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<div class="moz-cite-prefix">Hi Jose,<br>
<br>
kick-map related parameters in ordered_solvent scope of parameters
are leftover that I forgot to remove back when I was working on
it. So you can see it as a minor bug. And yes, you can't change
them. Sorry about delayed answer (I saw the email on phenixbb but
did note reply immediately and it sank in the flood of other
stuff).<br>
<br>
Pavel<br>
<br>
On 12/10/12 11:04 AM, Jose M de Pereda wrote:<br>
</div>
<blockquote cite="mid:50C63223.3040009@usal.es" type="cite">
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Dear Phenix Team,<br>
<br>
Last week I sent an e-mail to the phenixbb regarding the
parameters that control de generation of averaged kick maps.
Unfortunately, I have not received any feedback from the
community.<br>
<div class="moz-forward-container"><br>
I wonder if you could give me some help on this subject.<br>
<br>
Probably, the calculation of averaged kick maps is already very
well optimized in phenix.refine and phenix.maps. Yet, I am still
curious.<br>
<br>
Thanks a lot in advance<br>
All the best<br>
<br>
�� Jose<br>
<br>
<br>
-------- Original Message --------
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Subject:
</th>
<td>[phenixbb] parameters for averaged kick maps</td>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Date:
</th>
<td>Tue, 04 Dec 2012 10:12:46 +0100</td>
</tr>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">From:
</th>
<td>Jose M de Pereda <a moz-do-not-send="true"
class="moz-txt-link-rfc2396E"
href="mailto:pereda@usal.es"><pereda@usal.es></a></td>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Reply-To:
</th>
<td>PHENIX user mailing list <a moz-do-not-send="true"
class="moz-txt-link-rfc2396E"
href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a></td>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">To: </th>
<td>PHENIX user mailing list <a moz-do-not-send="true"
class="moz-txt-link-rfc2396E"
href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a></td>
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<br>
<br>
<pre>Dear all,
I would like to compare averaged kick maps obtained using different �kick sizes�.
Is it possible to define the kick size and the number of kicks in phenix.refine and/or phenix.maps?
In phenix.refine, the �ordered_solvent� section has keywords to control the generation of kick maps:
kick_map {
kick_size = 0.5
number_of_kicks = 100
}
But, it seems to me that these can not be used during the generation of maps or maps� coefficients.
Related with this issue, does phenix.refine always use the same kick
size or does it adjust it ad hoc (e.g. based on ML error estimates)?
Thanks a lot,
Jose
</pre>
<br>
<br>
<pre class="moz-signature" cols="72">--
------------------------------------------------------------
Jose M de Pereda, PhD
Instituto de Biologia Molecular y Celular del Cancer (IBMCC)
Spanish National Research Council - University of Salamanca
Campus Unamuno s/n
E-37007 Salamanca, Spain
Phone: +34-923-294817
Fax: +34-923-294795
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://xtal.cicancer.org/">http://xtal.cicancer.org/</a>
------------------------------------------------------------</pre>
<br>
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