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Hi Irina,<br>
<br>
what's the resolution?<br>
<br>
Try Cartesian SA instead. Also you can calculate 2mFo-DFc map and
run real-space refinement - it has large convergence radius.<br>
<br>
If the model is more or less in place rigid body refinement may not
be necessary. <br>
<br>
Pavel<br>
<br>
<br>
<div class="moz-cite-prefix">On 5/1/15 3:29 PM, Irina PROKHOROVA
wrote:<br>
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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>
</p>
<p>Irina<br>
</p>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
color="#000000" face="Calibri, sans-serif"><b>От:</b> Pavel
Afonine <a class="moz-txt-link-rfc2396E" href="mailto:pafonine@lbl.gov"><pafonine@lbl.gov></a><br>
<b>Отправлено:</b> 30 апреля 2015 г. 15:30<br>
<b>Кому:</b> Irina PROKHOROVA; <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<b>Тема:</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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