Re: [ccp4bb] Refining residues as rigid bodies

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

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Subject: Re: Solubilization buffer
From: natrajan natrajan {- at -} EMBL {- dot -} FR
Date: 2009-12-03

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Subject: Re: Bad geometry for alt. conformation refined in Refmac5
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2009-12-03

Subject: Re: Refining residues as rigid bodies
From: MARTYN SYMMONS martainn_oshiomains {- at -} BTINTERNET {- dot -} COM
Date: 2009-12-03

Discussing with Fred Vellieux offlist I suggested the following: would it be useful to have a sort of 'simulated annealing' of the B-factor values? - in refinement I often try resetting them to higher values (Moleman has a function for this I think) and then see which ones refine back down nicely - but it would be good to have some sort of randomization method - that would be a test of how much the values are inherited from the modelling early on - say from the MR probe model for example.

We could do multiple B-factor refinements with different starting kicks to the values and look for the best final Rfree or some measure of map quality?

Martyn

Martyn F. Symmons
Cambridge
'Chan fhiosrach mur feòraich.'
Gaelic proverb - Nothing asked, nothing learned.

________________________________
From: Pavel Afonine
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, 2 December, 2009 22:52:45
Subject: Re: [ccp4bb] Refining residues as rigid bodies

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 à :
>>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: Solubilization buffer
From: natrajan natrajan {- at -} EMBL {- dot -} FR
Date: 2009-12-03

Next message:
Subject: Re: Bad geometry for alt. conformation refined in Refmac5
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2009-12-03