[phenixbb] strategy suggestion ???

ChenTiantian chentiantian2010 at gmail.com
Mon May 30 18:31:51 PDT 2011

I just started learning crystallography months ago, and the software I used
most is XDS, HKL2000, phenix and coot.
Now I am working on a series of datasets-----the same target protein with
various ligands. The following is my refinement workflow:
1, Processing data with XDS (or HKL2000 for some of the datasets)
2,Molecule replacement with phaser.
3,Check and modify the structure residue by residue with COOT,
4,phenix.refine with the following command line:

phenix.refine protein.1.mtz protein.pdb \
strategy=individual_sites+individual_sites_real_space+individual_adp+tls \
simulated_annealing=true simulated_annealing.start_temperature=1000 \
simulated_annealing.cool_rate=10 main.number_of_macro_cycles=5 \
ordered_solvent=true refinement.input.xray_data.labels="F,SIGF" \

5,Fit the ligand and redo step 3&4; stop refining when the Rwork and Rfree
looks reasonable.
6,Chage the strategy line to
strategy=individual_adp adp.individual.isotropic=all \
to remove the ANISOU lines in pdb file.

Any suggestion for this workflow ? or how do you always deal with the
similar case ? cause I'm new about this field,maybe I did something stupid.
Ps, the value of Rwork and Rfree are too close, like,
Final: r_work = 0.1741 r_free = 0.1817 bonds = 0.036 angles = 1.818
Is that reasonable ?

Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences
Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park,
Pudong New Area, Shanghai, 201203, P.R. China
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