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I am not familiar with CNS restraints, but whatever the program restraints are - if you do a omit map, or just set the occupancies of the metal and its surroundings to 0.00 and do a few cycles of refinement, I believe any model bias will disappear and what you see will be pretty accurate description of the metal.
When you include that atom  in the refinement it is usually necessary to at least set distance restraints up - otherwise the heavier metal density will tend to swallow any water molecules around about
Eleanor

On 14 May 2012 15:19, Ed Pozharski <[log in to unmask]> wrote:
On Sat, 2012-05-12 at 08:48 -0400, Dave Roberts wrote:
> However, I just want to make sure the metal environment is not due to
> the fact that I did something wrong in my refinement script - thus
> making it tetrahedral because it was refined as tetrahedral.
...
> I don't use CCP4 for refinement, I use CNS, but I'm hoping somebody
> will be able to guide me here.
>

AFAIK, CNS does not generate any geometry restraints for metal ions
*automatically*.  You may want to make sure (if you didn't yet) that you
use a correct residue name, e.g. NI2 (and atom name NI+2) for Ni++.  CNS
libraries would use different values for the radii and scattering
factors of these.


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