Re: [ccp4bb] phenix.refine and refmac

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

Previous message:
Subject: protein expression
From: Daniel Jin jin_xiechen {- at -} YAHOO {- dot -} COM
Date: 2008-03-04

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Subject: Re: protein expression
From: wu donghui wdh0972 {- at -} GMAIL {- dot -} COM
Date: 2008-03-04

Subject: Re: phenix.refine and refmac
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2008-03-04

Hi Yang Li,

0) Cool down -:)

1) To see if the refinement is converged in phenix.refine is easy: just
look how R-factors change from macro-cycle to macro-cycle (this is
reported in PDB file header and in .log file). If they don't change
much, then it is "converged". If they still going down, then simply
increase the number of macro-cycles, say from default 3 to 5 or 10 (the
keyword is "main.number_of_macro_cycles=5").

2) I would also suggest to run your final refinement with
"optimize_wxc=true". This will optimize the relative Xray/Geometry
weight. Since it is slow, just run it overnight.

3) Note that phenix.refine does not perform TLS refinement if you run it
with all default parameters, so if you want to do TLS refinement then
you need to use appropriate keyword to request it. (I emphasize this
just because you mentioned that you ran phenix.refine using default
settings but as at the same time you said that you included TLS).

4) Also make sure that you use "ordered_solvent=true" so the ordered
solvent gets updated and refined automatically as the refinement progresses.

Cheers,
Pavel.

On 3/4/2008 6:35 PM, yang li wrote:
> 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
>
>

CCP4bb navigation

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

Previous message:
Subject: protein expression
From: Daniel Jin jin_xiechen {- at -} YAHOO {- dot -} COM
Date: 2008-03-04

Next message:
Subject: Re: protein expression
From: wu donghui wdh0972 {- at -} GMAIL {- dot -} COM
Date: 2008-03-04