Re: [ccp4bb] question about getting rid of model bias in refinement

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: chromophore in GFP
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2008-08-02

Next message:
Subject: D-Amino acids to L-Amino acids
From: Yusuf Akhter yusuf {- dot -} akhter {- at -} EMBL-HAMBURG {- dot -} DE
Date: 2008-08-02

Subject: Re: question about getting rid of model bias in refinement
From: Sun Tang suntang2222 {- at -} YAHOO {- dot -} COM
Date: 2008-08-02

Hello Eleanor,

Thank you very much for your reply. I don't know whether or not the conformation is model biased or not. I just want to make sure the conformation is model free of model bias because these residues are important. The refinement moved the residue back may indicate the previous conformation is correct. I want to know whether there are any other methods to cross-verify the result.

Thank you very much for your opinions.

Best,

Sun

--- On Thu, 7/31/08, Eleanor Dodson wrote:

From: Eleanor Dodson
Subject: Re: [ccp4bb] question about getting rid of model bias in refinement
To: suntang2222@yahoo.com
Date: Thursday, July 31, 2008, 11:41 AM

Sun Tang wrote:
> Hello Everyone,
>
> I have a question about getting rid of model bias in refinement with
refmac. I solved the structure with molecular replacement. After final
refinement of the structure, I found out some key amino acids in the structure
and wanted to make sure their conformations are correct. I omitted these amino
acids (by setting occupancy to zero) and refined the structure. I manually fit
the amino acids into the density and refined the structure again. I found these
amino acids return to the precious conformations even though the conformations I
fit were different. Should I omit these amino acids from the beginning of the
refinement? What is the best way to get rid of the model bias? Your suggestions
are greatly appreciated!
>
> Best,
>
> Sun
>
>
>
>
>

This seems rather strange!
The bias would usually disappear especially if you have a) set occs to
0.0 for selected residues, b) done several cycles of refinement.

Could there be 2 conformations for these residues?
One where it was originally and one where you have built them?
Eleanor

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: chromophore in GFP
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2008-08-02

Next message:
Subject: D-Amino acids to L-Amino acids
From: Yusuf Akhter yusuf {- dot -} akhter {- at -} EMBL-HAMBURG {- dot -} DE
Date: 2008-08-02