[phenixbb] HLs not recognised

Mon May 12 09:07:17 PDT 2014

Hi Tim,

I think we ignore arrays with *all* zeros (as Nat pointed out), not just 
select Miller index entries that have data value zero. That is if you 
have 1000 of Fobs and all 1000 of them are equal to zero such an array 
will be ignored. Perhaps this also depends on the specific program.

All the best,
Pavel

On 5/12/14, 8:54 AM, Tim Gruene wrote:
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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
>>
>>
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> - -- 
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
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