[phenixbb] fix rotamers question
petgxray at gmail.com
Wed Oct 20 06:38:25 PDT 2010
Thank you very much for these clarifications,
On Wed, Oct 20, 2010 at 6:27 AM, Jeff Headd <jjheadd at lbl.gov> wrote:
> Hi Peter,
> > - How Phenix chooses which rotamers need to be fixed ?
> Rotamers that need to be examined are identified as those that are
> either rotamer outliers as defined by the Richardson rotamer library
> or are sidechains whose real-space CC is below a user-definable
> threshold (0.9 by default).
> > - Does Phenix really re-calculate the three maps after correcting each
> > rotamer ? For very large structures this is very time-consuming and one
> > settle for calculating a new map every 10-20 residues. Perhaps this could
> > a user-controlled parameter ?
> The maps are not calculated after each rotamer correction, but instead
> are recalculated after all flagged rotamers have gone through the
> correction protocol once. Each correction is then validated against
> the recalculated maps, and those sidechains that are not an
> improvement over the original orientation are returned to the original
> orientation. This whole process is considered a macrocycle, and the
> number of macrocycles for rotamer correction may be specified by the
> > -Can you please explain how fix_rotamers works together with ncs
> > ?
> This is a great question and I'm not sure of the answer. Perhaps one
> of the other developers can weigh in on this point?
> phenixbb mailing list
> phenixbb at phenix-online.org
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