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.
