On Wed, Mar 28, 2012 at 9:05 AM, Subhani Bandara
I have refined a protein with a metal-chelate complex at 1.4 resolution and saw positive density around some metals that are on a two fold. I refined those chelator complexes with fixed occupancy to avoid the negative density seen around it as they are partially occupied. Also I had to avoid xyz refinement after fixing them on special position, to avoid moving away from two fold. I have attached a figure of one of those complexes. If I increase occupancy then it shows negative density. How can I get rid of this positive density.
Are you using anisotropic B-factor refinement? If not, making the metal anisotropic might help (and at 1.4A, there's a good chance you can refine the non-hydrogen protein atoms anisotropically too). But the difference density could also be just Fourier truncation artifacts - these are pretty common around heavy atoms. If anisotropy doesn't fix the problem, I'd just ignore it. -Nat