[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
> >     _______________________________________________
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> >     phenixbb at phenix-online.org
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>
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