<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; ">
<div>Hi Tom,</div>
<div><br>
</div>
<div>Thanks very much for the tips. I wonder if I need to increase peak separation in case of a long protein?</div>
<div><br>
</div>
<div>Best,</div>
<div><br>
</div>
<div>William</div>
<div>---</div>
<div><br>
</div>
<span id="OLK_SRC_BODY_SECTION">
<div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt">
<span style="font-weight:bold">From: </span>"Terwilliger, Thomas Charles" <<a href="mailto:terwilliger@lanl.gov">terwilliger@lanl.gov</a>><br>
<span style="font-weight:bold">Date: </span>Friday, 3 July 2015 18:08<br>
<span style="font-weight:bold">To: </span>William Chao <<a href="mailto:william.chao@crick.ac.uk">william.chao@crick.ac.uk</a>><br>
<span style="font-weight:bold">Cc: </span>"<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>" <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>>, "Terwilliger, Thomas Charles" <<a href="mailto:terwilliger@lanl.gov">terwilliger@lanl.gov</a>><br>
<span style="font-weight:bold">Subject: </span>RE: Optimal settings for finding NCS from density<br>
</div>
<div><br>
</div>
<div dir="ltr"><style type="text/css" id="owaParaStyle"></style>
<div style="word-wrap:break-word; color:rgb(0,0,0); font-size:14px; font-family:Calibri,sans-serif" fpstyle="1" ocsi="0">
<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">
<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Hi William,
<div><br>
</div>
<div>For find_ncs_from_density the shape of the molecule itself is not so important. What matters is if there is some local part of the molecule that is recognizable in both copies. So I would try default parameters first. I assume you did that and it didn't
give you a useful answer...so then I would do these things:</div>
<div><br>
</div>
<div>1. try many locations : <span style="font-size: 10pt;">n_center_use=20</span></div>
<div>This is the best option...it will try 20 times using density at 20 different locations to search. If you have an older version of phenix you may need to download a nightly build to do this.</div>
<div><br>
</div>
<div>2. Try varying the resolution</div>
<div><br>
</div>
<div>3. Try varying the angular spacing of the search (<span style="font-size: 10pt;">delta_phi)</span></div>
<div><br>
</div>
<div>All the best,</div>
<div>Tom T</div>
<div><br>
<div style="font-family:Times New Roman; color:#000000; font-size:16px">
<hr tabindex="-1">
<div id="divRpF417852" style="direction:ltr"><font face="Tahoma" size="2" color="#000000"><b>From:</b> CCP4 bulletin board [<a href="mailto:CCP4BB@JISCMAIL.AC.UK">CCP4BB@JISCMAIL.AC.UK</a>] on behalf of William Chao [<a href="mailto:William.Chao@CRICK.AC.UK">William.Chao@CRICK.AC.UK</a>]<br>
<b>Sent:</b> Friday, July 03, 2015 10:24 AM<br>
<b>To:</b> <a href="mailto:CCP4BB@JISCMAIL.AC.UK">CCP4BB@JISCMAIL.AC.UK</a><br>
<b>Subject:</b> [ccp4bb] Optimal settings for finding NCS from density<br>
</font><br>
</div>
<div></div>
<div>
<div>Dear all,</div>
<div><br>
</div>
<div>What would be the best settings to look for NCS using phenix.find_ncs_from_density on an elongated (~150A) molecule? No coordinate is available unfortunately and there should be 2 copies in a P21 space group.</div>
<div><br>
</div>
<div>Many thanks in advance!</div>
<div><br>
</div>
<div>William</div>
<div>---</div>
<p style="color:rgb(112,113,115); font-family:'Trebuchet MS','Lucida Grande'; font-style:italic; font-size:10pt">
The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 215 Euston Road, London NW1 2BE.
</p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</span>
<p style="color:rgb(112,113,115);font-family: 'Trebuchet MS', 'Lucida Grande'; font-style: italic; font-size: 10pt;">
The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 215 Euston Road, London NW1 2BE.
</p>
</body>
</html>