[phenixbb] Modeling Disordered Domains
pafonine at lbl.gov
Tue Apr 5 22:31:00 PDT 2011
> In the other 5 copies, a entire domain (~25kDa) is largely disordered
> (some have patchy residual density, but not readily interpretable).
> Altogether, this means that I am missing ~20% of the total protein in
> the AU. It seems that how you model this much "missing" material
> could have a significant effect on the final refined model. This is
> something we have observed a number of times, so I am wondering if
> anyone can suggest ways to deal with this aside from just leaving the
> domains out entirely.
> Regarding missing or patchy domains, Pavel recently added a feature
> that should at least improve the phases and refinement behavior
this is still ongoing project that Tom and myself are working on. It
still need some work and a lot of testing. You can try it now by using
"use_statistical_model_for_missing_atoms=true" in phenix.refine (you
need the latest version for this), and there is no documentation yet, sorry.
Actually, I was looking for a real case where there is a significant
amount of model missing. If you send me the data, your best current
model and the sequence, I will use it for testing and
optimizing/training the algorithms that we are developing right now.
For some details see pages #17-19 here:
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