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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