Hi,<br>I just started learning crystallography months ago, and the software I used most is XDS, HKL2000, phenix and coot.<br>Now I am working on a series of datasets-----the same target protein with various ligands. The following is my refinement workflow:<br>
1, Processing data with XDS (or HKL2000 for some of the datasets)<br>2,Molecule replacement with phaser.<br>3,Check and modify the structure residue by residue with COOT,<br>4,phenix.refine with the following command line:<br>
<br>phenix.refine protein.1.mtz protein.pdb \<br>strategy=individual_sites+individual_sites_real_space+individual_adp+tls \<br>simulated_annealing=true simulated_annealing.start_temperature=1000 \<br>simulated_annealing.cool_rate=10 main.number_of_macro_cycles=5 \<br>
ordered_solvent=true refinement.input.xray_data.labels="F,SIGF" \<br>output.prefix=myprotein<br><br>5,Fit the ligand and redo step 3&4; stop refining when the Rwork and Rfree looks reasonable. <br>6,Chage the strategy line to<br>
strategy=individual_adp adp.individual.isotropic=all \<br>to remove the ANISOU lines in pdb file.<br><br>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. <br>
Ps, the value of Rwork and Rfree are too close, like,<br>Final: r_work = 0.1741 r_free = 0.1817 bonds = 0.036 angles = 1.818<br clear="all">Is that reasonable ?<br><br>-- <br>Drug Discovery and Design Center,<br>Shanghai Institute of Materia Medica, Chinese Academy of Sciences<br>
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