Installing Prime Third-Party Software and Databases on Windows
Prime allows you to do both web-based searches of the BLAST and PDB databases and searches of a local copy of these databases. The required Prime third-party software is included in the Prime installer, and is installed into the thirdparty folder of the installation by default. The databases needed for web-based searches are also included in the Prime installer, and are installed by default. When you do a default installation of Prime, you need not do anything more to enable web-based searches (for finding homologs, secondary structure prediction, and alignments). If you have a web proxy server, you may have to configure it—see Access to the Web via a Proxy for Schrödinger Applications.
If you want to use local databases, you must install the databases and set the appropriate environment variables.
The required Prime third-party databases can be installed directly from the web. When you install the databases, you should consider installing them to a network-mounted disk, because of the space required and so that they can be used by multiple users. If you do so, you must set environment variables to identify these databases—see Software Requirements for Prime. You should not install the databases into the Schrödinger software installation.
Note: PSIPRED is not supported on Windows.
To update or download the BLAST and PDB databases:
| 1. | Choose Start → All Programs → Schrodinger-2026-1 → Schrodinger Command Prompt. |
A DOS command prompt window opens, in which you can type the required commands.
| 2. | Set the path to the third-party databases by typing the following command: |
set SCHRODINGER_THIRDPARTY=thirdparty-location
If you installed the third-party databases in the default location, or if the SCHRODINGER_THIRDPARTY environment variable is already set, skip this step.
| 3. | Run the rsync_pdb utility by typing the following command: |
rsync_pdb
| 4. | Run the update_BLASTDB utility by typing the following command: |
update_BLASTDB -b
The download starts, and the progress of the process is printed in the shell window. When it is finished, you can close the command prompt window.
Note: The copy of the PDB database installed as described here does not include an all folder. While this does not affect the running of Schrödinger software, its absence might affect the running of other software that relies on the presence of this folder.