PHASING categories and data names

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Hello there -

Jiansheng Jiang writes -

> Still I could not find the PDB subset
> cif for SF from mmCIF 0.9.0.
> 
> >  _phasing_MIR_refln.der_id   . . . . . . . . . . . . . .    74
> >  _phasing_MIR_refln.F_calc   . . . . . . . . . . . . . .    79
> >  _phasing_MIR_refln.F_calc_au  . . . . . . . . . . . . .    85
> >  _phasing_MIR_refln.F_meas   . . . . . . . . . . . . . .    91    99   104
> >  _phasing_MIR_refln.F_meas_au  . . . . . . . . . . . . .    95
> >  _phasing_MIR_refln.F_meas_sigma   . . . . . . . . . . .    98
> >  _phasing_MIR_refln.F_meas_sigma_au  . . . . . . . . . .   103
> >  _phasing_MIR_refln.index_h  . . . . . . . . . . . . . .   108
> >  _phasing_MIR_refln.index_k  . . . . . . . . . . . . . .   112
> >  _phasing_MIR_refln.index_l  . . . . . . . . . . . . . .   116
> >  _phasing_MIR_refln.phase_calc   . . . . . . . . . . . .   120

Perhaps a little history would help clear up the mystery here.  Some years
ago, the PDB needed a set of CIF definitions for their structure factor
files.  Providing data items for the native data was a simple matter of
added a few more data items to the REFLN category than were already present
in the mmCIF draft.  But the PDB also asked us for data items for MIR data,
and here we generated something based on the still (at that point) evolving
PHASING categories in the mmCIF draft.

Subsequent to that, the mmCIF draft dictionary went out for community review,
and one of the changes that we were asked to make was to provide for storing
all of the MIR (or MAD) data sets used in a phase determination within the
same data block as the native data (the data against which the structure
was eventually refined.)  This had not been our original data model - we had
thought that users would store derivative data in separate data blocks.

But people seemed to want them in the same data block as the native, so we
redesigned the data model in the PHASING category to provide for this.  At
present, the PHASING_SET categories are where the reflections are actually
stored, and then the PHASING_MIR or PHASING_MAD categories can refer to those
data sets by their set id.  This revised model for the PHASING categories was
implemented in summer of 1995, and has been part of the mmCIF draft since
that time.

It seems that we have left some of the data names developed for the PDB
structure factor files dangling in the process of responding to the desires
of the community - I am sorry for that.  The question is how to fix the
situation, and I see two paths.  The simplest would be for the PDB to switch
to the data names in the current data model.  If for some reason that poses a
difficulty, we would be happy to provide a compatability dictionary that
aliases the old-style names to their current forms.  Please tell us which
path you prefer to take, and we will act accordingly.

Best wishes - Paula 

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 Dr. Paula M. D. Fitzgerald  ______________ voice and FAX: (908) 594-5510
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