pdb2cif update

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• Previous message: Herbert J. Bernstein: "ciftbx update"

pdb2cif has been updated to release 2.3.2 of 22 Sep 96.  The following is
a summary of the most recent changes:

Release 2.3.2 has several changes for compliance with the mmCIF
dictionary version 0.8.02, in response to some problems discovered by
John Westbrook and the checking provided by his ciflib routines. The most
visible changes are the listing of the standard residues used in an entry
in the CHEM_COMP category, changing use of a quoted blank field as a
value for _atom_site.auth_aym_id to a period, and moving some data items
common to a loop into the loop itself.

Release 2.3.1 corrects some minor problems in release 2.3.0. In
particular a problem with a bad item count and a bad date on machines
running some older versions of perl has been corrected.   Extra
warnings for NMR entries with unusual uses of B-values or occupancies
have been added.

Release 2.3.0 was an update to Release 2.2.7 correcting some minor
problems with data item types, long publication names, and a failure to
report CSD codens.

Release 2.2.7 was the first pdb2cif release after PDB entries compliant
with the February 1996 V2.0 PDB format became available. The format of
data items in ATOM_SITE lists derived from V2.0 entries was corrected,
and the mapping of HETNAM and HETSYN moved from ENTITY_NAME_SYS to
ENTITY_NAME_COM.

For prior revisions, see CHANGES in the release.

Compliance

This version is intended to produce mmCIF files conforming to mmCIF
version 0.8.02 and above.
Full compliance is not possible in some areas. In particular, the most of
values used for
_exptl.method, and some of the values used for _struct_conf_type.id do
not conform to the enumerations in the dictionary. Full compliance would
require agreement
between the PDB and COMCIFS on equivalent lists of values.

The following definitions would have to be appended to the mmCIF
dictionary for validation of pdb2cif output:

save__struct_conn.ptnr1_atom_site_id
    _item_description.description
;              The id of an atom site for the first partner in a bond

               This data item is a pointer to _atom_site.id in the
               ATOM_SITE category.
;
    _item.name                  '_struct_conn.ptnr1_atom_site_id'
    _item.mandatory_code          no
    _item.category_id             struct_conn
    _item_linked.child_name     '_struct_conn.ptnr1_atom_site_id'
    _item_linked.parent_name    '_atom_site.id'
     save_

save__struct_conn.ptnr2_atom_site_id
    _item_description.description
;              The id of an atom site for the second partner in a bond

               This data item is a pointer to _atom_site.id in the
               ATOM_SITE category.
;
    _item.name                  '_struct_conn.ptnr2_atom_site_id'
    _item.mandatory_code          no
    _item.category_id             struct_conn
    _item_linked.child_name     '_struct_conn.ptnr2_atom_site_id'
    _item_linked.parent_name    '_atom_site.id'
     save_

save__atom_site.label_model_id
    _item_description.description
;              A component of the macromolecular identifier for this atom
               site.
               The value of _atom_site.label_model_id associates the atom
               site with a particular nmr model.

;
    _item.name                  '_atom_site.label_model_id'
    _item.mandatory_code          no
    _item.category_id            'atom_site'
    _item_type.code               code
     loop_
    _item_linked.child_name
    _item_linked.parent_name
         '_struct_mon_prot.label_model_id'     '_atom_site.label_model_id'
         '_struct_mon_prot_cis.label_model_id' '_atom_site.label_model_id'
     save_


save__struct_mon_prot.label_model_id
    _item_description.description
;              This data item is a pointer to _atom_site.label_model_id
               in the ATOM_SITE category.
;
    _item.name                  '_struct_mon_prot.label_model_id'
    _item.mandatory_code          no
    _item.category_id             struct_mon_prot
     save_

save__struct_mon_prot_cis.label_model_id
    _item_description.description
;              This data item is a pointer to _atom_site.label_model_id
               in the ATOM_SITE category.
;
    _item.name                  '_struct_mon_prot_cis.label_model_id'
    _item.mandatory_code          no
    _item.category_id             struct_mon_prot_cis
     save_

save__struct_ref_seq_dif.db_seq_num
    _item_description.description
;              The sequence position in the referenced database entry
               corresponding to this point difference position.

               The use of . for _struct_ref_seq_dif.db_seq_num when
               a value has been given for _struct_ref_seq_dif.seq_num
               indicates that there has been an insertion at this
               position.

               The use of . for _struct_ref_seq_dif.seq_num when
               a value is given for _struct_ref_seq_dif.db_seq_num
               indicates that there has been a deletion at this
               position.
;
    _item.name                  '_struct_ref_seq_dif.db_seq_num'
    _item.mandatory_code          no
    _item.category_id             struct_ref_seq_dif
     loop_
    _item_range.maximum
    _item_range.minimum
                                  .    1
                                  1    1
    _item_type.code               int

     save_

-- Herbert J. Bernstein (yaya@bernstein-plus-sons.com)

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