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<div class="moz-cite-prefix">Thanks Pavel.<br>
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Abhinav </font>
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JCSG@SSRL, SLAC <br>
(650) 926-2992 <br>
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On 08/01/2012 12:50 PM, Pavel Afonine wrote:<br>
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<blockquote cite="mid:50198898.8090207@lbl.gov" type="cite">
<pre wrap="">Hi Abhinav,
</pre>
<blockquote type="cite">
<pre wrap="">The default minimum distance that a water gets placed near
protein/water atoms using 'ordered_solvent=true' option in
phenix.refine is 1.8.
Isn't this too close?
</pre>
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<pre wrap="">
Possibly. Though we pick waters into Fourier maps (which are different
from exact electron density distribution due to finite number of Fourier
coefficients = finite resolution) so the peaks may be shifted. The
smaller threshold distance is meant to account for this. As a side
effect it increases the risk of interpreting bad pick. How big this risk
(given all other peak selection criteria) - that I don't know: can take
a few days to investigate.
Also, it's a parameter - you can change it to match your taste.
</pre>
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<pre wrap="">Also, if two waters can't get placed in the density due to distance
criterion, can phenix place one water in dual conformations in that
density?
</pre>
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<pre wrap="">
Currently not, but would be good to have, I agree.
Pavel
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