Changes between Version 1 and Version 2 of mmCIFWriting

Timestamp:

Feb 5, 2018, 11:43:16 AM (8 years ago)

Author:

Greg Couch

Comment:

--

mmCIFWriting

@@ -13 +13 @@
 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.
 
-After that, for completeness, we should add the **entity** and **chem_comp** tables.  And the **audit_conform** table with our annotation that all keywords are in lowercase.
+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.
 
-Next, we should add support for writing the **atom_site** table with fixed width columns and add that annotation to the **audit_conform** table.
+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.
 
 == Completing Connectivity ==
@@ -29 +29 @@
 == Secondary Structure ==
 
-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.)
+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 ==
+
+ChimeraX keeps and uses other metadata that is only valid if the structure is not edited incompatibly.  For example, adding or removing hydrogens would be okay, adding a missing residue should be okay, deleting some residues may or may not be okay.  Not sure what to do yet, the safest thing to do, is to skip writing the metadata.  An initial conservative approach would be to modify the code to mark when the structure has been edited for any reason, and only write the metadata if it hasn't been edited.  If we could handle this issue, our original goal of writing what we read could be met.