Dear Mark,
if these really are riding hydrogens, they should not be present in your PDB
file from phenix or refmac5 - at least in refmac5 you have the option not to
include the riding hydrogens in the output. That remedies your problem.
If you were using shelxl for refinement, there would be not option not to
include them in the output - in that case you could simply ignore them in coot
(by not displaying them), because the actual coordinates are ignored by shelxl
as long as the AFIX command is present and correct.
Tim
On Wed, Mar 16, 2011 at 02:45:13PM -0400, 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.
>
> Mark
> --
--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
phone: +49 (0)551 39 22149
GPG Key ID = A46BEE1A
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