Installing Local Copies of the Prime Third-Party Software and Databases

If you want to use a local copy of the PDB and BLAST databases, you can download them from the relevant web sites or obtain them from Schrödinger on separate DVDs. Instructions are given in Installing Prime Third-Party Software and Databases on Linux, Installing Prime Third-Party Software and Databases on Windows, and Installing Prime Third-Party Databases on a Mac. It is highly recommended that you install the PDB and BLAST databases in a location outside the Schrödinger software installation.

If you install your own copy of the PDB database, 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

The exception is Windows, where the data/structures/all subdirectory is absent (and is not required).

If you choose to use your own installations of the third-party software, the following versions are required:

• BLAST+
• PSIPRED 3.x
• HMMER 3.0 and Pfam 26.0.

Note: The current version of Pfam is incompatible with previous versions distributed with Schrödinger software. If you have been using a version of Pfam that is installed outside the Schrödinger installation, you should ensure that you set the appropriate environment variables to point to a compatible version—see Table 1.