Changes between Version 4 and Version 5 of mmCIFWriting


Ignore:
Timestamp:
Mar 3, 2018, 5:35:00 PM (8 years ago)
Author:
Greg Couch
Comment:

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  • mmCIFWriting

    v4 v5  
    1414
    1515 v1::
    16   The minimal set of tables needed to properly reconstruct the connectivity are the **entity_poly_seq**, **atom_site**, and **struct_conn** tables.  Minimal work for the **struct_conn** table, just disufide and inter-residue metal coordination bonds
     16  Add the **entity** and **chem_comp** tables.  And the **audit_conform** table with our annotation that all keywords are in lowercase.  Reuse entity descriptions from metadata if possible.
    1717
    1818 v2::
    19   For completeness (define stuff that **id**'s refer to), add the **entity** and **chem_comp** tables.  And the **audit_conform** table with our annotation that all keywords are in lowercase.  Reuse entity descriptions from metadata if possible.
     19  The minimal set of tables needed to properly reconstruct the polymeric connectivity are the **entity_poly_seq** and **atom_site** tables. **atom_site_anisotrop** is easy, so do it also.
    2020
    2121 v3::
    22   Add support for writing the **atom_site** and **atom_site_anisotrop** tables with fixed width columns and add that annotation to the **audit_conform** table.
     22  Add secondary structure annotations.  Just output helices and each strand in a separate sheet.  Fix someday when sheet information becomes available.
    2323
    2424 v4::
    25   Add secondary structure annotations.  Just output helices and each strand in a separate sheet.  Fix someday when sheet information becomes available.
     25  Add symmetry metadata if saved (**pdbx_struct_assembly**, **pdbx_struct_assembly_gen**, **pdbx_struct_oper_list**)
    2626
    2727 v5::
    28   Add symmetry metadata if saved (**pdbx_struct_assembly**, **pdbx_struct_assembly_gen**, **pdbx_struct_oper_list**)
     28  Initial version of the **struct_conn** table, just disufide and inter-residue metal coordination bonds
    2929
    3030 v6::
    … …  
    3838
    3939 v9::
     40  Add support for writing the **atom_site** and **atom_site_anisotrop** tables with fixed width columns and add that annotation to the **audit_conform** table.
     41
     42 v10::
    4043   Embed residue templates (**chem_atom** and **chem_bond** tables), like the [[http://www.pdbe.org|PDBe]] does in its "updated" mmCIF files.  Residues with metal coordination bonds in them have "ambiguous" connectivity.
    4144
    42  v10::
     45 v11::
    4346   Review other metadata that is keep and try to incorporate it.
    4447