[phenixbb] Red patches of electron density

Pavel Afonine pafonine at lbl.gov
Sun Dec 1 22:50:48 PST 2013

Hi Bishal,

it's difficult to tell what's going on without looking at data, model 
and maps. From what you describe it sound like you do everything all 
right. If you want me to have a closer look, please send me model, data 
and eff files, and tell which residues you are concerned about.


On 11/25/13, 8:15 AM, Singh, Bishal wrote:
> Hi,
>   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
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