Re: [ccp4bb] too good R/Rfree with resolve

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

Previous message:
Subject: Re: refmac,tlsanl vs TLS, B and anisou
From: Kevin P Madauss kevin {- dot -} p {- dot -} madauss {- at -} GSK {- dot -} COM
Date: 2008-03-30

Next message:
Subject: Re: too good R/Rfree with resolve
From: "Thomas C {- dot -} Terwilliger" terwilliger {- at -} LANL {- dot -} GOV
Date: 2008-03-30

Subject: Re: too good R/Rfree with resolve
From: Partha Chakrabarti ppchak {- at -} GMAIL {- dot -} COM
Date: 2008-03-30

Hi,

Just a newbie question:

Could someone explain what might have gone wrong in this case? I guess
the structure factors should not change anyway! I am a bit confused
because I have used solve resolve several times for experimental
phasing, never had such a problem, on the other hand, have not heard
about density modification for MR apart from one posting (from Prof.
Lawrence Perl I think).

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..

Any insight would be highly appreciated..
Regards, Partha

On Fri, Mar 28, 2008 at 2:35 PM, Garib Murshudov 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
> >
> > _________________________________________________________________
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> >
>

--
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: Re: refmac,tlsanl vs TLS, B and anisou
From: Kevin P Madauss kevin {- dot -} p {- dot -} madauss {- at -} GSK {- dot -} COM
Date: 2008-03-30

Next message:
Subject: Re: too good R/Rfree with resolve
From: "Thomas C {- dot -} Terwilliger" terwilliger {- at -} LANL {- dot -} GOV
Date: 2008-03-30