CCP4 refmac

http://hyuan.imb.sinica.edu.tw/protocol/06_Jun_04_Lauren.ppt

Phenix

http://www.phenix-online.org/documentation/refinement.htm#anch38

Creating R-free flags

If not present in the input reflection files

% phenix.refine data.hkl model.pdb xray_data.r_free_flags.generate=True 

To change the default maximal number of test flags to be generated and the fraction: 

% phenix.refine data.hkl model.pdb xray_data.r_free_flags.generate=True xray_data.r_free_flags.fraction=0.05 xray_data.r_free_flags.max_free=500

Examples of frequently used refinement protocols

1.Starting refinement from high R-factors.

%phenix.refine data.hkl model.pdb  main.number_of_macro_cycles=10 simulated_annealing=true strategy=rigid_body+individual_sites+individual_adp

2. Depending on data resolution, refinement of individual ADP may be replaced with grouped B refinement.

% phenix.refine data.hkl model.pdb simulated_annealing=true strategy=rigid_body+individual_sites+group_adp main.number_of_macro_cycles=10 

3.Adding TLS refinement may be a good idea. 

% phenix.refine data.hkl model.pdb simulated_annealing=true strategy=rigid_body+individual_sites+individual_adp+tls main.number_of_macro_cycles=10 

4.If NCS is present - once can use it

% phenix.refine data.hkl model.pdb simulated_annealing=true strategy=rigid_body+individual_sites+individual_adp+tls main.ncs=true main.number_of_macro_cycles=10 tls_group_selections.params rigid_body_selections.params 

5.  Add water

 ordered_solvent=true 

Optimizing target weights (final run) 

phenix.refine uses automatic procedure to determine the weights between X-ray target and stereochemistry or ADP restraints. To optimize these weights (that is to find those resulting in lowest Rfree factors):

% phenix.refine data.hkl model.pdb optimize_wxc=true optimize_wxu=true 

where optimize_wxc will turn on the optimization of X-ray/stereochemistry weight and optimize_wxu will turn on the optimization of X-ray/ADP weight. Note that this could be very slow since the procedure involves a grid search over an array of weights-candidates. It could be a good idea to run this overnight for a final model tune up.

The default value for wxc_scale is 0.5. Increasing wxc_scale will make the X-ray target contribution greater and restraints looser.

The default value for wxu_scale is 1.0. Increasing wxu_scale will make the X-ray target contribution greater and therefore the B-factors restraints weaker.