[phenixbb] HLs not recognised
Nathaniel Echols
nechols at lbl.gov
Mon May 12 08:35:07 PDT 2014
Here is the problem:
phenix.mtz.dump resolve_1_190_phenix.mtz
...
HLA xxxxx 100.00% 0.00 0.00 A: phase probability
coefficients (Hendrickson/Lattman)
HLB xxxxx 100.00% 0.00 0.00 A: phase probability
coefficients (Hendrickson/Lattman)
HLC xxxxx 100.00% 0.00 0.00 A: phase probability
coefficients (Hendrickson/Lattman)
HLD xxxxx 100.00% 0.00 0.00 A: phase probability
coefficients (Hendrickson/Lattman)
We ignore arrays with all zeros, since they're obviously not correct -
however, the feedback given to the user is deficient. I am open to
suggestions about how we can improve this, but I am reluctant to assault
users with pop-ups every time bogus information is detected, especially
since this will increase the latency of the GUI.
The file from AutoSol you should actually use is probably named
overall_best_refine_data.mtz, which contains the original, purely
experimental phases (along with data and R-free flags, of course). We
don't recommend using the density-modified phases as restraints. (I am not
sure why Resolve would output all zeros; that is a question for Tom. I did
however notice the same thing in a file generated by AutoSol for a tutorial
dataset.)
-Nat
On Mon, May 12, 2014 at 8:21 AM, Jonathan Grimes
<jonathan at strubi.ox.ac.uk>wrote:
>
> hi nat
>
> i created this mtz file.....by taking a resolve.mtz
> and putting it back thru phenix.
>
> from the GUI and from the command line phenix
> doesnt like my HLs coeffs.
>
> thanks
> jon
>
> Dr. Jonathan M. Grimes,
> NDM Senior Reseach Fellow Diamond Research
> Fellow
> University Research Lecturer Diamond Light
> Source
> Division of Structural Biology Diamond House
> Wellcome Trust Centre for Human Genetics Harwell Science Campus
> University of Oxford Didcot
> Roosevelt Drive, OX11 0DE
> Oxford OX3 7BN, UK
>
> Email: Jonathan at strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk
> Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547
>
>
>
> ---- Original message ----
> >Date: Mon, 12 May 2014 07:44:14 -0700
> >From: Nathaniel Echols <nechols at lbl.gov>
> >Subject: Re: [phenixbb] HLs not recognised
> >To: Jonathan Grimes <jonathan at strubi.ox.ac.uk>
> >Cc: PHENIX user mailing list <phenixbb at phenix-online.org>
> >
> > This is a little strange - the GUI should not be
> > allowing you to select an array that won't work for
> > refinement. Could you please send me (off-list!)
> > both MTZ files that you tried using? (I don't
> > think I need data or anything else for this.)
> > thanks,
> > Nat
> >
> > On Mon, May 12, 2014 at 5:49 AM, Jonathan Grimes
> > <jonathan at strubi.ox.ac.uk> wrote:
> >
> > i have now used phenix to read in the mtz file,
> > read all the arrays
> > and make a new mtz file.
> >
> > phenix recognised the HLs as Hend/latt coeffs.
> >
> > i used the eff file to run phenix.refine at the
> > command line
> > and got this error
> >
> > Not a suitable array of experimental phases:
> > refinement.input.experimental_phases.labels=HLA,HLB,HLC,HL
> >
> > The phases were orginally derived by Phenix
> > using the auto solve GUI.
> > Jon
> >
> > Dr. Jonathan M. Grimes,
> > NDM Senior Reseach Fellow
> > Diamond Research Fellow
> > University Research Lecturer
> > Diamond Light Source
> > Division of Structural Biology
> > Diamond House
> > Wellcome Trust Centre for Human Genetics
> > Harwell Science Campus
> > University of Oxford
> > Didcot
> > Roosevelt Drive,
> > OX11 0DE
> > Oxford OX3 7BN, UK
> >
> > Email: Jonathan at strubi.ox.ac.uk, Web:
> > www.strubi.ox.ac.uk
> > Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 -
> > 287547
> >
> > ---- Original message ----
> > >Date: Mon, 12 May 2014 11:32:39 +0100
> > >From: phenixbb-bounces at phenix-online.org (on
> > behalf of Jonathan Grimes
> > <jonathan at strubi.ox.ac.uk>)
> > >Subject: [phenixbb] HLs not recognised
> > >To: phenixbb at phenix-online.org
> > >
> > >
> > > I am trying to refine a structure at low
> > resolution and would like to
> > > use phase restraints. using the GUI even
> > though HLs are present
> > > in the MTZ file, and are type
> > “A”…checked with CAD…..i am not given
> > > the option of selecting them.
> > >
> > > not clear to me what I’m doing wrong.
> > >
> > > hints most wellcome
> > > thanks
> > > jon
> > >
> > >
> > >Dr. Jonathan M. Grimes,
> > >NDM Senior Reseach Fellow
> > >University Research Lecturer
> > >DIAMOND Research Fellow
> > >
> > >Division of Structural Biology
> > >Wellcome Trust Centre for Human Genetics
> > >University of Oxford
> > >Roosevelt Drive,
> > >Oxford OX3 7BN, UK
> > >
> > >Email: Jonathan at strubi.ox.ac.uk, Web:
> > www.strubi.ox.ac.uk
> > >Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 -
> > 287547
> > >
> > >_______________________________________________
> > >phenixbb mailing list
> > >phenixbb at phenix-online.org
> > >http://phenix-online.org/mailman/listinfo/phenixbb
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
>
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