[phenixbb] Additional residue info in coot

Pavel Afonine PAfonine at lbl.gov
Wed Mar 10 12:42:22 PST 2010

Hi Breann,

>  I am currently refining a model of a zinc-binding protein and 
> after refinement there is additional positive Fo-Fc density at the 
> zinc site. This is the fourth independent structure of this 
> particular protein solved in my lab so we are confident the metal 
> is in fact zinc. 

- Are you applying any restraints to ZN position? It may be a good idea. In my experience, this usually fixes problems similar to yours. To do so:

phenix.metal_coordination model.pdb

this will give you a file that defines these restraints. Have a look at it and edit if you find it necessary.

Then use this file in refinement.

- Try refining occupancy of ZN.

> I noticed that after refinement the "residue info" 
> in Coot has two lines for the zinc atom. The first line reads 
> "G/121 ZN/ZN 1.00 44.30" while the second line reads G/121 ZN/ 0.00 
> 0.00. 

Can't say anything about it.

If you still need more help with this - please send me the data, model files and input parameters you used and I will have a look.


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