Prime User Manual - ISP

Prime User Manual
Appendix B: Environment Variables
Appendix B
The only environment variable that must be set before you can run Prime is SCHRODINGER.
The following list is presented for your convenience in case you prefer a different location for
any Prime-related directories.
General
SCHRODINGER_THIRDPARTY: Directory containing third-party software and databases, which
can be installed with the installers supplied by Schrödinger. The databases are installed in the
database subdirectory; the software in the bin subdirectory. Each third-party product has its
own subdirectory under these subdirectories. The default location if this environment variable
is not set is $SCHRODINGER/thirdparty.
PDB
SCHRODINGER_PDB: Full path to a user-supplied copy of the PDB database. The default for
this directory is $SCHRODINGER/thirdparty/database/pdb if only SCHRODINGER is set;
if SCHRODINGER_THIRDPARTY is set, the default is $SCHRODINGER_THIRDPARTY/
database/pdb. The copy of the database must retain the directory hierarchy used by the PDB
and must include the following subdirectories to be usable with Prime:
data/structures/all/pdb
data/structures/divided/pdb
data/structures/obsolete/pdb
On Windows the data/structures/all subdirectory is absent (and is not required).
Blast
PSP_BLAST_DIR: Location of Blast executables. Default is $SCHRODINGER_THIRDPARTY/
bin/platform/blast/bin, with the default for SCHRODINGER_THIRDPARTY noted above.
PSP_BLAST_DATA: Location of Blast matrices. Default is $SCHRODINGER_THIRDPARTY/
bin/platform/blast/data, with the default for SCHRODINGER_THIRDPARTY noted above.
PSP_BLASTDB: Location of Blast databases. The BLAST databases distributed with Prime are
formatted with version 2.2.16. If your BLAST database does not conform to this format, you
might experience problems with Prime. Default is $SCHRODINGER_THIRDPARTY/
database/blast, with the default for SCHRODINGER_THIRDPARTY noted above.
Prime 2.1 User Manual 123