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.
On Mar 28, 2010, at 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?
I would recommend running geometry regularization on the shaken model: phenix.pdbtools model.pdb --geometry_regularization -Nat -------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
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
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
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
phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
On Mar 30, 2010, at 7:05 AM, r n wrote:
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.
If you can't do restrained refinement, your options are basically limited to what Pavel and I already posted: shake the coordinates and regularize, or run simulated annealing without the X-ray term. (We probably need to create a separate command for this.) These have the disadvantage of potentially introducing distortions that are far from the native state of the protein in the crystals, and which won't be corrected by rigid-body refinement. Resetting all of the B-factors to something appropriate (the Wilson B, for instance) is a good idea, especially since it won't distort the model. However, if you have access to the original R-free set, you should really use that instead. My (uninformed) guess is that if you're only using rigid-body refinement, the probability of overfitting badly is low anyway, but you will still have some model bias. (PS. I would recommend including TLS refinement, with each domain or chain as a separate group.) -Nat -------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
Hi,
I do have a data is at very low resolution, so only possible to do rigid body refinement.
it depends what you call "low resolution". In small molecule crystallography ~1A resolution is "low resolution" (Acta Cryst. (2007). D63, 160-170). So, without knowing what the resolution of your data is I can't really tell whether you need to refine individual anisotropic B-factors or the whole model as just one TLS group. Anyway, if by "low resolution" you mean what comes to my mind this very minute, you can still try: Coordinates: - Simulated Annealing refinement in torsion angle space; - Highly restrained refinement of individual coordinates; - Optimize weights against Rfree. - You may need to use secondary-structure restrains (available in recent PHENIX versions). ADP: - combined refinement of TLS+individual or group B-factors; - Highly restrained individual ADP refinement; - Simple group ADP refinement (where the size of groups depends on resolution or/and data-to-parameters ratio) - Optimize target weights. NCS: - use if available. Bulk-solvent: - optimize mask parameters (r_solvent and r_shrink) using optimize_mask=true (this is will done automatically in future versions of phenix.refine). Multi-Start SA: - people find it useful (Andrei Korostelev, Martin Laurberg, and Harry F. Noller "Multistart simulated annealing refinement of the crystal structure of the 70S ribosome". PNAS 2009 106:18195-18200). Good luck! Pavel.
participants (4)
-
Francois Berenger -
Nathaniel Echols -
Pavel Afonine -
r n