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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb