<html dir="ltr">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-8-i">
<style>
<!--
@font-face
{font-family:"Cambria Math"}
@font-face
{font-family:Calibri}
@font-face
{font-family:Tahoma}
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif"}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline}
a:visited, span.MsoHyperlinkFollowed
{color:purple;
text-decoration:underline}
p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
{margin:0in;
margin-bottom:.0001pt;
font-size:8.0pt;
font-family:"Tahoma","sans-serif"}
span.EmailStyle17
{font-family:"Calibri","sans-serif";
color:#1F497D}
span.BalloonTextChar
{font-family:"Tahoma","sans-serif"}
.MsoChpDefault
{font-family:"Calibri","sans-serif"}
@page WordSection1
{margin:1.0in 1.0in 1.0in 1.0in}
-->
</style><style type="text/css" id="owaParaStyle"></style>
</head>
<body lang="EN-US" link="blue" vlink="purple" fpstyle="1" ocsi="0">
<div style="direction: ltr;font-family: Arial;color: #0000FF;font-size: 10pt;">
<div>Hi Jacob,</div>
<div><br>
</div>
My guess is that answer (or hint) is here (taken from this link : https://www.phenix-online.org/documentation/faqs/refine.html#targets-and-restraints):
<div><br>
</div>
<div>
<p style="color: rgb(0, 0, 0); font-family: Verdana, Helvetica, Arial, sans-serif; font-size: 21.6px;">
<strong>I have ions very close to water molecules/protein atoms, and phenix.refine keeps tring to move them apart. How can I prevent this?</strong></p>
<p style="color: rgb(0, 0, 0); font-family: Verdana, Helvetica, Arial, sans-serif; font-size: 21.6px;">
Use <tt class="docutils literal">phenix.ready_set</tt> or <tt class="docutils literal"><u>phenix.metal_coordination</u></tt> to generate custom bond (and optionally, bond angle) restraints, which will be output to a parameter file ending in ".edits". If you
are using the PHENIX GUI, there is a toolbar button for ReadySet in the phenix.refine interface, which will automatically load the output files for use in phenix.refine.</p>
<div><br>
<div style="font-family:Tahoma; font-size:13px">
<div><font face="Times New Roman" size="3"></font>I have not used it myself but I assume that the sigmas for the restraints would be in the *.edits files that you'll generate. </div>
<div><br>
</div>
<div>Hope this helps.</div>
<div><br>
</div>
<div> Boaz</div>
<div><font face="Times New Roman" size="3"></font> </div>
<div><font color="#000080" face="Times New Roman" size="3"><em>Boaz Shaanan, Ph.D.
<br>
Dept. of Life Sciences <br>
Ben-Gurion University of the Negev <br>
Beer-Sheva 84105 <br>
Israel <br>
<br>
E-mail: bshaanan@bgu.ac.il<br>
Phone: 972-8-647-2220 Skype: boaz.shaanan <br>
Fax: 972-8-647-2992 or 972-8-646-1710 </em></font></div>
<div><font color="#000080" face="Times New Roman" size="3"><em></em></font> </div>
<div><font color="#000080" face="Times New Roman" size="3"><em></em></font> </div>
<div><font face="Times New Roman" size="3"><em><font color="#000080">
<br>
<br>
</font></em></font></div>
<font face="Times New Roman" size="3"></font></div>
</div>
<div style="font-family: Times New Roman; color: #000000; font-size: 16px">
<hr tabindex="-1">
<div id="divRpF371855" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> Keller, Jacob [kellerj@janelia.hhmi.org]<br>
<b>Sent:</b> Wednesday, December 30, 2015 4:09 PM<br>
<b>To:</b> Nigel Moriarty<br>
<b>Cc:</b> ��� ����; phenixbb@phenix-online.org<br>
<b>Subject:</b> RE: [phenixbb] Modifications for Ca-binding site<br>
</font><br>
</div>
<div></div>
<div>
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">How does one change the ideal bond length/sigma in Phenix?</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">JPK</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt; font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt; font-family:"Tahoma","sans-serif""> Nigel Moriarty [mailto:nwmoriarty@lbl.gov]
<br>
<b>Sent:</b> Tuesday, December 29, 2015 10:12 AM<br>
<b>To:</b> Keller, Jacob<br>
<b>Cc:</b> Boaz Shaanan; phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] Modifications for Ca-binding site</span></p>
<p class="MsoNormal"> </p>
<div>
<p class="MsoNormal">Jacob</p>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Boaz has some sage advice. I recommend not excluding the Ca-O coordination but changing the ideal to better reflect the distances in your files.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">PS I'd also like the PDB files, directly, so as not to put noise on the list.</p>
