[phenixbb] phaser_x.mtz, resolve_x.mtz and exptl_fobs_phases_freeR_flags.mtz give different Rfree's using same model?

Tom Terwilliger terwilliger at lanl.gov
Tue May 20 09:25:41 PDT 2008


Hi Francis,

If you want to refine using anomalous data, then it is best to use 
your original dtrek data.  You can supply the freeR_flags from

exptl_fobs_phases_freeR_flags.mtz

if you want. Or you can generate freeR flags from your original data 
-- but then you must use these freeR flags from the beginning and 
redo everything involving model-building..

All the best
-Tom T




At 10:07 AM 5/20/2008, you wrote:
>Thanks Tom
>
>With option #3, have F+ and F- merged in
>exptl_fobs_phases_freeR_flags_xx.mtz? How can I refine with anomalous
>flags at this point?
>
>Thanks
>
>FR
>
>On May 20, 2008, at 9:47 AM, Tom Terwilliger wrote:
>
> > Hi Francis,
> >
> > I don't know how to explain the refinement results, but here are
> > some comments:
> >
> > 1. if you use defaults in autosol, then resolve_xx.mtz will have all
> > zeros for the HL coeffs. If you want the HL coeffs you have to say
> >
> > hl_in_resolve=true
> >
> > 2. I'd recommend refining using the HL coeffs from phaser_xx.mtz or
> > solve_xx.mtz, but yes, you can refine against the HL coeffs from
> > resolve_xx.mtz and it seems to work ok. Paul Adams did a test a while
> > back and the two worked about the same if I recall correctly. My
> > logic for using experimental phases in MLHL refinement is that this
> > is the independent information that is available; anything from
> > density modification as information about where the model is located
> > and flatness of solvent mixed in with the experimental information,
> > and this duplicates information from the refinement process.
> >
> > 3. So in general I'd use  exptl_fobs_phases_freeR_flags_xx.mtz from
> > autosol, or if you don't build a model in autosol,
> > exptl_fobs_phases_freeR_flags.mtz from autobuild.
> >
> >
> > All the best,
> > -Tom T
> >
> >
> >
> > At 09:17 AM 5/20/2008, you wrote:
> >> Ok. I think I have a case where I can't refine unless I use density
> >> modified experimental phases.
> >>
> >> I did an autosol run where I specified build=False so I don't have an
> >> exptl_fobs_phases_freeR_flags.mtz, but I do have phaser_1.mtz and
> >> resolve_1.mtz.
> >>
> >> However, when I refine my model using mlhl my Rfree drops below 30
> >> when using resolve_x.mtz and not phaser_x.mtz nor using the original
> >> d*trek ref using the same model? Using any of the other mtz's results
> >> in Rfree's in the mid 30s. Interestingly refining against the
> >> original
> >> d*trek results in an increase of Rfree with macro cycle?
> >>
> >>
> >>
> >> I checked the log file for resolve_x.mtz and although it says it's
> >> using the mlhl refinement target, it seems to be using FP, SIGFP (not
> >> the HL coefficients that I thought phased refinement would use) as
> >> evidenced by the .log file under 'Non-default parameters'. In this
> >> section it doesn't read in the HL cofficients? Is there any
> >> indication
> >> that it's actually refining against the phases?
> >>
> >> Any insight as to which mtz to use for final refinement would be
> >> suggested.
> >>
> >>
> >> Thanks
> >>
> >> FR
> >>
> >> P.S.
> >>
> >> What is the refinement target ml_sad?
> >>
> >> ---------------------------------------------
> >> Francis Reyes M.Sc.
> >> 215 UCB
> >> University of Colorado at Boulder
> >>
> >> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
> >>
> >> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
> >>
> >> _______________________________________________
> >> phenixbb mailing list
> >> phenixbb at phenix-online.org
> >> http://www.phenix-online.org/mailman/listinfo/phenixbb
> >
> >
> >
> >
> > Thomas C. Terwilliger
> > Mail Stop M888
> > Los Alamos National Laboratory
> > Los Alamos, NM 87545
> >
> > Tel:  505-667-0072                 email: terwilliger at LANL.gov
> > Fax: 505-665-3024                 SOLVE web site: http://
> > solve.lanl.gov
> > PHENIX web site: http:www.phenix-online.org
> > ISFI Integrated Center for Structure and Function Innovation web
> > site: http://techcenter.mbi.ucla.edu
> > TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
> >
> >
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://www.phenix-online.org/mailman/listinfo/phenixbb
>
>---------------------------------------------
>Francis Reyes M.Sc.
>215 UCB
>University of Colorado at Boulder
>
>gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>
>8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
>
>_______________________________________________
>phenixbb mailing list
>phenixbb at phenix-online.org
>http://www.phenix-online.org/mailman/listinfo/phenixbb




Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web 
site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB





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