I think if you cant see it dont build it, but deposit the data..
There are many (most?) structures with missing loops
Eleanor
Pavel Afonine wrote:
This might help:
Acta Cryst. (1997). D53, 540-543 Local Improvement of
Electron-Density Maps
Pavel.
PS> It will be implemented in PHENIX sometime in future, but for the
moment you will need to so some scripting.
On 12/8/2008 11:08 AM, Andy Millston wrote:
I am trying to build a model of a 60000 Da protein from the
diffraction data collected at 2.0 A resolution. There is a 10-residue
stretch that has such bad electron density that even at 0.4 sigma
level one can hardly see any well defined density for residues with
long side chains.
My question is: are such poorly defined regions left unmodeled in
protein structures? Or is it conventional to model the whole chain no
matter how poor the density? The region in question is in the middle
of the chain and has several long side chain residues - both charged
and uncharged.
AM