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<p>Thanks, it worked but not the way I expected.</p>
<p>It definitely found problematic regions in the model but moved it not correctly. Should I adjust the parameters of SA? (I did torsion SA with a default settings and before MR and rigid-body by domains)</p>
<p>I am still improving the model since it has some clashes. There are also disordered regions and tiny movements of big domains. Is it neccessary to adjust the model as much as possible with rigid-body before SA?</p>
<p><br>
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<p>Irina<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><b>��:</b> Pavel Afonine <pafonine@lbl.gov><br>
<b>����������:</b> 30 ������ 2015 �. 15:30<br>
<b>����:</b> Irina PROKHOROVA; phenixbb@phenix-online.org<br>
<b>����:</b> Re: [phenixbb] SA</font>
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<div>Hi Irina,<br>
<br>
SA scope of parameters needs "refinement." prefix:<br>
<br>
refinement.simulated_annealing {<br>
mode = every_macro_cycle second_and_before_last once *first first_half<br>
}<br>
<br>
Let me know if it doesn't do it!<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 4/30/15 2:20 AM, Irina PROKHOROVA wrote:<br>
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<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Hello,<br>
<br>
I am trying to run coordinate refinement 5 cycles with first cycle of simulated annealing (torsion) via command line. Here is a part of my params file that I adapted from my colleges:<br>
<br>
refinement.main {<br>
number_of_macro_cycles = 5<br>
target = *ml mlhl ml_sad ls<br>
simulated_annealing_torsion = True<br>
}<br>
<br>
simulated_annealing {<br>
mode = every_macro_cycle second_and_before_last once *first first_half<br>
}<br>
<br>
refinement.refine {<br>
strategy = *individual_sites individual_sites_real_space rigid_body \<br>
individual_adp group_adp tls occupancies group_anomalous<br>
sites {<br>
individual = segid *A<br>
individual = segid *B<br>
}<br>
<br>
<br>
<br>
As a result I get the Error
<blockquote type="cite">Unused parameter definitions:<br>
simulated_annealing.mode (file "refine.params", line 26)<br>
</blockquote>
Could you help me with the syntax, please. Should I include sites definition for simulated annealing?<br>
<br>
Irina<br>
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<br>
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