[phenixbb] Something that came up on the CCP4 list...

Pavel Afonine pafonine at lbl.gov
Thu Sep 16 06:26:11 PDT 2010

  Hi Simon,

> Could I just seek some clarification? I was under the impression that 
> phenix.refine calculated riding hydrogens by default and took these 
> into account as a restraint on the geometry?

if you want hydrogen atoms to be used in refinement (as "riding model" 
or explicit) your need to make sure the PDB file that you give to 
phenix.refine contains H atoms. That is you need to add them using 
programs like phenix.reduce or phenix.ready_set or using corresponding 
functionality in the GUI.

phenix.refine will not add them internally as part of refinement IF 
hydrogen atoms are NOT present in input PDB file.

Adding hydrogen atoms as 'riding model' does not add any refinable 
parameters, but the scattering contribution from them is included most 
of the time. This is why we do not use H atoms silently but require them 
to be in input PDB file - simply to make sure the reported statistics 
(such as R-factors) is easily reproducible.

All the best!

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