structures align 100% but according to the PDB coordinates are only rotated relative to one another. The dipole.py scipt is calculating them as two different
dipoles. Can you help me with this?</div>
<div class="">Thanks,</div>
<div class="">Vatsala Sagar</div>
</div>
</div>
_______________________________________________<br class="">
Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">
Chimera-users@cgl.ucsf.edu</a><br class="">
Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
</div>
</span></div>
</div>
</span>
</div>
</body></html>