[phenixbb] HLs not recognised

Tim Gruene tg at shelx.uni-ac.gwdg.de
Mon May 12 08:54:28 PDT 2014


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Dear Nat,

I don't know the formula for HL by heart and I don't see the
Miller-Indices, but couldn't centric reflections have all four HLs = 0
if the two-fold ambiguity is resolved and those reflections have
phi=0? I thought phi=0 corresponds to A=B=C=D=0.

Best,
Tim

On 05/12/2014 05:35 PM, Nathaniel Echols wrote:
> 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
>> 
> 
> 
> 
> _______________________________________________ phenixbb mailing
> list phenixbb at phenix-online.org 
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> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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