Re: PDB EXPDTA records

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• Previous message: Paula Fitzgerald: "Re: secondary structure"
• Maybe in reply to: Frances Bernstein: "PDB EXPDTA records"

Frances Bernstein writes:

> PDB entries contain a record called EXPDTA that describes the
> type(s) of experimental data used to determine the structure.
> The PDB currently has the following types defined:
> 
>        ELECTRON DIFFRACTION
>        FIBER DIFFRACTION
>        FLUORESCENCE TRANSFER
>        NEUTRON DIFFRACTION
>        NMR
>        NMR SOLID STATE
>        NMR SOLUTION
>        SYNCHROTRON X-RAY DIFFRACTION
>        THEORETICAL MODEL
>        X-RAY DIFFRACTION
> 
> For NMR entries the keyword can be followed by a comma and additional
> information:
> 
> EXPDTA    NMR, 29 STRUCTURES
> EXPDTA    NMR, MINIMIZED AVERAGE STRUCTURE
> 
> If more than one type of experiment was performed the two sets of
> information will be separated by a semi-colon:
> 
> EXPDTA    X-RAY DIFFRACTION; NEUTRON DIFFRACTION
> 
> I was unable to find a field in the mmCIF dictionary that is designed
> to carry this information.  Note that we have had several entries
> over the years that used more than one type of data so this must be
> handled as a list in mmCIF.
> 
> I am aware that the NMR people are designing extensions to CIF for
> their special purposes but I feel that this aspect must be handled in
> mmCIF itself because it is directly relevant to the coordinates of a
> macromolecule (and because a joint x-ray and NMR study is not out of
> the question).
> 
> Would it possible to design keywords and a format to carry this information?

This is something that we have talked about doing at more CIF working group
meetings than I can count, but one of the many things that we knew that had
to be taken care of that we somehow just never got around to.  That's the
beauty of this review process - someone out there is watching and these things
are finally getting done.

I have created data items _exptl.method and _exptl.method_details to deal
with this information - they are given below.  But you will see that the
enumeration list I have generated is rather different than the one that Fran
included in her message.  I haven't changed things to try and be difficult,
but rather to try and be consistent.  After all, fiber diffraction is most
likely to be x-ray diffraction as well.  And synchrotron X-ray diffraction
(from Fran's list) is just a special case of X-ray diffraction - if we give
it a separate experimental indicator, then we would need to distinguish
between sealed-tube X-ray diffraction and rotating-anode x-ray difrraction
and combinations of the two.

It does occur to me that the list I am proposing could be broken out into
sample type (i.e., single-crystal, fiber, solution, solid-state) and 
experimental technique (X-ray diffraction, neutron diffraction, nmr, etc),
and I would be willing to consider that possibility.  However, I thought
we were looking for a simplifying keyword here, and it may be that we
want a far more minimal list than what I give below.  Debate is welcome.

- - - - -

save__exptl.method
    _item_description.description
;              The method used in the experiment.
;
    _item.name                  '_exptl.method'
    _item.category_id             exptl
    _item.mandatory_code          yes
    _item_type.code               char
     loop_
    _item_enumeration.value      'single-crystal x-ray diffraction'
                                 'single-crystal neutron diffraction'
                                 'single-cyrstal electron diffraction'
                                 'fiber x-ray diffraction'
                                 'fiber neutron diffraction'
                                 'fiber electron diffraction'
:                                 single-crystal joint x-ray and neutron
                                  diffraction
;
:                                 single-crystal joint x-ray and electron
                                  diffraction
;
                                 'solution nmr'
                                 'solid-state nmr'
                                 'theoretical model'
     save_

save__exptl.method_details
    _item_description.description
;              A description of special aspects of the experimental method.
;
    _item.name                  '_exptl.method_details'
    _item.category_id             exptl
    _item.mandatory_code          no
    _item_type.code               char
     loop_
    _item_examples.case          '29 structures'
                                 'minimized average structure'
     save_

- - - - -

Paula

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 Dr. Paula M. D. Fitzgerald  ______________ voice and FAX: (908) 594-5510
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• Previous message: Paula Fitzgerald: "Re: secondary structure"
• Maybe in reply to: Frances Bernstein: "PDB EXPDTA records"