[phenixbb] Modeling Disordered Domains

Pavel Afonine pafonine at lbl.gov
Tue Apr 5 22:31:00 PDT 2011

Hi Damian,

>  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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