Prime User Manual - ISP

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Chapter 12: Command-Line Utilities
12.5 Database Update Utilities
Prime uses two databases, the PDB database and the BLAST database. As these databases are
continually being updated, the versions distributed with the software will not have the latest
contributions. Utilities have been provided for updating these databases from the web sites.
12.5.1 update_BLASTDB
This utility updates the BLAST database from a copy on the Schrödinger web site that is
synchronized nightly with the BLAST web site. The preformatted database files are downloaded.
Syntax:
$SCHRODINGER/utilities/update_BLASTDB
The BLAST database is installed in the first location found in the following list:
• $PSP_BLASTDB
• $SCHRODINGER_THIRDPARTY/database/blast
• $SCHRODINGER/thirdparty/database/blast
These environment variables are described in Appendix B. You must have permission to write
to the destination in order to run this utility.
12.5.2 rsync_pdb
This utility creates or updates a local mirror of the PDB.
Syntax:
$SCHRODINGER/utilities/rsync_pdb
The PDB is installed in the first location found in the following list:
• $SCHRODINGER_PDB
• $SCHRODINGER_THIRDPARTY/database/pdb
• $SCHRODINGER/thirdparty/database/pdb
These environment variables are described in Appendix B. You must have permission to write
to the destination in order to run this utility.
This utility uses an rsync server on the Schrödinger web site that enables the files to be downloaded.
The files are written in the new remediated format. The Schrödinger site is updated
nightly from the PDB.
Prime 2.1 User Manual