<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="">Your structures are rotated 180 degrees relative to one another, not 90 degrees. And the charge is not the same of the two copies, HIS 53 has different charges. Removing HIS 53 (del :53) gives exactly opposite dipole vectors as expected.<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jan 6, 2017, at 7:09 AM, Sagar, Vatsala (NIH/NEI) [F] wrote:</div><br class="Apple-interchange-newline"><div class="">
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<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>
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<span style="font-weight:bold" class="">From: </span>Tom Goddard <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]" <br class="">
<span style="font-weight:bold" class="">Subject: </span>Re: [Chimera-users] dipoles<br class="">
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Hi Vatsala,
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<div class=""> I guess you are refering to the dipole.py script on the Chimera Python scripts web page:</div>
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<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>
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Tom</div>
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<div class="">On Jan 4, 2017, at 11:17 AM, Sagar, Vatsala (NIH/NEI) [F] wrote:</div>
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<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>
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