Installing Prime Third-Party Software and Databases on Linux

Prime third-party products are included in the web download and are installed by default. The Pfam database is also installed by default, as well as data required for web-based BLAST searches. PSIPRED is not included or required, but is highly recommended.

Prime can obtain PDB files and run BLAST searches on the web or on a local database. For web-based searches, the default Prime installation is sufficient. For local database access the PDB and BLAST databases must be installed.

If you already have any of the third-party products installed and want to use the existing installation rather than installing another copy, you can do so by setting the appropriate environment variables, which are described in Software Requirements for Prime. Likewise, if you want to install any of these products in a location other than the standard location in $SCHRODINGER/thirdparty, you should use that location in the relevant steps below, and set the appropriate environment variables. The instructions below assume that you are installing into the standard location.

It is assumed that you have already installed the Prime software and set the SCHRODINGER environment variable.

To install the PDB and BLAST databases:

Run the following scripts:

$SCHRODINGER/utilities/update_BLASTDB

$SCHRODINGER/utilities/rsync_pdb

The BLAST databases are installed in the first location found in the following list:

The location specified by the -f option.
$PSP_BLASTDB
$SCHRODINGER_THIRDPARTY/database/blast
$SCHRODINGER/thirdparty/database/blast

Likewise, the PDB is installed in the first location found in the following list:

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

If an environment variable in these lists is not defined, the list item is skipped. The environment variables are described in Software Requirements for Prime.

To compile and install PSIPRED:

Create a directory in which to download and build PSIPRED.

This directory will be referred to as the build directory and labeled build-dir.

Download the desired version into the build directory from the PSIPRED download site:

http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/

(If this location changes, the PSIPRED home page is located at http://bioinf.cs.ucl.ac.uk/psipred.)

Change to the build directory and unpack the source code:

cd build-dir
tar xzvf psipredversion.tar.gz

Compile the code:

cd src
make
make install
cd ..

5. Create a directory in $SCHRODINGER for the software (if it does not already exist):

mkdir -p $SCHRODINGER/thirdparty/bin/Linux-x86_64/psipred

6. Copy the bin and data directories from the build directory:

cp -r bin/ $SCHRODINGER/thirdparty/bin/Linux-x86_64/psipred/
cp -r data $SCHRODINGER/thirdparty/bin/Linux-x86_64/psipred/

Check the final layout:

ls -R $SCHRODINGER/thirdparty/bin/Linux-x86_64/psipred/

The layout should look as follows:

.:
   bin  data
 
   ./bin:
   pfilt  psipass2  psipred  seq2mtx
 
   ./data:
   weights.dat   weights.dat3  weights_p2.dat  weights_s.dat2
   weights.dat2  weights.dat4  weights_s.dat   weights_s.dat3