Dictionary Status Update ... At last ...

• Messages sorted by: [ date ][ subject ][ author ]
• Previous message: Lynn Ten Eyck: "Re: names"

Dear Folks:

Greetings from New Jersey.  Helen, John and I are sitting here, trying very
hard to get caught up on the many issues that all of you have sent in over
the last few months.  We feel badly that this has all gotten so out of phase
with your contributions, but the only thing to do now is to get caught up
and to stay caught up.

Hence, we will not be replying to your individual contributions in the style
that I had previously established - rather, we will tell you what has been
done to address many of the specific issues, and we will tell you why we
are not planning to take any action of some of the other issues.  We are
trying to deal with everything, but some details will certainly fall through
the cracks - please feel free to raise issues again if you aren't satisfied
with the action we have taken, or with our reasons for deciding not to 
taking any action

This message is being written midway through our afternoon of updating the
dictionary.  What we have done so far is to deal with a large number of
the smaller issues.  The larger issues, the ones that require either more
thought or larger alternations to the dictionary, will be addresses as soon
as we tell you what has been done so far.

What we *have* done is summarized in the audit trail - you will note that
this covers two versions of the dictionary (1995-12-11 was never publicly
released because I never got around to writing the messages summarizing the
changes):

  0.7.29 1995-12-11
;
  Changes (PMDF):
    + Changes to my title and Brian's in header information.
    + Enhanced description of the 'Hill system' of element ordering in
        the definition of _chem_comp.formula.
    + Added _item.mandatory_code to _phasing_mir_der.native_set_id
    + Added DATABASE_PDB_CAVEAT category.
    + Changed supercedes to superseded in DATABASE category description.
    + Changed DATABASE_NEW to DATABASE_2 in category description.
    + Changed SRUCT_SHEET_TOPOLOGY to STRUCT_SHEET_TOPOLOGY in category
        description.
    + Changed examples for STRUCT_SHEET_RANGE to contain only
        _struct_sheet_range.symmetry, not _struct_sheet_range.beg_symmetry and
        _struct_sheet_range.end_symmetry
    + Added cell.Z_PDB data item
    + Changed _atoms_sites.cartn_tran_matrix to atom_sites.cartn_transf_matrix
        in definition of _atom_sites.cartn_transform_axes
    + Changed _chem_comp.nstd_class to _chem_comp.mon_nstd_class in
        definition of _chem_comp.mon_nstd_flag
    + Added data items for _chem_link_bond.value_angle and
        _chem_link_bond.value_angle_esd
    + Changed reference to _chemical_formula.appendix to CHEMICAL_FORMULA
        category description in definition of _chemical_formula.moiety
    + Changed _comp.prog.version to _comp_prog.version and 
        _comp.prog.citation_id to _comp_prog.citation_id in COMP_PROG example
    + Changed reference to _computing.phasing_mir in _phasing_mir.method to
        a reference to the COMP_PROG category.
        Similarly with _computing.phasing_averaging in 
        _phasing_averaging.method and _computing.phasing_mad in
        _phasing_mad.method and _computing.save_reduction in
        _reflns.data_reduction_method
    + Changed _entity.name_com.name to _entity_name_com.name in 
        ENTITY_NAME_COM example
    + Changed reference to _exptl_crystal.face_ to data items in the 
        EXPTL_CRYSTAL_FACE category in the definition of 
        _exptl_crystal.description.
    + Changed _diffrn.attenuator_code to _diffrn_attenuator.code in
        the definition of _diffrn_refln.attenuator_code
    + Changed _exptl.crystal_preparation to _exptl_crystal.preparation in the
        definition of _exptl.details
    + Changed _geom_bond.distance to _geom_bond.dist in the definition of
        _geom_bond.dist_esd
    + Added data items for _refine.ls_d_res_high and _refine.ls_d_res_low
    + Changed _refine.d_res_high to _refine.ls_d_res_high and
        _refine.d_res_low to _refine.ls_d_res_low in the definition of
        _refln.status
    + Changed _reflns_scale_group.code to _reflns_scale.group_code in the
        definition of _refln.scale_group_code
    + Changed _struct_site_view_details to _struct_biol_view.details in the
        rotation matrix element definitions in the STRUCT_BIOL_VIEW
        category (even though I realize that this isn't really correct in
        terms of the definition of _struct_biol_view.details)
    + Changed _symmetry.equiv_pos_as_xyz to _symmetry_equiv.pos_as_xyz in
        the definition of _symmetry.space_group_name_H-M
    + Changed _struct_mon.details_RSSR to _struct_mon_details.RSSR and
        _struct_mon.details_RSR to _struct_mon_details.RSR in a number of
        definitions in the STRUCT_MON_PROT and STRUCT_MON_NUCL categories
    + Changed _reflns_shell.possible_%_obs to _reflns_shell.percent_possible_obs
        in the REFLNS_SHELL example
    + Corrected alphabetical order of data items in the REFLNS_SHELL category
    + Changed _struct_sheet.number_details to _struct_sheet.details in the
        STRUCT_SHEET examples
    + Replaced _struct_sheet_range.beg_symmetry and
        _struct_sheet_range.end_symmetry with _struct_sheet_range.symmetry
        in the STRUCT_SHEET_RANGE category and fixed example itself
    + Changed _refine.ls_number_reflns to _refine.ls_number_reflns_obs in the
        definitions of _refine.ls_restrained_S_all and
        _refine.ls_restrained_S_obs
    + Changed _refine_ls_shell.reflns to _refine_ls_shell.number_reflns_obs in
        the REFINE_LS_SHELL example
    + Removed example from DATABASE category as it was not longer valid
;
  0.7.30 1996-01-29
;
  Changes (PMDF, HB, JDW):
    + Added data items for pseudorotation in STRUCT_MON_NUCL.
    + Globally changed future tense usage to present tense (eg. will be -> is)
    + Added _citation.book_publisher_city.
    + Changed _citation.journal_coden_PDB to _citation.journal_coden_CSD.
    + Added _citation.journal_coden_CAS.
    + Generalized the defintion of _atom_site.calc_flag.
    + Corrections to definitions defining beginning and ends of ranges in 
      category STRUCT_SHEET_HBOND.
    + Added data items _diffrn_refln.scan_rate and _diffrn_refln.scan_time_backgd
    + Added HELX_LH_27_P and HELX_RH_27_P helix enumeration types.  
    + Added figure of merit data item _refln.fom.
;

