[phenixbb] Question related to Phenix refinement

Engin Özkan eozkan at uchicago.edu
Tue Jan 20 08:54:20 PST 2015


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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>
>
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