<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="">Hi Vatsala,<div class=""><br class=""></div><div class=""> To change the arrow thickness change the line of code in the dipole.py script</div><div class=""><br class=""></div><div class=""><span style="font-family: monospace; font-size: 11px; background-color: rgb(238, 238, 221);" class="">bildString </span><span class="o" style="font-weight: bold; font-family: monospace; font-size: 11px; background-color: rgb(238, 238, 221);">=</span><span style="font-family: monospace; font-size: 11px; background-color: rgb(238, 238, 221);" class=""> </span><span class="s" style="color: rgb(187, 136, 68); font-family: monospace; font-size: 11px; background-color: rgb(238, 238, 221);">".arrow </span><span class="si" style="color: rgb(187, 136, 68); font-family: monospace; font-size: 11px; background-color: rgb(238, 238, 221);">%g</span><span class="s" style="color: rgb(187, 136, 68); font-family: monospace; font-size: 11px; background-color: rgb(238, 238, 221);"> </span><span class="si" style="color: rgb(187, 136, 68); font-family: monospace; font-size: 11px; background-color: rgb(238, 238, 221);">%g</span><span class="s" style="color: rgb(187, 136, 68); font-family: monospace; font-size: 11px; background-color: rgb(238, 238, 221);"> </span><span class="si" style="color: rgb(187, 136, 68); font-family: monospace; font-size: 11px; background-color: rgb(238, 238, 221);">%g</span><span class="s" style="color: rgb(187, 136, 68); font-family: monospace; font-size: 11px; background-color: rgb(238, 238, 221);"> </span><span class="si" style="color: rgb(187, 136, 68); font-family: monospace; font-size: 11px; background-color: rgb(238, 238, 221);">%g</span><span class="s" style="color: rgb(187, 136, 68); font-family: monospace; font-size: 11px; background-color: rgb(238, 238, 221);"> </span><span class="si" style="color: rgb(187, 136, 68); font-family: monospace; font-size: 11px; background-color: rgb(238, 238, 221);">%g</span><span class="s" style="color: rgb(187, 136, 68); font-family: monospace; font-size: 11px; background-color: rgb(238, 238, 221);"> </span><span class="si" style="color: rgb(187, 136, 68); font-family: monospace; font-size: 11px; background-color: rgb(238, 238, 221);">%g</span><span class="s" style="color: rgb(187, 136, 68); font-family: monospace; font-size: 11px; background-color: rgb(238, 238, 221);"> .1 .2 .9"</span></div><div class=""><br class=""></div><div class="">The values at the end control the shape, the “.1” is the cylinder radius, the “.2” is the arrow tip cone radius, and the “.9” is the fraction of the arrow length taken by the cylinder. This is described in the Chimera BILD format documentation here</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html" class="">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jan 25, 2017, at 10:02 AM, Sagar, Vatsala (NIH/NEI) [E] wrote:</div><br class="Apple-interchange-newline"><div class="">
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<div class="">Hi Tom, </div>
<div class="">Do you know how to change the dipole vector thickness. I am using dipole.py program to calculate dipoles in Chimera, and it is giving me a very thin line. </div>
<div class="">Thanks a lot, I sincerely appreciate it,</div>
<div class="">Vatsala Sagar</div>
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<span style="font-weight:bold" class="">From: </span>"Sagar, Vatsala (NIH/NEI) [F]" <br class="">
<span style="font-weight:bold" class="">Date: </span>Friday, January 6, 2017 at 10:09 AM<br class="">
<span style="font-weight:bold" class="">To: </span>Tom Goddard , "<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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<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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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
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=""><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>
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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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