<!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 Andy,<br>
<br>
<blockquote
cite="mid:39AF62D77705A347AEAE4226BC2DFF43147AB5B496@MBXC.exchange.cornell.edu"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<meta name="Generator" content="Microsoft Word 12 (filtered
medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Consolas;
panose-1:2 11 6 9 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";
color:black;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
pre
{mso-style-priority:99;
mso-style-link:"HTML Preformatted Char";
margin:0in;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";
color:black;}
span.HTMLPreformattedChar
{mso-style-name:"HTML Preformatted Char";
mso-style-priority:99;
mso-style-link:"HTML Preformatted";
font-family:Consolas;
color:black;}
span.apple-style-span
{mso-style-name:apple-style-span;}
span.EmailStyle20
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<div class="WordSection1"><span style="font-size: 11pt;
font-family: "Calibri","sans-serif";
color: rgb(31, 73, 125);"> I’m looking for a
description of how the “secondary_map_and_map_cc_filter”
parameter operates. The default is set to be a
2mFobs-DFmodel, and I assume it’s calculating a correlation
coefficient as the basis for filtering waters that are present
in the mFobs-DFmodel maps (i.e. primary map) but not in the
2mFo-DFc map. However, I’d like to confirm my assumption is
true and also learn whether the cutoff value for whether or
not a putative water molecule gets culled can be changed. I
haven’t found the information in the online documentation or
the Phenixbb archives. </span></div>
</blockquote>
<br>
yes, the second map, 2mFo-DFc is used to computed map CC
(poor_cc_threshold<span style="color: blue;"></span>). Also, it is
used to filter waters by the absolute value of the 2mFo-DFc map
computed at water oxygen center (poor_map_value_threshold).<br>
<br>
The default values are good for most of cases (I hope).<br>
<br>
Pavel.<br>
<br>
<br>
</body>
</html>