[phenixbb] Red patches of electron density

Singh, Bishal b.singh at dkfz-heidelberg.de
Mon Nov 25 08:15:38 PST 2013

 I am solving a crystal structure at 1.2 Å with completeness 97.3% in the highest resolution shell. There are few small patches of red electron densities on the main chain of a flexible loop at a contour level of ~3sigma of difference ED map. Refinement parameters were following: XYZ coordinates, individual B-factor, optimize X-ray/stereochemistry weight, optimize X-ray/ADP weight and individual Anisotropic ADP for amino acids excluding hydrogen. Target weights are as default in phenix.refine.

I already have observed two alternative conformation for this region in another crystal structure. Therefore I am thinking that these red patches are because of lower occupancy of these residues. Please suggest me what shall I do. I shall be grateful for your words.

With regards,
Bishal Singh
University of Heidelberg, Germany

More information about the phenixbb mailing list