<html><head><title>autoSHARP [Sushi 3.4.0] run (Project MIRAS28, User brent)</title></head>
<body bgcolor="#fffaf0" text="#000000" alink="#ff0000" link="#0000c0" vlink="#800080">
<center>
<h1><u>autoSHARP</u> run<br>(Project MIRAS28, User brent)<br> [Sushi 3.4.0]</h1>
(start: Thu Jan 4 15:24:49 EST 2007)
</center>
<hr size="4" noshade="noshade">
<pre>
Copyright (C) 1999-2005 <b>Clemens Vonrhein</b> and the
Buster Development Group.
All rights reserved.
<u>Use of this program implies acceptance of conditions</u>
<u>given in the SHARP licence agreement.</u>
(please reload this document from time to time!)
<u><b>Please cite:</b></u>
Vonrhein, C, Blanc, E., Roversi, P and Bricogne,
G. (2005). Automated structure solution with autoSHARP. In
"Crystallographic Methods", S Doublie, Ed., Humana Press,
Totowa, NJ, submitted.
</pre>
<b>Title : </b><u>running autoSHARP on MIRAS data using S184C and S193C derivatives</u><br><br>
<!-- insert .HtmlMenu here-->
<!--===================================================================-->
<hr size="4" noshade="noshade">
<a name="SECTION1">
<h1>1. Preparation</h1></a>
<!------------------------------------------------------------------->
<hr noshade="noshade">
<a name="SECTION1.1">
<h3> 1.1 Checking supplied information</h3></a>
<a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/CHECKS/LISTautoSHARP.html">(details)</a>
<a href="http://maya:8080/manual/autoSHARP3.html#checks" target="ManualWindow" onclick="ManualWindow=window.open('/manual/autoSHARP3.html#checks','ManualWindow');ManualWindow.focus();return false;">(explanation)</a>
[<a href="#CCP4">2</a>, <a href="#MerrittXXXX">3</a>]
<small>(2 seconds)</small>
<br>
<table>
<tbody><tr valign="top">
<td> </td>
<td>
<b><font color="#ee6600">2 warnings :</font></b>
<ul>
<li><a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/CHECKS/LISTautoSHARP.html#WarningNum1">No # of residues</a>
</li><li><a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/CHECKS/LISTautoSHARP.html#WarningNum2">CCP4 version unsupported</a>
</li></ul>
</td>
<td> </td>
<td>
<b><font color="#000088">2 important notes (out of ~ 14) :</font></b>
<ul>
<li><a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/CHECKS/LISTautoSHARP.html#NoteNum1">Speed/Accuracy rate set to 5</a>
</li><li><a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/CHECKS/LISTautoSHARP.html#NoteNum4">116 amino acid residues in sequence</a>
</li></ul>
</td>
</tr>
</tbody></table>
<!------------------------------------------------------------------->
<hr noshade="noshade">
<a name="SECTION1.2">
<h3> 1.2 Converting files</h3></a>
<a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/CONVERT/LISTautoSHARP.html">(details)</a>
<a href="http://maya:8080/manual/autoSHARP3.html#convert" target="ManualWindow" onclick="ManualWindow=window.open('/manual/autoSHARP3.html#convert','ManualWindow');ManualWindow.focus();return false;">(explanation)</a>
<small>(8 seconds)</small>
<!------------------------------------------------------------------->
<hr noshade="noshade">
<a name="SECTION1.3">
<h3> 1.3 Extracting additional information</h3></a>
<a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/GETINFO/LISTautoSHARP.html">(details)</a>
<a href="http://maya:8080/manual/autoSHARP3.html#getinfo" target="ManualWindow" onclick="ManualWindow=window.open('/manual/autoSHARP3.html#getinfo','ManualWindow');ManualWindow.focus();return false;">(explanation)</a>
[<a href="#Wilson1942">4</a>, <a href="#Matthews1968">5</a>, <a href="#Kantardjieff2003">6</a>]
<small>(10 seconds)</small>
<br>
<table>
<tbody><tr valign="top">
<td> </td>
<td>
<b><font color="#000088">2 important notes (out of ~ 29) :</font></b>
<ul>
<li><a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/GETINFO/LISTautoSHARP.html#NoteNum23">most likely 2 molecules and solvent fraction of 0.553</a>
</li><li><a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/GETINFO/LISTautoSHARP.html#NoteNum26">overall resolution = 30.00 2.80 Å</a>
