Update ADIT-NMR dictionary on BMRB-only platform

The dictionaries

There are two sets of dictionaries:

  1. files used by ADIT-NMR, and
  2. files used by the validator “post-processor”.

Both sets should be installed at the same time to keep the versions in sync.

Dictionary files are stored in their own subversion repository.

As of the time of this writing ADIT-NMR on programmer and QA platforms is installed in /adit/www.

svn checkout

Check out http://svn.bmrb.wisc.edu/svn/nmr-star-software-dictionaries into e.g. ~. Initial checkout:

cd ~
svn co http://svn.bmrb.wisc.edu/svn/nmr-star-software-dictionaries

After that you can just

cd ~/nmr-star-software-dictionaries
svn up

to fetch the updates.

ADIT-NMR dictionaries

  1. should be in ~/nmr-star-software-dictionaries/adit-nmr-2015
  2. Copy all files to ADIT-NMR's dictionaries directory:
    cd ~/nmr-star-software-dictionaries/adit-nmr-2015
    cp View-bmrb.cif adit_nmr_upload_tags.csv bmrb_1.view default-entry.cif dict.cif mmcif_bmrb.dic nmrcifmatch.cif refdb.str table_dict.str /adit/www/dictionaries/
  3. Build the binary version of main ADIT-NMR dictionary (cif_bmrb.dic.odb):
    cd /adit/www/dictionaries/
  4. Copy files to ADIT-NMR's config directory:


    cp View-bmrb.cif adit_nmr_upload_tags.csv bmrb_1.view cif_bmrb.dic.odb default-entry.cif dict.cif mmcif_bmrb.dic nmrcifmatch.cif table_dict.str /adit/www/adit/config/bmrb-adit/


  5. Build binary versions of the view file (View-bmrb.cif) and entry template file (default-entry: it's used to prepopulate new sessions when the “BEGIN” button is pressed, it contains a few snippets of NMRIF data to represent a few default values that force some flags to start out the way we want).
    cd /adit/www/adit/config/bmrb-adit/


    ../../../cgi-bin/bmrb-adit/prebuild-binary-templates View-bmrb.cif default-entry.cif View-bmrb.odb default-entry.odb


Validator dictionary

  1. should be in ~/nmr-star-software-dictionaries/validator/production
  2. copy validict.3.str file to ADIT-NMR's config and dictionaries directories:
    cp validict.3.str /adit/www/adit/config/bmrb-adit/
    cp validict.3.str /adit/www/dictionaries/

(File refdb.str is part of the validator, however, the version in validator/production includes data for a lot of non-standard residues that makes it quite big and slow to load. Since that data is not used by ADIT-NMR post-processor, there is a separate “trimmed-down” version of refdb.str in adit-nmr repo.)


At this point the dictionary is installed and can be tested – test only by starting a new deposition from the beginning.

Depositions make their own cached copy of the dictionary files that were present in the adit/config/bmrb-adit/ directory at the moment the deposition began, and they continue using that version of the dictionary throughout, so any dictionary changes won't be seen in previous sessions that were already begun before the update happened. This is quite a deliberate choice, as the data files for a session use binary data tables that would be corrupted if the dictionary added a new field and suddenly changed the program's idea of how many columns there are supposed to be in the table.