[phenixbb] fix rotamers question

Jeff Headd jjheadd at lbl.gov
Tue Oct 19 21:27:29 PDT 2010

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 can
> settle for calculating a new map every 10-20 residues. Perhaps this could be
> 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 restraints
> ?

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?


More information about the phenixbb mailing list