Re: [phenixbb] HLs not recognised

12 May 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
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: [email protected], 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 
Subject: Re: [phenixbb] HLs not recognised
To: Jonathan Grimes 
Cc: PHENIX user mailing list 
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
   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: [email protected], 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: [email protected] (on
    behalf of Jonathan Grimes
    )
    >Subject: [phenixbb] HLs not recognised
    >To: [email protected]
    >
    >
    >  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: [email protected], Web:
    www.strubi.ox.ac.uk
    >Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 -
    287547
    >
    >_______________________________________________
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