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Re: [ccp4bb] phenix.refine and refmac
 

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CCP4bb <-- 2008 <-- March 2008 <-- 04 March 2008
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Subject: Re: multiple sequence alignment from multiple pairwise structural alignments
From: Ashley Buckle ashley {- dot -} buckle {- at -} MED {- dot -} MONASH {- dot -} EDU {- dot -} AU
Date: 2008-03-04 		Next message:
Subject: protein expression
From: Daniel Jin jin_xiechen {- at -} YAHOO {- dot -} COM
Date: 2008-03-04


Subject: Re: phenix.refine and refmac
From: yang li robertcatrukie {- at -} GMAIL {- dot -} COM
Date: 2008-03-04
Thanks for your replies. I did use default settings in phenix refine,
included TLS in it. This is an about 2.3A data, and the number Rfree used to
refine is big enough. I also kept the same Rfree in two programs. In refmac
I also tried diffenrent weighting sets--from defaut 0.3 to 0.02, TLS
included--maybe there are some other ways to define the restrains. The R and
Rfree will increase as the weighting is set too low, and the gap
didnot improve much. I donnot know in this case if the phenix refine has
converged, but the not stable Rfree in refmac made me nervous. Simply,
in this case, which one should I choose? Certainly to my private opinion I
would prefer to Scott's answer, Rfree is the most obvious parameter than
something esle like geometry, eg. Just looks good. :)


On 3/5/08, Partha Chakrabarti wrote:
>
> One point which I don't understand is how can someone compare the two
> different programs when they don't use the same numbers for
> xray:geometry terms? Taking the default settings for a given
> resolution might not be enough.. !
>
>
>
>
> On Tue, Mar 4, 2008 at 7:58 PM, Savvas Savvides
> wrote:
> > Hi Yang
> > how many reflections do you have in your test-set for calculating
> > R-free? Too few reflections, typically less than 500, may not
> > constitute a statistically robust cross-validation data set, and thus
> may
> > lead to fluctuations in R-free plus a tendency for R-free to increase
> > as a function of refinement cycle. Some of the early
> > publications from Axel Brunger on crystallographic cross-validation
> > address the need for enough reflections (>500) in the test-set. In
> > addition, the presence of even a handful of strong but inaccurately
> > measured/integrated low-resolution reflections in a limited test-set
> > can aggravate abnormal behavior in R-free.
> >
> > Best wishes
> > Savvas
> >
> >
> > toQuoting yang li :
> >
> > > Dear All,
> > > I have post a similar question about CNS and refmac before, now
> in
> > > another structure I met a similar problem. I have an almost finished
> > > structure, the Rfree of which
> > > is about 0.28 by refmac. Then I used phenix to refine it, below is
> the
> > > result:
> > > REMARK ******************** REFINEMENT SUMMARY: QUICK FACTS
> > > *******************
> > > REMARK Start: r_work = 0.1970 r_free = 0.2892 bonds = 0.006 angles =
> 1.213
> > > REMARK Final: r_work = 0.1917 r_free = 0.2617 bonds = 0.008 angles =
> 1.374
> > > REMARK
> > >
> ************************************************************************
> > > Since the map from phenix couldnot be opened by coot directly--or
> I
> > > donnot know how to--I used refmac to get a mtz map file. But I found
> that at
> > > the first several cycle of
> > > refmac the Rfree decreased, then both the R and Rfree
> values continued
> > > increasing and FOM decreasing.
> > > The best R/Rfree/FOM during the refinement is
> > >
> > >
> -----------------------------------------------------------------------------
> > > Overall R factor = 0.1932
> > > Free R factor = 0.2513
> > > Overall figure of merit = 0.8168
> > >
> -----------------------------------------------------------------------------
> > > And after 40 cycles the final result is:
> > >
> -----------------------------------------------------------------------------
> > > Overall R factor = 0.2008
> > > Free R factor = 0.2772
> > > Overall figure of merit = 0.7902
> > >
> -----------------------------------------------------------------------------
> > > The values looks like keep going up if increase the cycles. Then
> which
> > > value should I take as the final result? The phenix or the best
> Refmac
> > > result or I have to take a converged
> > > value from refmac?
> > >
> >
>
>
>
>
> --
> MRC National Institute for Medical Research
> Division of Molecular Structure
> The Ridgeway, NW7 1AA, UK
> Email: pchakra@nimr.mrc.ac.uk
> Phone: + 44 208 816 2515
>
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