- - - - -

That is the easy part - it takes a few more words to discuss the items where
we have decided to take no action.

* We decided not to change explt to expt - exptl comes from the core, and we
  would generate more heat than light by changing it at this point.

* We decided not to changes entity to mol, or mon(monomer) to residue - 
  the first decision again comes from a desire not to generate confusion, as
  we chose entity to be a term distinct from molecule, which already means
  something specific to most people.  We also chose monomer instead of 
  residue to be neutral over proteins, nucleic acids, and sugars.

* We didn't add citation keywords, mostly because it would be a lot of trouble.
  As keywords are a list, they would require a separate category and pointers
  back to citation, and it didn't seem that they added enough that was 
  critical to the archive to generate yet another list.  This decision can
  be revisited is there if a general desire for this list.

* We talked about the Q atom types for NMR structures.  It seemed to us that
  Q atoms can easily be thought of as either dummy or (more likely) calcalated
  atomic positions, and that the current list of enumerations suffices.  We
  did, however, change the defintion of d in that enumeration list so that 
  'diffraction' became 'experiment', and thus technique-neutral.

* With respect to the format for names, it was my recollection that COMCIFS
  has already discussed how to deal with Jr, III, etc.  We have written to
  Brian MaMahon to see if he can tell us what the decision was.

* PDB TER records.  We believe that this is a software issue, not a data
  structure issue.  All of information necessary for generating a TER record
  can be generated from the coordinate and sequence data items.

* We consider the discussion of "looped aliases" to be resolved.  There were
  a number of mail messages about this, but since no one seems to still be
  pushing the point, we assume that this issue has been clarified to every-
  one's satisfaction.

* We have looked in detail at the many points Dale has made about the domain,
  if you will, in which experimental vs. model data items should be stored.
  These points are well taken, but we don't think that they are issues to be
  decided at the dictionary level.  Rather they are organizational issues to
  be decided by whoever is using this data structure to archive data - that
  could be either a public database or your home lab.

* We are not currently enforcing a a 32-charcter length for data item names.

* We are not using GLOBAL declarations in either dictionaries or data files.

* We are assuming that . and ? are part of the STAR grammar.  As such, they
  do not need to be included in each regular expression.  The assumption
  is that a parser would check for . and ? first, and, failing to find them,
  proceed to validate the item against the regular expression.

* Units extensions are obsolete.  Although they existed in the original
  core dictionary, they have been dropped from DDL 1.4 (and they never
  existed in DDL 2.1).

* The issue of chain ids has come up from several directions.  In order
  to correctly cross reference data items, chain ids are mandatory.

* With respect to psuedorotations, Helen has come up with a list of data
  items appropriate for the pseudorotation angles found in nucleic acids.
  But that is a special case, and it is appropriate that a more general
  set of definitions should also be added.  Perhaps Dale, who has already
  given this some thought, could contribute to the generation of those
  data items.

OK, that it is for round one and we will now proceed to round two.  We'll
be back.

Paula, Helen, John 

****************************************************************************
*  John Westbrook                       Ph:  (908) 445-4290                *
*  Department of Chemistry              Fax: (908) 445-4320                *
*  Rutgers University                                                      *
*  PO Box 939                        e-mail: jwest@rutchem.rutgers.edu     *
*  Piscataway, NJ 08855-0939                                               *
****************************************************************************

• Previous message: Lynn Ten Eyck: "Re: names"