[phenixbb] question on bad geometry

Jeff Headd jjheadd at lbl.gov
Wed Sep 1 11:25:36 PDT 2010

Hi Fengyun,

On Wed, Sep 1, 2010 at 11:12 AM,  <fn1 at rice.edu> wrote:
> I am now checking the model manually. With the "rotamer analysis" in coot,
> the plot shows that most of the rotamer outliers are Leu. Is this the common
> case that Leu appears as the rotamer outlier most often?

Yes, Leu sidechains are often misfit.  It's very easy at medium
resolution to fit a Leu sidechain ~180 degrees backward, which is
almost always an unfavorable conformation.  Flipping them back around
should arrive at a highly populated, favorable conformation.  This
problem also effects Thr and Val sidechains, and Ile at times, too.

You can read more about this here:

Coot is very good at fixing these errors with the 'autofit best
rotamer' tool, and most should also be fixed with the PHENIX 'fix
rotamers' tool.


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