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Increase the number of allowed clashes in Phaser, and examine the
resulting solution in Coot to see if (1) electron density is
reasonable, and (2) molecular packing is reasonable. It is very
common that a search model has some surface loops in alternate
locations compared to your target that generate the clashes. These
loops can be deleted in your search model if desired, or, if you
have sufficient data quality, you can try using the initial phases
obtained to autobuild the target.<br>
<br>
_______________________________________<br>
Roger S. Rowlett<br>
Gordon & Dorothy Kline Professor<br>
Department of Chemistry<br>
Colgate University<br>
13 Oak Drive<br>
Hamilton, NY 13346<br>
<br>
tel: (315)-228-7245<br>
ofc: (315)-228-7395<br>
fax: (315)-228-7935<br>
email: <a class="moz-txt-link-abbreviated" href="mailto:rrowlett@colgate.edu">rrowlett@colgate.edu</a><br>
<br>
<div class="moz-cite-prefix">On 7/2/2015 8:55 AM, Almudena Ponce
Salvatierra wrote:<br>
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<div>Hi everyone, <br>
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I am running Phaser (from Phenix) and while checking
the .log file (it is still running) I realize that it
found some solutions with a TFZ score over 7, but it
won't take them I guess because the number of clashes
is higher than allowed (>12, I guess they're not so
many either).<br>
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My models are poor and for so I would like to check
these solutions that for now Phaser will reject. However
in the input I don't want to increase the allowed number
of clashes because this will then affect all the other
solutions and this will take forever... <br>
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So my question is: can I tell phaser somehow to write
down/save the solutions for which the TFZ score will be
higher than 7? Even though the clashes<br>
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Thanks a lot in advance<br>
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All the best, <br>
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Almu<br clear="all">
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-- <br>
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<div dir="ltr">Almudena Ponce-Salvatierra
<div>Macromolecular crystallography and
Nucleic acid chemistry</div>
<div>Max Planck Institute for Biophysical
Chemistry</div>
<div>Am Fassberg 11 37077 G�ttingen</div>
<div>Germany</div>
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