Re: [phenixbb] shaking a PDB without introducing clashes

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]