[phenixbb] Twinning in phenix.autobuild?

Tom Terwilliger terwilliger at lanl.gov
Mon Sep 10 10:59:27 PDT 2007


You can tell autobuild to use phenix.refine maps instead of 
density-modified maps with:

two_fofc_in_rebuild=Yes

Here is the documentation on this keyword:

            You can choose to use a sigmaa-weighted 2Fo-Fc map in
            all cycles of rebuilding instead of a density-modified
            map. If the model is poor this can sometimes allow
            model-building in place to work even when it will not
            for density-modified maps.

In the GUI you can set this keyword in the General Parameters window 
(screen 4). It has the label "Use 2Fo-Fc map in rebuild?"

All the best,
Tom T


At 11:41 AM 9/10/2007, you wrote:
>An example of mytwinrefinement.eff looks like this:
>
>refinement.twinning {
>   twin_law = "-h-k,k,-l"
>   detwin {
>     mode = algebraic proportional *auto
>     map_types {
>       twofofc = *two_m_dtfo_d_fc two_dtfo_fc
>       fofc = *m_dtfo_d_fc gradient m_gradient
>       aniso_correct = False
>     }
>   }
>}
>
>I think it would make sense to (re)build in the maps from phenix.refine
>rather than using density modified maps, if the model is complete enough
>that is.
>Tom, do you have some comments on this?
>
>Greetings
>
>Peter
>
>
>
>
>
>Tom Terwilliger wrote:
> > Hi Francis,
> >
> > Unfortunately we have not yet incorporated twin refinement directly
> > into autobuild.  However you can specify this in a
> > "mytwinrefinement.eff" file that tells phenix.refine what to do, and
> > then you can read this in to autobuild with (command-line version):
> >
> > refine_eff_files_list=mytwinrefinement.eff
> >
> > (or from the GUI by filling in the blank under "Refinement parameters
> > files (optional)".
> >
> > All the best,
> > Tom T
> >
> >
> > At 11:16 AM 9/10/2007, Francis E Reyes wrote:
> >
> >> Hello all
> >>
> >>
> >> So I discovered from xtriage that my crystal is twinned.  I have a
> >> pretty decent model that xtriage says has an r/rfree of 30/30 to a
> >> resolution of 2.6. I wanted to try a phenix.autobuild at 2.8A.  I
> >> couldn't find a parameter flag for autobuild that turns on twinning.
> >>
> >> I already autobuilt this model once, and the xtriage log did find
> >> that the crystal was twinned, but twinning in refinement of the
> >> model during rebuilding wasn't turned on.
> >>
> >> Is there a way to tell autobuild to rebuild using twinning?
> >>
> >> Thanks
> >>
> >> FR
> >>
> >> ---------------------------------------------
> >> 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
> >>
> >>
> >>
> >> _______________________________________________
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> >> 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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> > phenixbb at phenix-online.org
> > http://www.phenix-online.org/mailman/listinfo/phenixbb
> >
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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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