[phenixbb] Fw: Question related to Phenix refinement

Dear All, Then what is rsrg? Smith On Wednesday, January 21, 2015 12:54 AM, Engin Özkan wrote: Just a correction: "adp" is not anisotropic displacement parameters, but "Atomic Displacement Parameters". ADP is actually the proper name for B-factors. In phenix.refine, "adp" step can include isotropic ADP refinement, anisotropic ADP refinement, TLS refinement, or combinations of those. There is also "nhq" or something like that among the steps phenix.refine performs. It is for flipping sidechains (by 180 degrees) of residues that are hard to distinguish one way or the other based on clashes and hydrogen bonding. Obviously, it involves Asn, Gln and His. This step, while time consuming sometimes, is useful and should be performed, to prevent yourself from embarrassment by claiming hydrogen bonds with no donors and two acceptors, for example. Engin On 1/20/15 4:17 AM, Christian Roth wrote:

Hi,

bss: bulk solvent scaling rsrl: real space rotamer refinement? Did you select rotamer correction or realspace refinement in your strategy? adp: ainsotropic displacement parameters means simple B-Factor refinement

Cheers

Christian

Am 20.01.2015 um 01:49 schrieb Smith Lee:

...

Dear All.

In the Phenix refine "run status" window, with the progression of the refinement, it occurs 3' bss, 3' rsrl, 3' xyz, 3' adp (for 3rd round of refinement). I guess xyz means the strategy is for x, y, z coordinates? Then what do bss, rsrl and adp mean?

I am looking forward to getting your reply.

Smith

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