[phenixbb] shaking a PDB without introducing clashes

Pavel Afonine PAfonine at lbl.gov
Sun Mar 28 19:13:08 PDT 2010

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!

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
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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