[phenixbb] strategy suggestion ???

Michael Thompson miket at chem.ucla.edu
Tue May 31 13:17:17 PDT 2011

I once used the following strategy to search for ligands when the apo structure had already been determined. I was using Refmac at the time, but I don't see why you couldn't do it with phenix.refine.

After you process your data, if your crystals with and without the ligands are isomorphous, then you don't necessarily need to do molecular replacement to get phases. After you process the data from your crystals with the ligands, you can take the mtz file and start refining with the pdb file for your apo structure. You can start with a rigid body refinement to account for any small shifts or rotations that may have taken place when you added the ligand. Then after that refine according to your protocol of choice.

The main place you can run into trouble is if you have a polar space group. If you do the rigid body refinement and get a horrible R-factor, the there's a good chance you have indexed the two data sets in opposite orientations. This can be corrected by reindexing, I think the phenix tool for this is xmanip but someone can correct me if I'm wrong.

Good luck,


----- Original Message -----
From: "ChenTiantian" <chentiantian2010 at gmail.com>
To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
Sent: Monday, May 30, 2011 6:31:51 PM GMT -08:00 US/Canada Pacific
Subject: [phenixbb] strategy suggestion ???

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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Michael C. Thompson

Graduate Student

Biochemistry & Molecular Biology Division

Department of Chemistry & Biochemistry

University of California, Los Angeles

miket at chem.ucla.edu

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