Quick navigation: Home   |    Site Map   ||    References   |    Biography   ||    Copyright   |    Other copyright   |    Contact us   |    Advert   |   
 

Re: [ccp4bb] Rigid body refinement as last 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: Off topic: Crystal degredation with age
From: "Edward A {- dot -} Berry" BerryE {- at -} UPSTATE {- dot -} EDU
Date: 2009-02-06		Next message:
Subject: Re: Rigid body refinement as last refinement?
From: "William G {- dot -} Scott" wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2009-02-06


Subject: Re: Rigid body refinement as last refinement?
From: Andy Millston andymillston {- at -} YAHOO {- dot -} COM
Date: 2009-02-06

Thank you for your responses.

Restrained refinement does a good job at refining most of the structure except a small region with poor density. Every time I refine it, it puts this region completely out of the map. It doesn't have much effect on overall geometrical factors as its a very small part of a relatively large molecule.
I am annoyed at the fact that Refmac doesn't seem to have much respect for the electron density map while refining this region, and all my attempts to keep the residues within the map go in vain. The refined residues are still ok according to Fo-Fc map, but they're completely out of the 2Fo-Fc map boundaries. Also, my model and the refined model both look bad on Ramachandran plot. But I think its a unique feature of the molecule, at least thats what the density suggests. Also, packing score and quality value plot suggest that there is nothing seriously wrong with my model.

As you've suggested I should try altering the restraints and see how it goes.

Thank you.

Andy



CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: Re: Off topic: Crystal degredation with age
From: "Edward A {- dot -} Berry" BerryE {- at -} UPSTATE {- dot -} EDU
Date: 2009-02-06		Next message:
Subject: Re: Rigid body refinement as last refinement?
From: "William G {- dot -} Scott" wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2009-02-06
ProteinCrystallography.org: Copyright 2006-2010 by Quid United Ltd