[phenixbb] R-free set for low resolution

Hi Follow up the shaking the coordinates, I was end up using different R-free set. I do have a data is at very low resolution, so only possible to do rigid body refinement. How can I avoid over fitting or model bias due to the different R-free set using phenix. Thanks ram ________________________________ From: Pavel Afonine To: PHENIX user mailing list Sent: Sun, March 28, 2010 10:13:08 PM Subject: Re: [phenixbb] shaking a PDB without introducing clashes Hi Francois, to add to Nat's reply: - you can also apply a systematic shift to the model by rotating+translating it: phenix.pdbtools model.pdb rotate="10 20 30" translate="1 2 3" - you can run SA "refinement" w/o X-ray term: phenix.refine model.pdb fake_data.mtz simulated_annealing=true main.bulk_solvent=false main.number_of_macro_cycles=10 output.prefix=distorted_model strategy=individual_sites My plan is to add a command line tool called phenix.fake_model_and_data that will create a model and corresponding fake data that will look like a real data and no-one could say that it is a fake data -:) To be available soon! All the best! Pavel. On 3/28/10 5:17 PM, Francois Berenger wrote:

Hello,

I recently used "phenix.pdbtools modify.sites.shake=..." in order to have some data from 0.1 to 5A. away from the true structure in order to test some scripts.

I think this introduced clashes in the "shaken" PDBs I got. Is there a tool/way to avoid this?

Best regards, Francois. _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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