[phenixbb] Fw: Question related to Phenix refinement
smith_lee123 at yahoo.com
Sat Feb 14 20:39:06 PST 2015
Then what is rsrg?
On Wednesday, January 21, 2015 12:54 AM, Engin Özkan <eozkan at uchicago.edu> 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
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.
On 1/20/15 4:17 AM, Christian Roth wrote:
> 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
> 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.
>> phenixbb mailing list
>> phenixbb at phenix-online.org
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> phenixbb at phenix-online.org
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