[phenixbb] query re local grid search in phenix.real_space_refine
pafonine at lbl.gov
Sat Feb 10 10:41:50 PST 2018
no, it does not do it for all residues. It does it for residues that
have poor fit to the map or unlikely rotameric state. There is a
potential to make this smarter and faster.
On 2/10/18 09:41, Oliver Clarke wrote:
> Related to the last message - when using local_grid_search, does phenix attempt to torsion-angle search every residue, or just outliers?
> It would seem like maybe using EMRinger or similar to identify residues where there is strong sidechain density, but in a non-rotameric position or with an incorrectly fit rotamer might be one way to make it more efficient if it is the former.
> I don’t want phenix trying to do a local grid search on residues with no sidechain density - these may be in an area of the map with poor local resolution, perhaps where I have docked a crystal structure, or carefully manually adjusted rotamers - local grid search in these regions is likely to make things worse if it is not focused on residues with clear sidechain density.
> phenixbb mailing list
> phenixbb at phenix-online.org
> Unsubscribe: phenixbb-leave at phenix-online.org
More information about the phenixbb