[phenixbb] R-free set for low resolution
ramme29 at yahoo.com
Tue Mar 30 07:05:57 PDT 2010
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.
From: Pavel Afonine <PAfonine at lbl.gov>
To: PHENIX user mailing list <phenixbb at phenix-online.org>
Sent: Sun, March 28, 2010 10:13:08 PM
Subject: Re: [phenixbb] shaking a PDB without introducing clashes
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!
On 3/28/10 5:17 PM, Francois Berenger wrote:
> 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,
> phenixbb mailing list
> phenixbb at phenix-online.org
phenixbb mailing list
phenixbb at phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the phenixbb