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
