Combi-Chem - Start-up and Configuration

Combi-Chem

2 Start-up and Configuration

This chapter describes configuring the Cerius² Combi-Chem module. It includes:

: Running Cerius2
: Daylight setup
: Oracle setup
: MDL ISIS setup

Running Cerius2

Prerequisites

To run the Combi-Chem module, your workstation should have:

A licensed copy of Cerius² version 3.8, including an appropriate set of modules from the Combi-Chem suite (see Role of Cerius2 combinatorial chemistry software suite).
A home directory in which you can create subdirectories.

If you do not have this version installed, please contact your MSI support office to obtain a Cerius² v.3.8 CD and the Cerius² Installation and Administration Guide. You should then proceed to a normal installation of the Cerius² v.3.8 software.

Starting the program

To start Cerius² 3.8, move (cd) to a directory in which you have write permission and enter at the UNIX prompt:


>	C2DIR/bin/Cerius²

where C2DIR is the original Cerius² 3.8 installation directory.

If you are not familiar with running Cerius², refer to the Cerius² Modeling Environment documentation, available on the Cerius² CD or from the MSI website.

Daylight setup

This release provides an interface to Daylight for computation of 2D fingerprints. This version uses Daylight code version 4.51. Other Daylight releases may work, but they have not been tested and are not supported.

Setting environment variables

For this interface to work properly, the Daylight environment variables should be properly defined before starting a Cerius² session. The following environment variables should be set:


>	setenv DY_ROOT Daylight_root_directory

>	setenv DY_LICENSEDATA Daylight_license_file

>	set path = ($DY_ROOT/bin $path)

The Daylight software should be installed on a specified machine. You must declare the location of the Daylight software installation in your .cshrc file by setting the environment variable DY_ROOT. Specifically, the environment variable DY_ROOT must be set to the value of the root directory of the Daylight software as seen on the machine on which it runs.

The environment variable DY_LICENSEDATA must be set to point to the Daylight license file.

Testing licenses

Of course, you must not only have the files installed and the environment variable DY_ROOT defined but also have licenses. You can test the presence of Daylight licenses by entering:


>	$DY_ROOT/bin/testlicense

Cerius2 setup

If Daylight is installed and licensed on the machine on which Cerius² is running, no further setup is required.

If Daylight is installed and licensed on a machine other than the one where Cerius² runs, then you must tell Cerius² to run the SMILES application on the Daylight machine rather than (as is the default) on the local machine.

Start the SMILES application on the appropriate remote machine by:

1. Start Cerius².

2. Select the Utilities/External Processes... menu item. The Process Management control panel appears.

3. In the Application list box, scroll down and select the application named SDK_SMILES. Then the Host list box is filled in with the allowed choices for remote host.

4. Select the host name where Daylight is installed and licensed.

5. Click the Start action button. You see a message like the following in your text window:


Application SDK_SMILES is served by process smiles on iris142 `/usr/people/moises/daylight/obj/irix/smiles.exe' successfully started


smiles.exe : revision 97.091

You are now ready to use Daylight functionality.

Note

The Daylight interface for the input/output of SMILES strings and for calculation of fingerprints and other descriptors is available only for SGI systems running IRIX 6.2 or higher.

The Daylight interface for the input/output of SMILES strings and for calculation of fingerprints and other descriptors is available only for SGI systems running IRIX 6.2 or higher.

Oracle setup

This release provides an interface to Oracle for importing relational data into Cerius² study tables. This version uses Oracle version 7. Other Oracle releases may work, but they have not been tested and are not supported.

Setting environment variables

You must define the Oracle environment variables before starting a Cerius² session. The following environment variables should be set:


>	setenv ORACLE_HOME Oracle_root_directory

If LD_LIBRARY_PATH is defined:


>	setenv LD_LIBRARY_PATH $ORACLE_HOME/lib:$LD_LIBRARY_PATH

If LD_LIBRARY_PATH is not defined:


>	setenv LD_LIBRARY_PATH $ORACLE_HOME/lib

MDL ISIS setup

This release provides an interface to MDL ISIS for computation of 2D fingerprints and ISIS database searching applications. This version uses ISIS Host version 2.1. Other ISIS releases may work, but they have not been tested and are not supported.

Setting environment variables

You must define the ISIS environment variables before starting a Cerius² session. The following environment variables should be set by sourcing the appropriate script:


>	source ISIS_root_directory/bin/mdlnames.csh

Last updated May 19, 2000 at 01:50PM Pacific Daylight Time.