Additional residue info in coot
Hello, 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. 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. The occupancy for the second line cannot be changed and it only appears after refinement. I carried out the same refinement using a previously solved structure of the same protein and the extra residue info line was not present. My question is where does this extra line in the residue info come from and could the zero occupancy be causing additional Fo-Fc density at the metal site? Thanks, Breann Breann L. Brown Page Laboratory Department of Molecular Pharmacology, Physiology and Biotechnology Brown University Providence, RI 02912
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. Pavel.
I think that the additional line in Coot in the "residue info" comes from
the pdb file that has a TER line after an end of a chain.
Maia
----- Original Message -----
From: "Pavel Afonine"
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.
Pavel.
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participants (3)
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Brown, Breann -
chern -
Pavel Afonine