Re: [ccp4bb] Refining residues as rigid bodies

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

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Date: 2009-12-04

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Subject: Re: Refining residues as rigid bodies
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-12-04

You can do it in phenix.refine. The prototype is:

for trial in trials:
phenix.refine model.pdb data.mtz main.random_seed=random_value
modify_start_model.adp.shake=true output.prefix=str(random_value)

where each refinement will start with the original B-factors that are
shaken by a certain value.

Pavel.

PS> You can use phenix.pdbtools to do any manipulations on your model,
such as shaking, setting, shifting of coordinates, b-factors,
occupancies, etc.

On 12/3/09 4:05 AM, MARTYN SYMMONS wrote:
> 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!
>>

CCP4bb navigation

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

Previous message:
Subject: Postdoctoral position at the Goethe University Frankfurt- Institute of Biochemistry
From: pos pos {- at -} EM {- dot -} UNI-FRANKFURT {- dot -} DE
Date: 2009-12-04

Next message:
Subject: Structural Biologist - permanent position in Central London
From: Andrew Turnbull aturnbull {- at -} CANCERTECHNOLOGY {- dot -} COM
Date: 2009-12-04