<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Hi Dialing,<br>
<br>
<blockquote
cite="mid:1321849199.89118.YahooMailNeo@web121714.mail.ne1.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: times new roman,new york,times,serif;
font-size: 12pt;">
<div style="font-family: times new roman,new york,times,serif;
font-size: 12pt;">
<div style="font-family: times new roman,new york,times,serif;
font-size: 12pt;">
<div style="right: auto;" id="yiv104674267">
<div style="right: auto;">
<blockquote style="right: auto;" type="cite">
<div style="right: auto;"
class="yiv104674267gmail_quote">
The default value of the starting tempera<var
id="yui-ie-cursor"></var>ture of Phenix refine
simulated annealing is 5000. At this temperature all
the protein structure will be destroyed.</div>
</blockquote>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<br>
it depends on parametrization. In phenix.refine you can use
10000-15000K and the model will not explode. Simply try it - that's
the best way to find out.<br>
<br>
<blockquote
cite="mid:1321849199.89118.YahooMailNeo@web121714.mail.ne1.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: times new roman,new york,times,serif;
font-size: 12pt;">
<div style="font-family: times new roman,new york,times,serif;
font-size: 12pt;">
<div style="font-family: times new roman,new york,times,serif;
font-size: 12pt;">
<div style="right: auto;" id="yiv104674267">
<div style="right: auto;">
<blockquote style="right: auto;" type="cite">
<div style="right: auto;"
class="yiv104674267gmail_quote">
<div style="right: auto;">Will you please explain
why we start the simulated annealing at 5000? </div>
</div>
</blockquote>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<br>
As with ~500-600 parameters in phenix.refine, the defaults are set
to the values that are "good in average, most of the time". If you
want to do aggressive SA refinement (eg.: Korostelev et al, PNAS
2009), then 5000K is too low, and 10000 may be way better. If you
want to get multi-start SA averaged map for a 1A resolution model,
then 5000 is too high, and 500-1000K is a better start.<br>
<br>
Pavel<br>
<br>
</body>
</html>