</div>
</div>
<div>
<p class="MsoNormal"><br clear="all">
</p>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal">Cheers</p>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Nigel</p>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">---</p>
</div>
<div>
<p class="MsoNormal">Nigel W. Moriarty<br>
Building 33R0349, Physical Biosciences Division<br>
Lawrence Berkeley National Laboratory<br>
Berkeley, CA 94720-8235<br>
Phone : 510-486-5709 Email : <a href="mailto:NWMoriarty@LBL.gov" target="_blank">
NWMoriarty@LBL.gov</a><br>
Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal"> </p>
<div>
<p class="MsoNormal">On Tue, Dec 29, 2015 at 5:49 AM, Keller, Jacob <<a href="mailto:kellerj@janelia.hhmi.org" target="_blank">kellerj@janelia.hhmi.org</a>> wrote:</p>
<p class="MsoNormal">Well, I think it's more of a data-vs-geometry battle, with the geometry dragging in the side chains towards the calciums, and the data pulling them out. When I real-space refine them in Coot, some of the Ca-O distances are pretty different
from the "ideal" values. Maybe I could just exclude them from xyz refinement in Phenix after making sure they're correct in Coot? I'll give that a shot.<br>
<br>
Kol tuv,<br>
<br>
Jacob</p>
<div>
<div>
<p class="MsoNormal"><br>
<br>
<br>
<br>
-----Original Message-----<br>
From: Boaz Shaanan [mailto:<a href="mailto:bshaanan@bgu.ac.il" target="_blank">bshaanan@bgu.ac.il</a>]<br>
Sent: Tuesday, December 29, 2015 7:52 AM<br>
To: Keller, Jacob; <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
Subject: RE: Modifications for Ca-binding site<br>
<br>
Hi Jacob,<br>
<br>
Sucking-up neighboring residues into the Calcium (or other heavier atoms) density is a known issue. Turning-off the Ca-O or other distance restraints around the Calcium is the last thing you want to do, in my experience. You'd better check those distance restraints
and verify that they're compatible with the distances in other (preferably high resolution, of course) structures with calcium binding sites similar to yours and then make sure they're given the appropriate weight during refinement. That's my view but Pavel
will give you more advices I'm sure.<br>
<br>
Cheers,<br>
<br>
Boaz<br>
<br>
<br>
Boaz Shaanan, Ph.D.<br>
Dept. of Life Sciences<br>
Ben-Gurion University of the Negev<br>
Beer-Sheva 84105<br>
Israel<br>
<br>
E-mail: <a href="mailto:bshaanan@bgu.ac.il" target="_blank">bshaanan@bgu.ac.il</a><br>
Phone: 972-8-647-2220 Skype: boaz.shaanan<br>
Fax: 972-8-647-2992 or 972-8-646-1710<br>
<br>
<br>
<br>
<br>
<br>
________________________________________<br>
From: <a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a> [<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a>] on behalf of Keller, Jacob [<a href="mailto:kellerj@janelia.hhmi.org" target="_blank">kellerj@janelia.hhmi.org</a>]<br>
Sent: Tuesday, December 29, 2015 4:44 AM<br>
To: <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
Subject: [phenixbb] Modifications for Ca-binding site<br>
<br>
I am getting a lot of problems with my calcium binding sites--there is clear density for the calciums and the protein side chains, but Phenix keeps sucking the side chains out of their density towards the calciums and also the calciums show some positive difference
density, perhaps due to too-high b-factors (or potentially partial occupancy by Na?). I think what might work best is to turn off the Ca-O bond length restraints somehow, but don't see where/how to do that. I tried releasing them from geometrical restraints,
but that made things worse, since things went haywire in the sidechains themselves.<br>
<br>
Is it possible to make Phenix ignore the Ca-O bond distance restraints?<br>
<br>
JPK<br>
<br>
*******************************************<br>
Jacob Pearson Keller, PhD<br>
Looger Lab/HHMI Janelia Research Campus<br>
19700 Helix Dr, Ashburn, VA 20147<br>
email: <a href="mailto:kellerj@janelia.hhmi.org" target="_blank">kellerj@janelia.hhmi.org</a><br>
*******************************************<br>
<br>
<br>
<br>
_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a><br>
<br>
_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></p>
</div>
</div>
</div>
<p class="MsoNormal"> </p>
</div>
</div>
</div>
</div>
</div>
</div>
</body>
</html>