[phenixbb] rotamer outlier reduction by coot

Nathaniel Echols nechols at lbl.gov
Mon Dec 5 10:54:11 PST 2011

On Mon, Dec 5, 2011 at 2:48 AM, Dialing Pretty <hdc123hdc123 at yahoo.com> wrote:
> After select a rotamer and acception, I find some hydrogens in the outlier
> rotamer will be isolated from the rotamer, and the rotamer will have new
> hydrogens at its new position. Is any influence by further refine by phenix?

This sounds like the classic "exploding hydrogens" problem.  You
should update to the latest version of Coot (possibly one of the
nightly builds), which has the new hydrogen definitions which are more
compatible with Phenix.

> After I save the new PDB file by coot after I selected the new rotamers to
> replace the outlier rotamers, I did a Phenix refine. There is an error
> message at the start says "Number of atoms with unknown nonbonded energy
> typensymbol: 2228". What does it mean and how to solve the problem?

We can't answer this accurately without knowing more about what atoms
it complains about.  Normally this indicates that restraints are
missing, but it's possible this is related to the problem with
hydrogen atoms.


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