Knowledge Base

First, you must install the extensions into your KNIME installation and install the Schrödinger software. See Article 1084.

To use the Schrödinger nodes, the KNIME installation must know where to find the Schrödinger software installation. You can use one of the following methods to start KNIME so that it finds the installation.

(1) Set preferences in KNIME to identify the Schrödinger software installation (2013-1 release on).

Go to File → Preferences, and under KNIME, choose Schrodinger. You can then set SCHRODINGER to the full path to the Schrödinger software installation. If this item is unavailable, it means that the installation has already been picked up from your environment variable settings. See the Installation Guide for details. You can also identify the PyMOL installation by setting PYMOL4MAESTRO. Restart KNIME after setting the preferences.

This is not sufficient if you want to use the native 2D renderer, for which you must use option (2) or (3) below. As of the 2014-3 release, there is a new Python-based 2D renderer, which does not require setting up the environment as done in option (2) or (3). The native renderer (labeled Canvas 2D-JNI) is still available but it is deprecated.

(2) Create a script that sets up the environment, place it in your standalone KNIME directory, and run this script.

Examples of the script to use are available for download for Linux, Windows, and Mac.

(3) If you already have a script that you use to set up the environment for KNIME, copy the contents of the appropriate example script mentioned in the previous item into your own KNIME startup script, and edit it as needed.

(4) Use the KNIME startup script in the Schrödinger installation.

On Linux or Mac, open a terminal window, set the SCHRODINGER environment variable to point to the Schrödinger installation, then run the following command:

$SCHRODINGER/knime -knimeInstallDir path-to-standalone-KNIME

On Windows, you can add the path to the KNIME installation to the shortcut installed with the Schrödinger software. Right-click on the shortcut and choose Properties, then add -knimeInstallDir path-to-standalone-KNIME to the end of the text in the Target text box. Make sure that you don't replace the existing text, and make sure that you add a space between the existing text and the new text.

(5) Use the run command in the Schrödinger installation.

On Linux or Mac, open a terminal window, set the SCHRODINGER environment variable to point to the Schrödinger installation, then run the following command:

$SCHRODINGER/run path-to-standalone-KNIME/knime

On Windows, you can open a Schrodinger Command Prompt window and run the following command:

run path-to-standalone-KNIME/knime