[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.


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