[phenixbb] strategy suggestion ???
Frederic.Vellieux at ibs.fr
Mon May 30 23:14:57 PDT 2011
You don't always need to carry out simulated annealing. Typically,
simulated annealing will be carried out for a "de novo" structure
determination; for molecular replacement I hardly ever use simulated
annealing (or not at all). However, if the initial electron density maps
after molecular replacement are of insufficient quality, and if the
resolution is high enough, then I send the starting model and mtz file
to the Arp / Warp server for automatic model rebuilding.
> 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
> 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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