[phenixbb] Additional residue info in coot

chern chern at ualberta.ca
Thu Mar 11 08:19:07 PST 2010

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.

----- Original Message ----- 
From: "Pavel Afonine" <PAfonine at lbl.gov>
To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
Sent: Wednesday, March 10, 2010 1:42 PM
Subject: Re: [phenixbb] Additional residue info in coot

> 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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