Re: [ccp4bb] Refining residues as rigid bodies

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

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From: Bernhard Rupp br {- at -} RUPPWEB {- dot -} ORG
Date: 2009-12-01

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Subject: methews coefficient and validation of 60mer
From: Pankaj Chauhan pankajimtech {- at -} GMAIL {- dot -} COM
Date: 2009-12-02

Subject: Re: Refining residues as rigid bodies
From: Frederic VELLIEUX frederic {- dot -} vellieux {- at -} ORANGE {- dot -} FR
Date: 2009-12-02

If the problem is B-factor refinement, you can do that easily at low resolution with CNS. You just give tight restraints.

You modify the file bindividual.inp

This section:
{* target sigma values for restrained B-factor refinement *}

{* mainchain bonds *}
{===>} bsig_main=1.5;
{* mainchain angles *}
{===>} asig_main=2.0;

{* sidechain bonds *}
{===>} bsig_side=2.0;
{* sidechain angles *}
{===>} asig_side=2.5;

I cannot remember in which direction the values have to go. I think up. I have done this with a very low resolution structures (4.5 A?) a few years ago, you get smoothly varying B values, very tightly restrained. I do not think we published that structure, we obtained a higher resolution structure later (I don't think the referees would have been very happy seeing B factor refinement at low resolution). But it worked.

Fred.

> Message du 01/12/09 23:51
> De : "Jason C Porta"
> A : CCP4BB@JISCMAIL.AC.UK
> Copie Ã :
> Objet : Re: [ccp4bb] Refining residues as rigid bodies
>
>
>Basically my reasoning for doing this is a low data-to-parameter ratio, which makes B-factor refinement unfeasible. So far I have had nice results with breaking the complex into rigid subdomains. So i was basically just thinking of a way I could refine the structure best, without using too many parameters.

I see now how this can be done in Phenix. I will give it a try.

Thanks for all of your suggestions!

CCP4bb navigation

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

Previous message:
Subject: only 20
From: Bernhard Rupp br {- at -} RUPPWEB {- dot -} ORG
Date: 2009-12-01

Next message:
Subject: methews coefficient and validation of 60mer
From: Pankaj Chauhan pankajimtech {- at -} GMAIL {- dot -} COM
Date: 2009-12-02