 |
 |
On Wednesday 03 February 2010 10:04:36 Pavel Afonine wrote: I always suggest to run these refinement jobs and see which > one gives the best result: > > 1) TLS + individual isotropic ADP refinement (tls+individual_adp); > 2) TLS + group individual ADP refinement (tls+group_adp); I do not think that your (2) is a physically plausible model. I would dis-recommend this option. > 3) individual isotropic ADP refinement; > 4) group individual ADP refinement (with one refinable B per residue); > 5) group individual ADP refinement (with two refinable B per residue). I also tend to agree with Ed that option (5) has little physical plausibility in its favour. Better to stick with individual Biso and tight B restraints. cheers, Ethan > + on top of it you can add automatic weights optimization to remove the > arbitrariness in what is "loose" and "tights" restraints. > > This will give the conclusive, rock solid answer about which ADP > parameterization and refinement protocol is good for given model and > data. An alternative is an endless speculation. > > In the future the proper parameterization will be chosen automatically > based on a large array of data, model and map characteristics. > > > The existing > > two-adp-groups-per-residue implementation (CNS and phenix) is, imho, an > > example of *improper* parametrization. > > As you see, in phenix.refine you can combine any B-factor refinement > strategy with any (group, individual iso, aniso, tls), and apply it to > any selected part of your structure. So, I assume at this point of the > software automation, it is up to a smart researcher to decide which > refinement strategy to use. You cannot blame the software for giving you > the freedom to do what you may want to do. For example, if you choose to > refine two-B-factors per residue when you could safely refine individual > B-factors, it will be the example of improper parameterization that you > have chosen (and not the software did for you). In phenix.refine > technically you can refine individual isotropic or anisotropic B-factors > at any resolution - the program will not crash, and it will be up to the > user whether he/she will enjoy the results. Like I said, in the future > the model parameterization will be done automatically. > > I guess I'm going off this discussion - otherwise phenix.refine will get > less new options in the future if I keep writing -:) > > All the best! > Pavel. > > -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742