User:Henning/OpenMMS

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[edit] Loading PDB data into a local relational database

Here you find some information about my modified version of the OpenMMS relational database loader. This application parses mmCIF files (provided by the PDB) and loads them into a SQL relational database.

For more information about OpenMMS see:

• http://openmms.sdsc.edu/
• http://openmms.sdsc.edu/OpenMMS-1.5.1_Std/openmms/docs/OpenMMS_Overview.html
• http://openmms.sdsc.edu/OpenMMS-1.5.1_Std/openmms/docs/guides/PDBase.html

In the modified version, there is a new command line parameter action for the executable PDBase which lets you do CIF loading in batch mode without the graphical user interface (see readme file in the downloadable archive for details).

There are some issues with remediated files:

• the compressed file format has changed, so pdbase can only process uncompressed cif files at the moment
• loading from manifest does not work for some reason

My pipeline for automatic updating is as follows:

1. rsync with the pdb ftp site (See http://www.wwpdb.org/downloads.html)
2. uncompress cif files
3. create a list of pdb codes to be loaded
4. load files with the 'load from list' option

I have previously had problems with some cif files which failed to load. This may have been fixed by now but to be safe you may want to exlude the following pdb codes from the list:

• 1htq
• 2hyn
• 2ad1
• 2gwh
• 2i2q
• 2j07 (unknown cifparse exception)
• 2etg (now obsoleted)

[edit] Download

openmms_new.zip

[edit] See also

http://sw-tools.pdb.org/apps/DB-LOADER/index.html