On 16/03/11 18:45, Dr. Mark Mayer wrote:
> Dear all,
>
> I'm rebuilding structure refined using phenix -1.7-650 using coot
> 0.6.2-pre-1-250.
> When I use the rotamers command to select new rotamers (flagged as
> bad by molprobity) some of the riding H atoms get left behind, which
> means the file is no good for further crystallographic refinement.
> Likewise, real space refinement produces the infamous flying hydrogens problem.
>
> Any ideas on fixing this? Our current work around is to remove H and
> then run reduce again prior to refinement in phenix.
>
>
This is not a Coot problem. There is a mismatch between the model and
the dictionary (presumably version 3.x and 2.3).
The dictionary needs to be upgraded to 3.x - it is not hard work but
needs to be done. I have scheduled it for 0.7 if it is not done before
I do it - for standard protein residues, RNA and DNA at least.
You are using the approved work-around.
Paul.
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