[phenixbb] geometry in phenix.refine
Pavel Afonine
PAfonine at lbl.gov
Thu Feb 21 14:57:48 PST 2008
>> the difference is most likely because of H atoms, indeed (deferent
>> "ideal" values used by phenix.reduce and Monomer Library that is
>> used in
>> phenix.refine). In the next version of phenix.refine the geometry of H
>> atoms will always be regularized (unless free refinement is
>> requested at
>> ultra-high resolution), so it will be always consistent with the
>> Monomer
>> Library definitions.
>>
>
> Why not just the same value to start with?
>
Because some programs tend to distort hydrogen's geometry completely
(for example, COOT after doing local RS fit) so you start refinement
with nonsense H positions. And since in riding model X-H distances are
fixed you keep having wrong values. Many users reported this problem.
Pavel.
I
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