Crystallographic refinement in Phenix

Phenix refinement setup:

Structure refinement in phenix can be carried out using the instructions available here. The main advantage of phenix is the ability of the interpreter to look at the input parameter files and guess what the attributes for various parameters are.

A simple refinement command can be as

phenix.refine input_from_refmac.mtz post32-coot-21.pdb simulated_annealing=true 

to carry out a refinement on a model with input mtz and pdb file using simulated annealinf refinement

In my case I have a model with NCS ( non-crystalographic symmetry) so I create a  NCS file and also set the program to use NCS restraints and refine the NCS ( Using NCS in refinement).

The ncs is specified in a ncs file called model.ncs . This file can be obtained by running the command

phenix.simple_ncs_from_pdb [pdbfilename]

refinement.ncs.restraint_group {
  reference = chain A resid 40:450
  selection = chain B and resid 40:450
  selection = chain C and resid 40:430
  selection = chain D and resid 40:450
}

The command I use is

phenix.refine  post32_number19_refmac3.mtz  post32-coot-21.pdb simulated_annealing=true model.ncs refinement.main.ncs=true --overwrite refinement.ncs.excessive_distance_limit=None >phenix_06_18_2008_1.log 

Here are the explanations for each input option

Often the program will stop and give a very detailed explanation of what went wrong. Follow the suggested input options to proceed with refnement.

For example if there are multiple possible sources of F_obs in the file you may need to specify which one to use for the refinement:

refinement.input.xray_data.<wbr/>labels="I3CplusRG_2.1.mtz:I_<wbr/>yfA6-1R(+),SIGI_yfA6-1R(+),I_<wbr/>yfA6-1R(-),SIGI_yfA6-1R(-)"