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@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@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@lbl.gov>
>Subject: Re: [phenixbb] HLs not recognised
>To: Jonathan Grimes <jonathan@strubi.ox.ac.uk>
>Cc: PHENIX user mailing list <phenixbb@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@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@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@phenix-online.org (on
>     behalf of Jonathan Grimes
>     <jonathan@strubi.ox.ac.uk>)
>     >Subject: [phenixbb] HLs not recognised
>     >To: phenixbb@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@strubi.ox.ac.uk, Web:
>     www.strubi.ox.ac.uk
>     >Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 -
>     287547
>     >
>     >_______________________________________________
>     >phenixbb mailing list
>     >phenixbb@phenix-online.org
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