[phenixbb] BRU error

Nathaniel Echols nechols at lbl.gov
Fri May 20 14:52:45 PDT 2011

On Fri, May 20, 2011 at 2:42 PM, Krystle Williams McLaughlin <
krystle_w at hotmail.com> wrote:

> I have already run a BRU molecule through ReadySet and when I use the cif
> file generated from this phenix.refine will run through but when the Bromine
> atom is in the structure has a large negative density peak in the Fo-Fc map.

This could just be radiation damage - assuming the Br is in the correct
position as judged by the 2Fo-Fc map, it doesn't have anything to do with
the restraints used.  I don't know if there's a reference for this, but I
was told that brominated nucleotides are extremely sensitive to radiation
damage, much worse than SeMet.  Did you use this for phasing?

 I think it may just be a naming thing. BRU is already in the monomer
> library so I don't understand why I get an error at first also without the
> readyset cif file.

It isn't in the version of the monomer library we distribute - many of the
files in the full version are incomplete, and we don't include those.
 ReadySet does have access to the Chemical Components Database definition of
BRU, however, which it probably used to make the restraints.

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