Thank you very much for these clarifications,<br>Peter.<br><br><br><div class="gmail_quote">On Wed, Oct 20, 2010 at 6:27 AM, Jeff Headd <span dir="ltr"><<a href="mailto:jjheadd@lbl.gov">jjheadd@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi Peter,<br>
<div class="im"><br>
> - How Phenix chooses which rotamers need to be fixed ?<br>
<br>
</div>Rotamers that need to be examined are identified as those that are<br>
either rotamer outliers as defined by the Richardson rotamer library<br>
or are sidechains whose real-space CC is below a user-definable<br>
threshold (0.9 by default).<br>
<div class="im"><br>
> - Does Phenix really re-calculate the three maps after correcting each<br>
> rotamer ? For very large structures this is very time-consuming and one can<br>
> settle for calculating a new map every 10-20 residues. Perhaps this could be<br>
> a user-controlled parameter ?<br>
<br>
</div>The maps are not calculated after each rotamer correction, but instead<br>
are recalculated after all flagged rotamers have gone through the<br>
correction protocol once. �Each correction is then validated against<br>
the recalculated maps, and those sidechains that are not an<br>
improvement over the original orientation are returned to the original<br>
orientation. �This whole process is considered a macrocycle, and the<br>
number of macrocycles for rotamer correction may be specified by the<br>
user.<br>
<div class="im"><br>
> -Can you please explain how fix_rotamers works together with ncs restraints<br>
> ?<br>
<br>
</div>This is a great question and I'm not sure of the answer. �Perhaps one<br>
of the other developers can weigh in on this point?<br>
<br>
Thanks,<br>
Jeff<br>
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</blockquote></div><br><br clear="all"><br><br>