Hello Anna, if you want to refine H atoms (coordinates, B-factors) individually then use hydrogens.refine=individual Note, this will only make sense if data resolution is high enough, say better than 0.9-0.7A or so. You can disable 'Fit rotatable H or D' by using hydrogens.real_space_optimize_x_h_orientation=False Note, this has nothing to do with torsion angle dynamics. Pavel On 1/7/15 8:26 AM, Anna Makal wrote:

Hi,

I would like to ask for advice concerning 'Fit rotatable H or D' refinement stage in phenix.refine.

I am attempting to run unconstrained refinement on a certain high-resolution protein dataset: just XYZ and ADPs refinement for every single atom in the structure, with hydrogen atoms treated with individual approach.

It turns out that when I set more then 3 macrocycles, the 'Fit rotatable H or D' refinement stage is activated in every macrocycle prior to 'XYZ individual' refinement stage. I am using version 1.9, release 1692 for windows. When I last worked with PHENIX, it was distribution 1342, and I am positive I have not come across such refinement stage. It seems that TARDY is involved at that stage.

As I specifically do not want to introduce any kind of torsion angle dynamics in my current refinement, I would like to ask, what command/option shall I use to deactivate this stage of H-atom fitting in my refinement?

With regards,

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