Crystallography‎ > ‎Refinement‎ > ‎

Phenix


Input labels when "multiple equally suitable arrays of observed xray data found"

scaling.input.xray_data.obs_labels=
refinement.input.xray_data.labels=

after = use for example:
IMEAN,SIGIMEAN

or:
F, SIGFP


Maps (compute)


phenix.refine model.pdb data.hkl strategy=none main.number_of_macro_cycles=1

Parameters for a typical phenix.refine job


phenix.refine data.hkl model.pdb refine.adp.tls="chain A" \ 
refine.adp.tls="chain B" 
main.number_of_macro_cycles=4 \ 
xray_data.high_resolution=2.5 
wxc_scale=3 
wxu_scale=5 \ 
output.prefix=my_best_model \
strategy=tls+individual_sites+individual_adp \ 
simulated_annealing.start_temperature=5000 \
twin_law=k,h,-l

R-factor from deposited PDB


phenix.model_vs_data

Rms deviations 

To calculate rms deviations between two sets of coordinates that are originating from two PDB files:

phenix.superpose_pdbs file1.pdb file2.pdb

will superpose two sets of coordinates and print RMS deviations before and after superposition:

RMSD between fixed and moving atoms (start): 0.575
RMSD between fixed and moving atoms (final): 0.563

Sequence (extract from pdb)


phenix.print_sequence model.pdb

Table1 (extract information for) 


phenix.model_vs_data model.pdb reflection.mtz