[phenixbb] individual anisotropic adps
Frank von Delft
frank.vondelft at sgc.ox.ac.uk
Thu Dec 11 09:08:16 PST 2008
Question at large: do any formalisms exist, or are any envisioned, that
deal with this question more rigorously? E.g. in principle everything
is always ADP, but as resolution decreases, the restraints are tightened
accordingly, so that there is an appropriately refined continuum from
fully ADP @ 1A to isotropic @ 2A to TLS only @ 3A?
I know for a fact I've heard about this somewhere, but can't remember where.
that in principle always refine ADP for everything, but tighten the
Pavel Afonine wrote:
> Hi Gerwald,
> from what I recall is if you refine anisotropic ADP at "too low"
> resolution in other refinement programs, they were often stopping
> complaining about non-positive definite U or unstable refinement. This
> seemed to me the main technical limit.
> In phenix.refine this does not happen but it doesn't mean that refining
> anisotropic ADP at "too low" resolution will yield meaningful results.
> I'm not sure that there is an exact resolution borderline for doing (or
> not doing) individual anisotropic ADP refinement. From my experience,
> I've never seen a case at ~1.5A and higher where switching from iso- to
> anisotropic model was not good. Then this question transforms into "at
> which resolution you start refining waters as anisotropic?"... A very
> rough number I would say is 1.2-1.1A and higher.
> In-between 1.5 and 1.7 (1.8A) is a "gray zone", where it is very likely
> that anisotropic ADP refinement will result in over-fitting, however
> there is a chance that it might still be valid.
> Summarizing, if I have a data at resolution between between 1.5 and 1.8A
> resolution, I just try two refinements: in one refining isotropic and in
> another refining anisotropic ADPs. Rfree is your best friend here (and
> Rfree-Rwork). In my opinion, this is the most robust and cheep way to
> get the answer.
> On 12/11/2008 7:48 AM, gerwald jogl wrote:
>> Hi All,
>> I was wondering if there is information/recommendations out there for
>> the resolution required to refine individual anisotropic adps. I think
>> the recommendation for shelx is at least 1.5 A resolution.
>> In addition, is phenix set up and would it make sense to combine tls
>> with individiual anisotropic adps?
>> All comments welcome,
>> phenixbb mailing list
>> phenixbb at phenix-online.org
> phenixbb mailing list
> phenixbb at phenix-online.org
More information about the phenixbb