Release of mmcif.1995.08.31

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Hello folks -

I promised you a new version of the dictionary before I left town at the end
of the day today, and I have amazingly managed to get something done before
that deadline.  Not so amazingly, I have not managed to get everything done.
What I will summarize in this message is things that have been taken care
of.  In a separate message I will summarize issues that are still
outstanding - these will get taken care of, but not before I get back on 19
Sep.

I am extremely grateful to both Herb and Frances Bernstein, who have been
looking that the dictionary very carefully from both a content and
consistency perspective (Frances) and from a syntactical perspective (Herb).
A large number of the changes in the version I am releasing today are the
result of things that they have found.  I'm not going to mirror all of the
mail that they have sent me, but you will find the sorts of things that have
been found and fixed by reading the audit trail at the end of this message.

But I will summarize a couple of things from Fran and Herb that deserve
comment, and then respond to issues raised by other folks.

- - - - -

Frances Bernstein writes:

5. You are not consistent in your use of tenses throughout the dictionary.
   An example is:
               Polymer entities will be expected to have corresponding
               ENTITY_POLY and associated entries.
               Water entities are not expected to have corresponding
               entries in the ENTITY category.
   I would recommend using the present tense, in general.

- -
 
I fixed the particular issue raised here (changing 'will be expected' to 'are
expected') but the question of tense is something that is going to have to be
explored globally in the entire dictionary.  Hence I will keep this item on
the StillToBeDealWith list as well.

- - - - -

Herb Bernstein writes:

I've run across another issue which I don't think is a problem,
but which confused me.  For the following blocks, you have
a loop of names and such with an unlooped alias:
     _atom_site.id, _atom_type.symbol, _chemical_conn_atom.number,
     _diffrn_radiation.wavelength_id, _diffrn_scale_group.code,
     _diffrn_standard_refln.code, _exptl_crystal.id,
     _reflns_scale.group_code
You explicitly say in the comments for _atom_site.id that the
intention is to link the alias to _atom_site.id, which is the
first name in the loop, so I am assuming that for all the rest
the intention is to link an unlooped alias to the first name when
the names are looped, and not to link that alias to any of the
other names.  My apologies if this is more properly a DDL
documentation question, but may I suggest adding an explict
comment about the intended linking to the blocks which don't
have such a comment, to avoid confusion for novices like me.

- -

I think I understand what Herb is asking here - in the save_ frames that
describes _atom_site.symbol (for instance) the data item is aliased to its
equivalent in the original cif core dictionary (_atom_site_symbol).  However,
the save_ frames also includes the tree of all data items that are children
of _atom_site.symbol, and it is *not* our intention that they all be assumed
to be alised to _atom_site_symbol.  I think that this is probably more a
DDL issue than a content issue, and perhaps John ans the other who think
carefully about DDL might want to give this some thought.  
 
- - - - -

Peter Keller writes:

A small point first: lines 13231 and 13232 are identical:

   '_phasing_MIR.entry_id'           '_entry.id'

Now, a lot of items have _item_type.code defined as char, when in fact,
they should clearly be text (the difference being that text can cover
several lines, where char is limited to one)...[much other stuff deleted]

- -
 
When I first read this, my reaction was "Oh dear, how can Peter have gotten
the wrong idea.  We don't made a distinction between char and text."  Then
I looked at the dictionary, and realized that there were indeed three data
items where we used 'text' instead of 'char.'  There were mistakes, and
they have been fixed, but my deepest apologies to Peter for sending him on
a wild goose chase through the dictionary, trying to find things that should
be text instead of char.  Again, remember, we make no such distinction.

- - - - -

Eldon Urich writes:

3.  Is there a data name for defining a chiral atom as having an R or S
configuration?  I could not find this in the ENTITY or CHEM_COMP sections.

The Klyne and Prelog reference given in the GEOM_TORSION group is, I
believe, a bit of misinformation carried over from the core CIF.  As
referenced this paper does not exist and the correct reference is
Experientia 16, 521-523 (1960).

- -

A data item has been added for the R vs S specification, and the reference
has been corrected.

- - - - -

While I was writing this, I received the list server copy of the posting I
thought I had made on Tuesday of this week.  It appears to have gotten stuck
somewhere for a couple of days - sorry for the delay.  I guess this way I get
to carry through on what I said I was going to do before you all ever knew I
had said it.

Here is the audit trail for the new version - I'll be back with you all in a
couple of weeks.

;
  0.7.25 1995-08-31
;
  Changes (PMDF):
    + Eliminated duplicate line in _entry_id parent/child table
    + Changed the three occurrences of _item_type.code text to char
        _atom_sites_alt.details
        _atom_sites_alt_ens.details
        _database_PDB_remark.text
    + Fixed Klyne and Prelog reference in GEOM_TORSION category description
    + Added data item _chem_comp_chir.atom_config
    + Added hyphen in non-crystallographic in definition sof
         _struct_ncs_ens.point_group
    + Changed Data Base to Database when referring to the CSD
    + Fixed four occurrances of 'the the' in definitions
    + Added _item_range.maximum and _item_range.minimum DDL items to
         _refine.ls_abs_structure_Flack and removed discussion of limits from
         the definition.
    + Changed two occurances of 'will be' to 'are' in the definition of
         _entity.type.
    + Changed ENTITY_NPOL to CHEM_COMP in definition of _entity.type.
    + Changes ATOM to HETATM for APS coordinates in Example 1 for the
          ATOM_SITE category
    + Corrected _item.category_id for _struct_mon_details.prot_cis.
    + Corrected _item.category_id for _refine_hist.details.
    + Rewrote header comments to emphasize use of the mmCIF listserver as the
      forum for the dictionary review process.
;

********************************************************************************
 Dr. Paula M. D. Fitzgerald  ______________ voice and FAX: (908) 594-5510
   Merck Research Laboratories ______________ email: paula_fitzgerald@merck.com
     P.O. Box 2000, Ry50-105     ______________ or bean@merck.com           
       Rahway, NJ 07065  USA 
         (for express mail use 126 E. Lincoln Ave. instead of P. O. Box 2000)  
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