Changes between Version 5 and Version 6 of mmcif-issues


Ignore:
Timestamp:
Mar 10, 2016, 1:51:43 PM (10 years ago)
Author:
gregc
Comment:

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  • mmcif-issues

    v5 v6  
    1 = Practical mmCIF Issues =
     1= (DRAFT) Practical mmCIF Issues =
    22(And some proposed solutions)
    33
    … …  
    1111    * [[#conn|Missing connectivity]]
    1212    * [[#metal|Metal coordination bonds]]
    13     * [[#water|Nonunique Waters]]
     13    * [[#water|Nonunique waters]]
    1414    * [[#size|Different sized models]]
    1515    * [[#optional|Missing why/when categories are optional]]
    … …  
    164164
    165165
    166 == wwPDB doesn't follow CIF standard markup conventions == #standard
     166== wwPDB doesn't follow CIF standard == #standard
    167167
    168 CIF text has a standard markup to write greek letters, accented letters, super- and subscripts, and some typographic style codes. mmCIF uses old PDB format markup. Ideally, text data values would use UTF-8 Unicode standard.
     168mmCIF files are for the most part CIF files.  But they don't follow the CIF standard for text markup.  Instead, they use the markup from PDB files.
     169CIF text has standard markup to write greek letters, accented letters, super- and subscripts, and some typographic style codes.
    169170
    170171=== Proposed fix: ===
    171172
    172 The mmCIF documentation needs be explicit about which parts of the CIF standard it conforms to.
     173* The mmCIF documentation needs be explicit about which parts of the CIF standard it doesn't conforms to.
     174* Eliminate most markup and use UTF-8 for text (except for data values that appear in the ''atom_site'' category, since UTF-8 would make the fixed width column optimization more difficult to generate).
    173175
    174176