Re: [ccp4bb] Refining residues as rigid bodies

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

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Subject: Re: decrease of background with distance?
From: John R Helliwell jrhelliwell {- at -} GMAIL {- dot -} COM
Date: 2009-12-02

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From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-12-02

Subject: Re: Refining residues as rigid bodies
From: MARTYN SYMMONS martainn_oshiomains {- at -} BTINTERNET {- dot -} COM
Date: 2009-12-02

IMHO this is a bad idea as the restraints can give undue weight to poorly ordered residues in order to favour the tighter distribution that you are specifying.

I have found bindividual.inp to perform at low resolution reasonably well, and I think it is more realistic than group B-factors. The overall weighting on these B-factor restraints is usually determined automatically by CNS I think.

The target sigmas in the distributed bindividual.inp file are too tight to start with and I would always follow previous suggestions on the bb - mainchain bond 2.0, mainchain angle 3.0, sidechain bond 4.5, sidechain angle 6.0. You can check the log file afterwards to see if the refinement is actually getting close to the values you set. Then you can manually set the B-factor restraint weighting if you are not happy with the program's choice. That would be a better way to restrain than changing the target distributions?

I think the PHENIX restrained B-factor refinement is very well thought out - based on ideas from Ian Tickle's analysis. And I would think that should be good at low resolution too - so perhaps worth a try? You can always do just B-factor refinement in PHENIX after geometric refinement in CNS if you want.

regards
Martyn

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

________________________________
From: Frederic VELLIEUX
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, 2 December, 2009 8:56:01
Subject: Re: [ccp4bb] Refining residues as rigid bodies

Dear Bulletin Board,

I received this information from Axel Bruenger, who rightly corrected me on the modification to be made to the bindividual.inp file:

>As an fyi, the sigmas should be made smaller to get a narrower B-factor
>differences.

My previous post:

> 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.

So the values have to go down. The precise values I used are somewhere on a DAT tape and we have no DAT reader here anymore...

Fred.

CCP4bb navigation

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

Previous message:
Subject: Re: decrease of background with distance?
From: John R Helliwell jrhelliwell {- at -} GMAIL {- dot -} COM
Date: 2009-12-02

Next message:
Subject: Re: Arp/wArp error
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-12-02