On Sun, Mar 30, 2008 at 07:08:14PM +0100, Partha Chakrabarti wrote:
> Is it by any chance that the FOMs were highly overestimated and that
> creates a problem with Maximum likelihood? That sort of reminds me of
> what I had heard for SHARP-solomon in a couple of instances..
The FOMs are never used in anything downstream from experimental
phasing and/or density modification - unless you calculate maps, but
even then you usually use some map coefficients directly. And to
describe the phase probability you should ideally use
Henrickson-Lattmann coefficients I guess.
Anyway, if you want to use experimental phase information in
refinement (good idea), make sure to use the Henrickson-Lattmann
coefficients from the phasing program. The HLs after density
modification are usually over-optimisitic (at least for classical
density modification programs like SOLOMON or DM).
I must admit I've never heard suspicions about the SHARP-solomon FOMs
before ... I could imagine people being generally supicious about FOMs
from any density modification program? I have very good experiences
using the HLs from SHARP afterwards during refinement. If you have
more details about this, I'd be very interested to hear!
Cheers
Clemens
>
> Any insight would be highly appreciated..
> Regards, Partha
>
>
> On Fri, Mar 28, 2008 at 2:35 PM, Garib Murshudov <[log in to unmask]> wrote:
> > make sure that you are using the original observation (Fobs and
> > corresponding sigmas) not that produced by density modification (e.g.
> > solve resolve) programs.
> >
> > Garib
> >
> >
> >
> > On 28 Mar 2008, at 10:43, stefano ricagno wrote:
> >
> > > Dear CCP4bb readers,
> > > this is my problem:
> > > I solved a structure by MR: the solution was easily found (molrep,
> > > phaser and balbes found always the same one), density looked
> > > generally reasonable (however in several places it was dubious) but
> > > R/Rfree were stuck at 42/47%.
> > > Then I tried some density modifications, resolve worked
> > > spectacularly the density became wonderful and several parts which
> > > were not in the model appeared.
> > > So I finished to build the model and everything looked good.
> > > The problem is now for a structure at 2.8 Å resolution I have R/
> > > Rfree of 8/9.5% respectively, which is clearly too good. Checking
> > > refmac log file it looked to me that refmac uses all the
> > > reflections in the .mtz file (that is as many reflections as before
> > > the resolve run).
> > > Ideas?
> > >
> > > thanks
> > >
> > > Stefano
> > >
> > > ps this is my last refmac:
> > >
> > > 2 mol in the AU, no NCS used, weighting term 0.01, no tls.
> > >
> > > Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND
> > > zBOND rmsANGL zANGL rmsCHIRAL $$
> > > $$
> > > 0 0.0943 0.1051 0.937 102149. 5673.2 0.0070
> > > 0.298 1.202 0.546 0.077
> > > 1 0.0910 0.1024 0.940 101442. 5642.4 0.0058
> > > 0.252 1.091 0.481 0.073
> > > 2 0.0898 0.1019 0.940 101221. 5634.0 0.0055
> > > 0.238 1.061 0.461 0.072
> > > 3 0.0891 0.1016 0.941 101080. 5628.8 0.0052
> > > 0.226 1.045 0.451 0.072
> > > 4 0.0884 0.1011 0.942 100947. 5622.7 0.0050
> > > 0.217 1.033 0.445 0.071
> > > 5 0.0877 0.1006 0.942 100824. 5617.0 0.0049
> > > 0.211 1.024 0.440 0.071
> > > 6 0.0872 0.1001 0.943 100708. 5611.4 0.0047
> > > 0.205 1.016 0.436 0.070
> > > 7 0.0866 0.0997 0.943 100593. 5606.5 0.0047
> > > 0.202 1.008 0.432 0.070
> > > 8 0.0861 0.0992 0.944 100483. 5601.5 0.0046
> > > 0.199 1.002 0.429 0.069
> > > 9 0.0857 0.0989 0.944 100391. 5597.5 0.0045
> > > 0.196 0.996 0.426 0.069
> > > 10 0.0852 0.0985 0.944 100313. 5593.5 0.0045
> > > 0.193 0.990 0.423 0.068
> > >
> > > _________________________________________________________________
> > > Explore the seven wonders of the world
> > > http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-
> > > US&form=QBRE
> > >
> >
>
>
>
> --
> MRC National Institute for Medical Research
> Division of Molecular Structure
> The Ridgeway, NW7 1AA, UK
> Email: [log in to unmask]
> Phone: + 44 208 816 2515
>
--
***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park
* Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group (http://www.globalphasing.com)
***************************************************************
|