[phenixbb] advice on 'Fit rotatable H or D' refinement stage in phenix.refine

Anna Makal amakal at chem.uw.edu.pl
Wed Jan 7 08:26:30 PST 2015


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

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