[phenixbb] Scattering from riding hydrogens?

Pavel Afonine pafonine at lbl.gov
Mon Nov 14 14:37:38 PST 2011

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).


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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