[phenixbb] Scattering from riding hydrogens?

Damian Ekiert dcekiert at scripps.edu
Mon Nov 14 16:12:27 PST 2011


Thanks for your response.  This question was motivated by discussions of whether or not to deposit riding hydrogens in the PDB, so perhaps I can ask a more general question.

As I understand things, the positions of the riding hydrogens (from an input PDB file) would would be incorporated into the calculation of Fcalc (I guess automatically now and before when contribute_to_f_calc = True).  If this is correct, then removing riding hydrogens before deposition seems very problematic, as they were effectively used in the calculation of R/R-free, etc.  However, if the contribution of hydrogens is more abstract (e.g., the riding hydrogens are not used in the calculation, but the presence of hydrogens in the protein in the crystal are accounted for in some other way), leaving them out of the deposition is somewhat less of a problem (setting aside for a moment any other reason for depositing them, such as the difficulties in re-hydrogenating the protein later on, etc.).

So in the context of Phenix and Fcalc, do the positions of the riding hydrogens matter?  And if they don't, does this mean that when an input model has zero hydrogens, Phenix is still trying in some way to account for the unmodeled/invisible hydrogens that we know are in there?



On Nov 14, 2011, at 2:37 PM, Pavel Afonine wrote:

> Hi Damian,
> the contribution of H atoms to the total model structure factor Fmodel 
> is refined in recent PHENIX versions, so these two parameters are not 
> necessary and in fact are leftovers that I forgot to remove when 
> switching to the new code. I will do it for the newer versions. Sorry 
> for the confusion.
> So, if you have H atoms in your input PDB file then you don't have to 
> change any parameter. If you don't want to use H atoms then simply make 
> sure they are not present in input PDB file.
> Current implementation of handling of hydrogen atoms in refinement is 
> partially inspired by
> J. Appl. Cryst. (2010). 43, 1100-1107
> and thoroughly tested by various numerical tests (that we should 
> probably publish in one of CCN issues).
> Pavel
> On 11/14/11 2:21 PM, Damian Ekiert wrote:
>> Hello,
>> I have a question regarding two parameters and how they affect riding hydrogens.
>>     contribute_to_f_calc = True
>>     high_resolution_limit_to_include_scattering_from_h = 1.6
>> At lower resolution, setting contribute_to_f_calc = false is frequently helpful when using riding hydrogens and has been discussed before.  But what is high_resolution_limit_to_include_scattering_from_h = 1.6 doing?  If scattering from hydrogens is only included at higher than 1.6A resolution, it would seem like contribute_to_f_calc = True/False would not have any effect at say, 3.5A, but comparing identical refinement runs with contribute_to_f_calc = True or contribute_to_f_calc = False clearly gives different results.  Can hydrogens contribute to Fcalc in a way aside from their scattering, or is their contribution accounted for independent of the position of the riding hydrogen (e.g., additional scattering term added to the associated heavy atom)?  I think I am misunderstanding what these two parameters are doing and would appreciate some clarification.
>> Thanks,
>> Damian Ekiert
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