Re: Fixes from Herb Bernstein

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Herb Bernstein writes:

> ...but in adapting Syd's ciftbx to ddl2 and mmCIF, it just
> told me that the aliases for
>   _atom_site_thermal_displace_type
>   _atom_site_aniso_label
>   _atom_site_aniso_type_symbol
> were not in the mmCIF dictionary I picked up recently, and, if I've
> typed correctly (which is not guaranteed) then grep seems to think
> that these names are in cifdic.c91 and .c94, but not in mmCIF.

The first item is this list a pure typo - some global grep had changed type
to item_type (and I can tell you exactly when *that* happened).

The second two are more complicated, as one of the trickier things that we
did was to create a separate ATOM_SITE_ANISOTROP category (for those users
who want to put anisotropic temperature factors in a separate loop).  In
doing this we moved some core dictionary items to the new category, but
forgot about aliases (it appears).  I've added _atom_site_aniso_label as an
alias to _atom_site_anisotrop.id and _atom_site_aniso_type_symbol as an alias
to _atom_site_anisotrop.type_symbol, but I'd like it is John Westbrook could
please check this over and make sure that what I have done doesn't create any
problems.

Herb also noted that:

> I don't know enough about CIF yet to know if this is intentional or
> not, but the following save frame names don't seem to conform to
> the model of _category.item:
>     _diffrn_standards.decay_%
>     _diffrn_standards.interval_count
>     _diffrn_standards.interval_time
>     _diffrn_standards.number
>     _diffrn_standards.scale_sigma
> They seem to have the category.id "diffrn" rather than
> "diffrn_standards".

> A similar problem (if it is a problem) may exist for:
>     _phasing_mad_expt.delta_delta_ph
>     _phasing_mad_expt.delta_phi
>      and several more _phasing_mad_expt... and _phasing_set...
> save frames.
> Hope this is helpful.
 
It sure is helpful - there is nothing like fresh eye looking at this this
beast for find problems.  All of the above have been fixed, and I am sending
a new version to Rutgers for posting on the web page.

The audit trail:

  0.7.24 1995-08-21
;
  Changes (PMDF):
    + Corrected category.id for data items in the DIFFRN_STANDARDS category
    + Corrected category.id for data items in the PHASING_MAD_EXPT category
    + Corrected category.id for selected data items in the PHASING_SET
        category
    + Corrected alias for _atom_site.thermal_displace_type
    + Introduced alias of _atom_site_aniso_label for _atom_site_anistrop.id
    + Introduced alias of _atom_site_aniso_type_symbol for
        _atom_site_anisotrop.type_symbol
;
 
Paula
 
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