Re: [ccp4bb] Refining residues as rigid bodies

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

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From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2009-12-02

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Subject: Re: Refining residues as rigid bodies
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-12-02

Hi,

you can do similar thing (that is resulting in similar outcome) in
phenix.refine by increasing the weight on ADP restraints term. Example:
increase "wu" or decrease "wxu_scale". Although I believe a regular
refinement of individual isotropic ADPs should normally work just fine
at 3A resolution in phenix.refine.

Pavel.

On 12/1/09 11:18 PM, Frederic VELLIEUX wrote:
> 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!
>

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

Previous message:
Subject: Re: decrease of background with distance?
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2009-12-02

Next message:
Subject: Solubilization buffer
From: megha goyal mgbiotec {- at -} GMAIL {- dot -} COM
Date: 2009-12-02