</li></ul>
</td>
</tr>
</tbody></table>
<!------------------------------------------------------------------->
<hr noshade="noshade">
<a name="SECTION1.4">
<h3> 1.4 Collecting and analysing all data</h3></a>
<a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/COLLECT/LISTautoSHARP.html">(details)</a>
<a href="http://maya:8080/manual/autoSHARP3.html#collect" target="ManualWindow" onclick="ManualWindow=window.open('/manual/autoSHARP3.html#collect','ManualWindow');ManualWindow.focus();return false;">(explanation)</a>
<small>(24 seconds)</small>
<br>
<table>
<tbody><tr valign="top">
<td> </td>
<td>
<b><font color="#ee6600">1 warning :</font></b>
<ul>
<li><a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/COLLECT/LISTautoSHARP.html#WarningNum1">Unusual ABS(DANO)/FMID ratio for 1 reflexion (DANOS184C/FS184C)</a>
</li></ul>
</td>
<td> </td>
<td>
</td>
</tr>
</tbody></table>
<!------------------------------------------------------------------->
<hr noshade="noshade">
<a name="SECTION1.5">
<h3> 1.5 Adding test set column</h3></a>
<a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/UNIQUEIFY/LISTautoSHARP.html">(details)</a>
<a href="http://maya:8080/manual/autoSHARP3.html#uniqueify" target="ManualWindow" onclick="ManualWindow=window.open('/manual/autoSHARP3.html#uniqueify','ManualWindow');ManualWindow.focus();return false;">(explanation)</a>
[<a href="#Bruenger1992">7</a>]
<small>(11 seconds)</small>
<br>
<table>
<tbody><tr valign="top">
<td> </td>
<td>
<b><font color="#000088">3 notes :</font></b>
<ul>
<li><a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/UNIQUEIFY/LISTautoSHARP.html#NoteNum1">Low anomalous completeness of 78% (derivative 1)</a>
</li><li><a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/UNIQUEIFY/LISTautoSHARP.html#NoteNum2">Low completeness of 84% (derivative 2)</a>
</li><li><a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/UNIQUEIFY/LISTautoSHARP.html#NoteNum3">Low anomalous completeness of 79% (derivative 2)</a>
</li></ul>
</td>
</tr>
</tbody></table>
<!--===================================================================-->
<hr size="4" noshade="noshade">
<a name="SECTION2">
<h1>2. Using unscaled data</h1></a>
<!------------------------------------------------------------------->
<hr noshade="noshade">
<a name="SECTION2.1">
<h3> 2.1 Scaling of merged data</h3></a>
<a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/SCALEIT/LISTautoSHARP.html">(details)</a>
<a href="http://maya:8080/manual/autoSHARP3.html#scaleit" target="ManualWindow" onclick="ManualWindow=window.open('/manual/autoSHARP3.html#scaleit','ManualWindow');ManualWindow.focus();return false;">(explanation)</a>
<small>(20 seconds)</small>
<br>
<table>
<tbody><tr valign="top">
<td> </td>
<td>
<b><font color="#ee6600">1 warning :</font></b>
<ul>
<li><a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/SCALEIT/LISTautoSHARP.html#WarningNum1">serious differences between datasets</a>
</li></ul>
</td>
<td> </td>
<td>
</td>
</tr>
</tbody></table>
<!------------------------------------------------------------------->
<hr noshade="noshade">
<a name="SECTION2.2">
<h3> 2.2 Additional analysis (NCS, sequence ...)</h3></a>
<a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/ANALYSE/LISTautoSHARP.html">(details)</a>
<a href="http://maya:8080/manual/autoSHARP3.html#analyse" target="ManualWindow" onclick="ManualWindow=window.open('/manual/autoSHARP3.html#analyse','ManualWindow');ManualWindow.focus();return false;">(explanation)</a>
[<a href="#RossmannBlow1962">8</a>, <a href="#Epp1971">9</a>]
<small>(1 minute 7 seconds)</small>
<!--===================================================================-->
<hr size="4" noshade="noshade">
<a name="SECTION3">
<h1>3. Using merged and scaled data</h1></a>
<!------------------------------------------------------------------->
<hr noshade="noshade">
<a name="SECTION3.1">
<h3> 3.1 Finding sites</h3></a>
