[phenixbb] Refinement with partial model - question

Pavel Afonine PAfonine at lbl.gov
Fri Apr 2 10:53:37 PDT 2010

Hi Ed,

> For instance, long time ago I, like many others before and after, have
> discovered that sometimes there are empty cavities inside proteins,
> which get filled with bulk solvent, resulting in negative density blobs.
> Not a big deal, really, but it was possible to appease the inner
> nitpicker by generating a mask in CNS, running it through USF's MAMA to
> remove isolated islands and supplying it to CNS refinement as an
> external mask.  I haven't seen much change in R-factors (naturally), but
> the negative density was gone.

do you still have that model and data available so I can quickly 
reproduce these negative density blobs? I would be happy to do this 
tonight (instead of having Friday's evening beer). That would be a 
starting point for me to think how we can do it better. I have some data 
from other people but I would like to have some more cases in my hands 
before I start doing anything.


More information about the phenixbb mailing list