On Sun, Apr 11, 2010 at 4:20 PM, Pascal Egea <span dir="ltr">&lt;<a href="mailto:pascal@msg.ucsf.edu">pascal@msg.ucsf.edu</a>&gt;</span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div>I am using the latest Phenix version (356) with the GUI and I would like to see the effect of optimization of the mask parameters.</div><div>How can I do this with the GUI in the latest version ( I am also using the secondary structure restraints)</div>

<div>in the manual I can see the command line</div><div>phenix.refine model.pdb data.mtz optimize_mask=true however I don&#39;t see such option in the GUI (I can&#39;t see it  listed  in the whole list of commands)<br></div>
</blockquote><div><br></div><div>I may have picked a poor caption for it.  It is labeled &quot;Refine mask parameters&quot; and it will be in the &quot;Miscellaneous settings&quot; dialog, but you need to set the user level to &quot;advanced&quot; to see it.  Opening Settings-&gt;Search parameters and searching for &quot;optimize&quot; also brings it up.  It is already on by default; apparently there is a slower protocol &quot;optimize_mask_thorough&quot; which is still False, but Pavel will have to explain what this means.</div>
<div><br></div><div>-Nat</div></div>