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Re: [ccp4bb] cns and refmac refinement
 

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CCP4bb <-- 2008 <-- February 2008 <-- 21 February 2008
Previous message:
Subject: Re: cns and refmac refinement
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-02-21 		Next message:
Subject: possible solutions for those troobleshooting ccp4 and ccp4i...
From: James Thompson Thompson {- dot -} James {- at -} MAYO {- dot -} EDU
Date: 2008-02-21


Subject: Re: cns and refmac refinement
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-02-21
"Then I used CNS to do annealing, then use refmac to do rigid body
refinement."

That can be why the R-factors went up. Rigid-body subsequent to simulated
annealing will (if anything) undo the refinement ...



Anastassis Perrakis wrote:
> Just to point out that I have missed the NCS presence; Lijun is
> *perfectly* correct; even more I should emphasize the point and
> say that at 3.0 A, Thou Must Use NCS (if I say again anything about
> Gospels and Kleywegt we end up with more facebook groups ...)
>
>> I think there is no reason at this resolution edge (~3A), making
>> bonds possibly resolvable, that NCS should not be used,
>
>>> By the way, it is a dimer and I didnot use NCS restarin
>>> during refinement. Below is from refmac log:
>
> I would however disagree with Lijun thats its instability. Of course
> the 180 cycles are of no use at all
> (10 cycles in Refmac are more than enough in 99% of cases), but Rfree
> shoots up from 32.6 to 36.2 in 12 cycles,
> which is clearly an indication of some sort of pathology, and not
> instability.
>
> Well, tight NCS is the best starting point in this case.
>
> Tassos
>
>

CCP4bb navigation

CCP4bb <-- 2008 <-- February 2008 <-- 21 February 2008
Previous message:
Subject: Re: cns and refmac refinement
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-02-21 		Next message:
Subject: possible solutions for those troobleshooting ccp4 and ccp4i...
From: James Thompson Thompson {- dot -} James {- at -} MAYO {- dot -} EDU
Date: 2008-02-21


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