[phenixbb] positive density around heavy metals

Nathaniel Echols nechols at lbl.gov
Wed Mar 28 09:18:39 PDT 2012

On Wed, Mar 28, 2012 at 9:05 AM, Subhani Bandara <ramssb17 at gmail.com> wrote:
> 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.


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