<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv=Content-Type content="text/html; charset=us-ascii">
<meta name=Generator content="Microsoft Word 12 (filtered medium)">
<!--[if !mso]>
<style>
v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style>
<![endif]-->
<title>How to turn off mask optimization</title>
<style>
<!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 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;}
p
{mso-style-priority:99;
mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:12.0pt;
font-family:"Times New Roman","serif";
color:black;}
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.EmailStyle20
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page Section1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.Section1
{page:Section1;}
-->
</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]-->
</head>
<body bgcolor=white lang=EN-US link=blue vlink=purple>
<div class=Section1>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Hi Pavel,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>I’m using 1.6.1 r393. The logfile shows 10 “Mask
optimization: start’ entries in 1 macrocycle total composed of rigid_body
(2 zones), individual positions and adp refinement. <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>I’ll try the latest built tomorrow and see if that makes a
difference.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Carsten<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div style='border:none;border-left:solid blue 1.5pt;padding:0in 0in 0in 4.0pt'>
<div>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";
color:windowtext'>From:</span></b><span style='font-size:10.0pt;font-family:
"Tahoma","sans-serif";color:windowtext'> phenixbb-bounces@phenix-online.org
[mailto:phenixbb-bounces@phenix-online.org] <b>On Behalf Of </b>Pavel Afonine<br>
<b>Sent:</b> Wednesday, May 26, 2010 3:57 PM<br>
<b>To:</b> PHENIX user mailing list<br>
<b>Subject:</b> Re: [phenixbb] How to turn off mask optimization<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Hi Carsten,<br>
<br>
It should be fast, if not then it's a bug.<span style='font-family:"Calibri","sans-serif"'><br>
<br>
main.optimize_mask = False works for me, I just tried. Which version are you
using?<br>
<br>
Pavel.<br>
</span><br>
<br>
<br>
On 5/26/10 12:49 PM, Schubert, Carsten [PRDUS] wrote: <o:p></o:p></p>
<p><span style='font-family:"Calibri","sans-serif"'>Hi,</span><o:p></o:p></p>
<p><span style='font-family:"Calibri","sans-serif"'>Is there a way to turn off
the mask optimization step in 393? I tried</span> <span style='font-family:
"Calibri","sans-serif"'>‘main.optimize_mask = False’ but that does
not work.</span> <span style='font-family:"Calibri","sans-serif"'>The program
spends a substantial amount of time in repeated mask optimizations and I am
trying to shave off a couple minutes for each run...</span><o:p></o:p></p>
<p><span style='font-family:"Calibri","sans-serif"'>Cheers,</span><o:p></o:p></p>
<p> <span style='font-family:"Calibri","sans-serif"'>Carsten</span><o:p></o:p></p>
<pre><o:p> </o:p></pre><pre style='text-align:center'>
<hr size=4 width="90%" align=center>
</pre><pre><o:p> </o:p></pre><pre>_______________________________________________<o:p></o:p></pre><pre>phenixbb mailing list<o:p></o:p></pre><pre><a
href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><o:p></o:p></pre><pre><a
href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><o:p></o:p></pre><pre> <o:p></o:p></pre></div>
</div>
</body>
</html>