<a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/SHELX/LISTautoSHARP.html">(details)</a>
<a href="http://maya:8080/manual/autoSHARP3.html#shelx" target="ManualWindow" onclick="ManualWindow=window.open('/manual/autoSHARP3.html#shelx','ManualWindow');ManualWindow.focus();return false;">(explanation)</a>
[<a href="#Schneider2002">10</a>]
<small>(53 minutes 58 seconds)</small>
<br>
<table>
<tbody><tr valign="top">
<td> </td>
<td>
<b><font color="#000088">1 important note (out of ~ 30) :</font></b>
<ul>
<li><a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/SHELX/LISTautoSHARP.html#NoteNum30">trial 1 (derivative 1 SIRAS - 4 sites): CC(E) = 0.297</a>
</li></ul>
</td>
</tr>
</tbody></table>
<!--===================================================================-->
<hr size="4" noshade="noshade">
<a name="SECTION4">
<h1>4. Using list of initial sites</h1></a>
<!------------------------------------------------------------------->
<hr noshade="noshade">
<a name="SECTION4.1">
<h3> 4.1 Create a SIN file</h3></a>
<a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/MKSIN/LISTautoSHARP.html">(details)</a>
<a href="http://maya:8080/manual/autoSHARP3.html#mkSIN" target="ManualWindow" onclick="ManualWindow=window.open('/manual/autoSHARP3.html#mkSIN','ManualWindow');ManualWindow.focus();return false;">(explanation)</a>
[<a href="#BricogneVonrheinFlensburgSchiltzPaciorek2003">11</a>, <a href="#Fortelle1997">12</a>]
<small>(1 second)</small>
<!------------------------------------------------------------------->
<hr noshade="noshade">
<a name="SECTION4.2">
<h3> 4.2 Run first round of SHARP</h3></a>
<a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/SHARP/LISTautoSHARP.html">(details)</a>
<a href="http://maya:8080/manual/autoSHARP3.html#sharp" target="ManualWindow" onclick="ManualWindow=window.open('/manual/autoSHARP3.html#sharp','ManualWindow');ManualWindow.focus();return false;">(explanation)</a>
[<a href="#Fortelle1997">12</a>, <a href="#BricogneVonrheinFlensburgSchiltzPaciorek2003">11</a>]
<small>(6 minutes 23 seconds)</small>
<br>
<table>
<tbody><tr valign="top">
<td> </td>
<td>
<b><font color="#000088">5 notes :</font></b>
<ul>
<li><a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/SHARP/LISTautoSHARP.html#NoteNum1">figure-of-merit [acentric/centric] = 0.21405/0.28257</a>
</li><li><a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/SHARP/LISTautoSHARP.html#NoteNum2">Compound 2 : phasing power ISO [acentric/centric] = 1.203/1.041</a>
</li><li><a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/SHARP/LISTautoSHARP.html#NoteNum3">Compound 2 : phasing power ANO = 0.219</a>
</li><li><a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/SHARP/LISTautoSHARP.html#NoteNum4">17 cycles</a>
</li><li><a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/SHARP/LISTautoSHARP.html#NoteNum5">results (maps) available</a>
</li></ul>
</td>
</tr>
</tbody></table>
<!------------------------------------------------------------------->
<hr noshade="noshade">
<a name="SECTION4.3">
<h3> 4.3 Cycling between residual map interpretation and SHARP</h3></a>
<!--...................................................................-->
<a name="SECTION4.3.1">
<br><b> 4.3.1 Automatic interpretation of residual maps</b></a>
<a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/RESID/LISTautoSHARP.html">(details)</a>
<a href="http://maya:8080/manual/autoSHARP3.html#resid" target="ManualWindow" onclick="ManualWindow=window.open('/manual/autoSHARP3.html#resid','ManualWindow');ManualWindow.focus();return false;">(explanation)</a>
<small>(3 seconds)</small>
<pre> <b><font color="#cc00ee">ERROR </font></b> : (see <a href="http://maya:8080/users/brent/logfiles/MIRAS28.0/RESID/LISTautoSHARP.html">RESID/LISTautoSHARP.html</a>)
</pre>
<hr noshade="noshade"><font size="-2">
<address><a href="http://www.globalphasing.com/">Buster Development Group</a></address>
</font></body></html>