[phenixbb] question on bad geometry

Ed Pozharski epozh001 at umaryland.edu
Tue Aug 31 22:23:03 PDT 2010

On Tue, 2010-08-31 at 20:37 -0500, fn1 at rice.edu wrote:
> Does  
> that mean I need to manually adjust the model? 

Autobuilder is a fantastic tool which greatly simplifies the model
building process, but you always must validate your structure by
inspecting the electron density.  I fully understand that (hopefully) it
is what you plan to do and this is more of a reaction to the alarming
number of obvious and easily correctable systematic errors one finds in
structures deposited in the PDB these days.

Thanks to Pavel for providing an excellent example to illustrate the
point.  One only needs to take a look at the model in context of
electron density maps to confirm that autobuilder will fix some errors
but also sometimes introduce some that require manual correction.



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