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<p>I know that feeling all too well!</p>
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<p>Cheers,</p>
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<p>Tristan<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> phenixbb-bounces@phenix-online.org <phenixbb-bounces@phenix-online.org> on behalf of Pavel Afonine <pafonine@lbl.gov><br>
<b>Sent:</b> Tuesday, 23 February 2016 1:47 AM<br>
<b>To:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] Feature request: multi-stage refinement protocols from the GUI?</font>
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<div>Hi Tristan,<br>
<br>
I've been willing to do this for years now. In fact it would help to automate refinement by dynamically casting refinement strategies and parameters as refinement progresses.
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<br>
Unfortunately no, this functionality is not available. It is not too difficult to implement, may be a week of focused work. The biggest problem is that the (only) way this can be done will brake a lot of backwards compatibility and will require a lot of changes
in the GUI because the main{} scope of parameters will have to become of type "multiple". So far this was the major demotivator for me to do it.<br>
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All the best,<br>
Pavel<br>
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<div class="moz-cite-prefix">On 2/22/16 15:36, Tristan Croll wrote:<br>
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<p>Hi all,</p>
<p><br>
</p>
<p>I'm personally a big fan of the Phenix GUI, in particular for its automated record keeping for different runs. One thing I really wish it had, though, is the option to define more complex refinement scenarios as a single run. An example of what I'm talking
about is the following protocol that has been working very well for me on a 3.6 � strucutre:</p>
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<p>- ~6 rounds of refinement of TLS, a single group B-factor and occupancies (the latter for a very small set of residues, mostly low-occupancy lead ions) with positions fixed</p>
<p>- ~8 rounds of TLS and individual B-factor refinement, still with positions fixed and with no further occupancy refinement</p>
<p>- ~8 rounds of TLS, B-factor and position refinement with torsion-angle restraints to the starting model</p>
<p>- ~8 rounds of position refinement with no restraints other than standard stereochemistry and metal bonds.</p>
<p><br>
</p>
<p>I know that all of this could be scripted quite easily from the command line, but it would be fantastic to be able to queue up such a protocol as a single continuous job in the GUI.</p>
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<p>Best regards,</p>
<p><br>
</p>
<p>Tristan<br>
</p>
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