<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Peter,<div><br></div><div>There's a new Phenix GUI for Phaser that's under development, and when that 's finished you'll be able to run all possible Phaser jobs from the GUI. In the meantime, it's probably easiest to use command scripts. </div><div><br></div><div>A number of the practical issues of using EM maps are the same as using density cut out from an X-ray</div><div>electron density map, e.g. making sure the cell is big enough (so that the interpolation of the transform of the density works) and knowing where the centre of the object is. These are discussed on our web page, at <a href="http://www-structmed.cimr.cam.ac.uk/phaser/density_as_model.html">http://www-structmed.cimr.cam.ac.uk/phaser/density_as_model.html</a>.</div><div><br></div><div>Assuming that your large P1 cell is at least 2.5 times as big in all directions as the small cell, then your approach sounds reasonable.</div><div><br></div><div>For EM maps, there's an extra issue. It seems that there is generally an uncertainty of several percent in the magnification factor, so you will want to adjust that up and down -- steps of 0.5% would probably be fine enough. The easiest way to do this is to scale the cell dimensions in the MTZ file containing the structure factors derived from the EM map. You could do that easily in sftools, and then run searches with all the scaled MTZ files.</div><div><br></div><div>Good luck! I'd be interested in hearing how you get on, and don't hesitate to ask any further questions.</div><div><br></div><div>Best wishes,</div><div><br></div><div>Randy Read</div><div><br><div><div>On 23 Jul 2009, at 16:08, Peter Grey wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Dear benevolent experts,<br><br>I am trying to use Phaser for molecular replacement with EM-map as a model.<br>The EM map, originally in a small P1 cell, was put in large P1 using CCP4's MAPROT and a mask that was defined by a certain cut-off level. <br> Could you please advise me how to derive the <font face="Courier New, Courier, mono"><font color="#0000ff">EXTEnt</font> and <font color="#0000ff">CENTre</font></font> parameters needed for ENSEmble building ?<br>Does the simple way of giving the size of the original P1 as the EXTEnt and its centre as CENTre sound reasonable ?<br> <br>I would be grateful for any advice and comments,<br><br>Peter.<br><br> _______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://www.phenix-online.org/mailman/listinfo/phenixbb<br></blockquote></div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div>------</div><div>Randy J. Read</div><div>Department of Haematology, University of Cambridge</div><div>Cambridge Institute for Medical Research Tel: + 44 1223 336500</div><div>Wellcome Trust/MRC Building Fax: + 44 1223 336827</div><div>Hills Road E-mail: <a href="mailto:rjr27@cam.ac.uk">rjr27@cam.ac.uk</a></div><div>Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk</div></span></div></span> </div><br></div></body></html>