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

Simon Kolstoe s.kolstoe at ucl.ac.uk
Thu Sep 16 08:49:53 PDT 2010

So just to clarify further -  if i am having problems with the final  
geometry of a model (eg clashscore as reported by molprobity), is it  
an appropriate trick to add hydrogens and then refine in phenix.refine  
using the riding hydrogens option, or does this not really change  


On 16 Sep 2010, at 14:26, Pavel Afonine wrote:

> 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!
> Pavel.
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