[phenixbb] positive density around heavy metals

Francis E Reyes Francis.Reyes at colorado.edu
Wed Mar 28 09:25:52 PDT 2012

Does phenix.refine use wavelength dependent form factor corrections for heavy (> C,N,O,S ) atoms?
This is quite helpful for eliminating FoFc density around metal centers .. especially if you took the data near an edge. 


On Mar 28, 2012, at 10:18 AM, Nathaniel Echols wrote:

> 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.
> -Nat
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list