[phenixbb] geometry in phenix.refine

[Pavel Afonine]

>> 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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