Changes between Version 2 and Version 3 of mmCIFWriting

Timestamp:

Feb 5, 2018, 4:20:00 PM (8 years ago)

Author:

Greg Couch

Comment:

--

mmCIFWriting

@@ -5 +5 @@
 * Information needed to reconstruct some tables is discarded after being used (//e.g.//, the sheet information for strands)
 * Whether or not the structure has been edited incompatibly is unknown, so associated metadata may or may not still be valid
-* intra-residue metal coordination bonds
 
-== First Pass ==
+== Milestones ==
 
-The [[http://www.rbvi.ucsf.edu/chimerax/docs/devel/mmcif.html|ChimeraX Fast mmCIF Guidelines]] give ChimeraX's requirements for reading.
+The [[http://www.rbvi.ucsf.edu/chimerax/docs/devel/mmcif.html|ChimeraX Fast mmCIF Guidelines]] gives ChimeraX's requirements for reading.
 
-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, for example, hydrogen bonds would be skipped.
+ v1::
+  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
 
-After that, for completeness, we should add the **entity**, **chem_comp**, and **atom_site_anisotrop** tables.  And the **audit_conform** table with our annotation that all keywords are in lowercase.
+ v2::
+  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.
 
-Next, we should 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.
+ v3::
+  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.
 
-== Completing Connectivity ==
+ v4::
+  Add secondary structure annotations.  Just output helices and each strand in a separate sheet.  Fix someday when sheet information becomes available.
 
-All of the issues for the **struct_conn** table should be addressed:
+ v5::
+  Add symmetry metadata if saved (**pdbx_struct_assembly**, **pdbx_struct_assembly_gen**, **pdbx_struct_oper_list**)
 
-* intra-residue metal coordination bonds
-* hydrogen bonds
-* bonds missing from residue templates
+ v6::
+  Add hydrogen bonds -- maybe limit to inter-strand h-bonds?
 
-At this point, we could embed the residue templates (**chem_atom** and **chem_bond** tables) like the [[http://www.pdbe.org|PDBe]] does in its "updated" mmCIF files.
+ v7::
+  Add bonds missing from residue templates
 
-== Secondary Structure ==
+ v8::
+   Make sure intra-residue metal coordination bonds are handled correctly.
+
+ v9::
+   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.
+
+ v10::
+   Review other metadata that is keep and try to incorporate it.
+
+== Secondary Structure Notes ==
 
 The secondary structure annotations, specifically the sheet annotations, are difficult since ChimeraX does not keep the original sheet information nor does it compute it.  Functionally, the currently needed secondary structure information can be computed with the internal DSSP code.  But those annotations don't always match the author's.  Ideally, the sheet information would both preserved and be computed, so the mmCIF file could contain that information.  (The sheet information would eventually be useful for a fancy cartoon representation too.)
-
-== Assemblies ==
-
-ChimeraX keeps the information needed to reconstruct various assemblies as metadata, and that can be written as is.  If the structure has been edited, it may or may not be valid.
 
 == Other Metadata ==