<div dir="ltr"><div><div>Dear Rex,<br><br></div>Here (<a href="http://www.phenix-online.org/documentation/reference/refinement.html#refinement-of-coordinates">http://www.phenix-online.org/documentation/reference/refinement.html#refinement-of-coordinates</a>) is some documentation for the command line version.<br></div>Basically <br><br><ol class=""><li><p class="">One rigid body group per chain (default behavior):</p>
<pre class="">% phenix.refine data.hkl model.pdb strategy=rigid_body
</pre>
</li><li><p class="">Multiple groups (requires a basic knowledge of the PHENIX atom
selection language, see below):</p>
<pre class="">% phenix.refine data.hkl model.pdb strategy=rigid_body \
sites.rigid_body="chain A" sites.rigid_body="chain B"
</pre>
<p>This will refine the chain A and chain B as two rigid bodies. The rest of
the model will be kept fixed.</p>
</li><li><p class="">If there are many rigid groups to define, typing them in the command line
may be a tedious exercise. In this case a better alternative is to create a
parameter file <tt class="">rigid_body_selections</tt> containing the following lines:</p>
<pre class="">refinement.refine.sites {
rigid_body = chain A
rigid_body = chain B
}
</pre>
<p>The command line will then be:</p>
<pre class="">% phenix.refine data.hkl model.pdb strategy=rigid_body \
rigid_body_selections.params
</pre>
<p>Files like this can be created, for example, by copy-and-paste from
the complete list of parameters (phenix.refine --show-defaults=all).</p></li></ol><p><br></p><p>And here (<a href="http://www.phenix-online.org/documentation/reference/refine_gui.html#refinement-settings">http://www.phenix-online.org/documentation/reference/refine_gui.html#refinement-settings</a>) is some documentation for the GUI.</p><p>So "Modify selections for" (choose Rigid body from the dropdown menu) will let you define the selections, either with text (e.g. "chain A and resseq 1:100"), or by using the "View/Pick" GUI, where you can select atoms.</p><p><br></p><p>Hope this helps!<br></p><p>Best regards,</p><p>Folmer<br></p><br><br><br><br><br><br></div><div class="gmail_extra"><br><div class="gmail_quote">2015-11-11 12:38 GMT+01:00 Rex Palmer <span dir="ltr"><<a href="mailto:rex.palmer@btinternet.com" target="_blank">rex.palmer@btinternet.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="color:#000;background-color:#fff;font-family:times new roman,new york,times,serif;font-size:16px"><div dir="ltr"><span>We have 1.5A resolution data for a heterodimeric protein with linked A and B chains. Phenix MR has produced a promising solution. We would now like to perform an initial refinement using Phenix with the A chain and B chain individually treated as rigid bodies.</span></div><div dir="ltr"><span>Is this possible with Phenix and if so how? </span></div><span class="HOEnZb"><font color="#888888"><div></div><div> </div><div>Rex Palmer<br><a href="http://www.bbk.ac.uk/biology/our-staff/emeritus-staff" target="_blank">http://www.bbk.ac.uk/biology/our-staff/emeritus-staff</a><br><a href="http://www.springer.com/978-1-4614-3954-7" target="_blank">http://www.springer.com/978-1-4614-3954-7</a></div></font></span></div></div><br>_______________________________________________<br>
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