ChemComp maintenance

This page contains very technical information on how chemComps get updated from the PDBe database.

Source information (PDBe database at the PDBe group, EBI, Cambridge):

• • Contains records per 'chemical component' (or 'chemical compound') on the wwPDB chemComps.

  • These records are updated each week Wednesday from the mmCIF chemical compound archive from the wwPDB.

  • During a big wwPDB remediation effort during 2008 and the beginning of 2009, all these chemical components were updated and cleaned up.

  • This PDBe database is different from the original (MSD) database that was used for the initial creation of CCPN chemComps.

CCPN chemComp status:

• • From November 2008, the CCPN chemComp archive is stored at the CcpForge site using CVS.

  • In March 2009, the CCPN chemComps were updated from the new remediated information from the wwPDB.

  • All scripts to deal with the conversion of the source data to CCPN were by this time updated (for use with the PDBe database and for CCPN v2.0 handling).

  • At this point, an automatic weekly update mechanism was created.

In below, 'data directory' refers to <ccpnmrdir>/data/pdbe/chemComp/.

File handling:

• • All chemComp(Coord) files are first saved to a temporary directory, then copied over to the final data directory (either archive/ or test/)

TODO (23rd March 2009):

• • Make sure ChemCompOverview.py is up-to-date with new chemComp info (problems with permissions for updateChemCompXmlWeb.py!)

  • Rerun cifCodeRedirect.py

  • Fix problems with uppercasing of new DNA residues

  • Make sure to set link information

  • Update using weekly update code after major rerun.

  • Set up automated weekly system (use TAG!)

  • PCA XEasy info (mails 18/02/2008)

TODO (not urgent):

• • Fix issues with IUPAC naming system (also then have to fix DataFormat, ...)

  • Use variant info from PDB for protein molType information (charges, smiles, ...)

  • Fix chemComp manual editor

Notes:

• • Check 'Backward compatibility' comments in exportChemComps.py to see where 'old' naming systems are re-inserted into newly made chemComps.