[phenixbb] question on bad geometry

Thomas C. Terwilliger terwilliger at lanl.gov
Wed Sep 1 05:25:18 PDT 2010

Hi Fengyun,

Just to emphasize what Ed points out here, an essential step in completing
a structure is to compare it, one residue, solvent molecule, or ligand at
a time, with your electron density map, fixing any inconsistencies between
the model and the map.  There are many wonderful tools in all the
crystallographic graphics programs to help you do this.

All the best,
Tom T

>> 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.
>> Cheers,
>> Ed.
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