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Article ID: 1361 - Last Modified: April 19, 2011

Where can I obtain the GPCR-specific BLAST sequences needed to run with the Align GPCR option in the Edit Alignment step?

The GPCR-specific BLAST sequences are included with the Prime software and third-party databases. If you install the BLAST database from a Prime distribution, these sequences are automatically included. They are updated when you run the utility update_BLASTDB.

If your BLAST database did not come from Schrödinger, you can download the GPCR-specific BLAST sequences from the Schrödinger ftp site. The sequences are provided in a compressed tar file, which can be found at:

ftp://ftp.schrodinger.com/support/hidden/gpcr/gpcr_blastdb.tar.gz

If you are prompted, the username is anonymous and the password is your email address. You will need to type the path name and file exactly as shown above, as the directories and contents are hidden.

When you have downloaded this file, extract it into the BLAST database directory, which is one of the following directories, depending on how your environment variables are set:

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

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