Multiple Sequence Viewer/Editor — Using BLAST and PDB Databases

To use a local BLAST or PDB database with the Multiple Sequence Viewer, you must first run a script to download or update the database, followed by setting an environment variable to point to the database.

Using a local BLAST database with the Multiple Sequence Viewer

To use a local BLAST database with the MSV, the update_BLASTDB utility updates the BLAST database from a copy on the Schrödinger website that is synchronized with the BLAST website, or via FTP from the NCBI website. The preformatted database files are downloaded. The syntax is:

$SCHRODINGER/utilities/update_BLASTDB [options]

For a description of the options, run the command with the -h option.

The BLAST database is installed in the first location found in the following list:

• $PSP_BLASTDB
• $SCHRODINGER_THIRDPARTY/database/blast
• $SCHRODINGER/thirdparty/database/blast

Using a PDB database with the Multiple Sequence Viewer

To use a local PDB database with the MSV, the rsync_pdb utility creates and updates a local mirror to the PDB. The syntax is:

$SCHRODINGER/utilities/rsync_pdb [options]

For a description of the options, run the command with the -h option.

The PDB database is installed in the first location found in the following list:

• $SCHRODINGER_PDB
• $SCHRODINGER_THIRDPARTY/database/pdb
• $SCHRODINGER/thirdparty/database/pdb

Using environment variables to point to the databases

You only need to set environment variables if any of the software or databases are outside of the Schrödinger installation. You can also use these environment variables if you have a customized copy of the databases, for example. If the BLAST and/or PDB databases are installed into the default location in the Schrödinger software installation ($SCHRODINGER/thirdparty), you do not need to set any extra environment variables.

However, when you install a new Schrödinger software release, you must make sure that these PDB and BLAST databases are installed into the new default location.

On Windows, if you are using an installed copy of the PDB to run Structure Prediction jobs, you must set the SCHRODINGER_PDB environment variable in Windows or UNC format. For use on a Linux host, you can set the environment variables for all users in /etc/profile.d. You can set the environment variables for remote hosts in the schrodinger.hosts file. For BLAST and PDB databases, the environment variables and descriptions are as follows:

• Additional Resources