Installing Discovery Studio on Linux systems

Console mode installation is provided for customers who are limited only to a terminal and unable to redirect a display.

Follow these instructions for installing Discovery Studio for general use on Linux systems. For installation on Windows systems, see Installing Discovery Studio on Windows systems.

Pre-installation checklist

You should be prepared with the following information before proceeding with the Discovery Studio installation. We recommend reading the entire installation procedure before beginning.

System specifications - the computer should meet the minimum requirements.
Installation location - you can choose to install the software to a particular folder on your system.
Available ports for HTTP and HTTPS services - installation of the server requires ports for communication purposes. The selected ports cannot be already in use by other applications on your computer. (This is not needed if installing only DS Visualizer and/or Client Applications.)

Instructions for the installation wizard

If you are installing a downloaded version of DS Visualizer, begin with step 3 below.

Mount the Discovery Studio 1.6 media.
Change directories to where the Discovery Studio media is mounted. For example, this typically might be /mnt/cdrom , /media/cdrecorder, or /mnt/dvd:
```
> cd /mnt/cdrom 
```
Get a directory listing and look for the script ds_setup_linux.sh.
```
> ls
```
Run the ds_setup_linux.sh script. The -silent flag is not supported.
```
> ./ds_setup_linux.sh
```
When the Welcome screen appears, click the Next button.
On the next screen, you are prompted to specify the location for the installation. You can accept the default installation location, enter an alternate location, or navigate to the alternate location by clicking the Browse button. When the desired location is entered in the Directory Name field, click the Next button. This step takes several minutes to complete before the next screen displays.
If you are installing only DS Visualizer, skip to step 8.

To customize your Discovery Studio install

During the installation process, you are presented with options for installation, some of which require specific licenses. This step details the available options so that you can configure the required custom installation.

Features that are not selected during installation are unavailable when working in Discovery Studio. You can run the installer again to modify these choices if you want to change your selection of features at a later time by deselecting the previously installed features.

Specify whether to install the Client Application or the Server Application or both. Note that these choices affect which screens you see as you complete this installation.

Under Client Application, select the subsets of features you would like installed and available for use. The following table describes the installation options:

Installation Option	Included Products	Description
DS Visualizer Pro	DS Visualizer Pro	If you choose Client Application, the Visualizer Pro option is automatically selected. Visualizer Pro is a required category for all Client Application installations. Visualizer Pro provides the high-quality visualization features for researchers in the life sciences who seek to explore chemical and biological information in 3D. It allows you to construct, view, and analyze complex models; to access multiple views on data for information rich analysis; and to open files from a wide variety of modeling and sequence analysis applications.
Protein Modeling	DS Protein Families, DS Protein Health, DS Protein Similarity Search, DS MODELER, DS Analysis, DS Biopolymer, DS CHARMm, CFF, DS CHARMm-Lite	This category provides methods for matching sequences to protein structure templates; PDB searching; aligning sequences, templates, or structures; and generating or analyzing 3D structures. It also allows you to study the energetic, dynamic, and electrostatic properties of a protein or protein complexes. Some of the methods are CHARMm, BLAST, MODELER, Align123, Align2D, and Profile s-3D.
Computational Chemistry	DS LigandScore, DS Ludi, DS LigandFit, DS Analysis, DS Biopolymer, DS CHARMm, CFF, DS CHARMm-Lite	This category allows you to explore potential binding modes of novel ligands via docking and scoring: extend docking with in situ minimization, scoring, and scoring to virtually screen libraries of compounds for potential hits; and generate, find, and optimize fragment ligands with de novo design tools. Some of the methods include Ludi, LigandFit, DockScore, Gold Docking, and Docking Refinement.

The Server Application option is required to execute server protocols through Pipeline Pilot on this machine.

Upon finalizing your choices on the Select Features screen, Click the Next button.
If you selected Server Application, you will be presented with the following:
The Pipeline Pilot Destination Folder screen opens. Accept the default or browse to a new location. Click the Next button to continue.
To set the for the HTTP and HTTPS port numbers to be used by Pipeline Pilot for the Apache process, accept the defaults or enter new values. Note that these ports must not be in use by other services. Click the Next button to continue.

On the File Association screen, select whether you want to associate files to automatically open with Discovery Studio.
If you are installing only DS Visualizer, click the Finish button on the Install Wizard Complete screen to complete the installation and skip all remaining steps.
On the Ready to Install the Program screen, click the Install button to complete the installation.
On the Accelrys License Pack Welcome screen, click the Next button.
On the Accelrys License Pack Destination screen, accept the default or browse to the location of your common License Pack installation shared by other Accelrys software installations. Click the Next button.
On the Select features screen, follow the instructions on the screen. Click the Next button.
On the Ready to Install the Program screen click the Install button to complete the Accelrys License Pack installation.
When the installer reports completion of the Discovery Studio 1.6 and Accelrys License Pack installation, click the Finish button.
The Accelrys License Administrator starts. Follow the online instructions for installing a temporary license. If you do not have a password, click the Close button to complete the installation. You can configure licensing, if necessary, after installation. If a temporary license is installed successfully, click the Finish button to complete the installation.

After the installation has completed, Discovery Studio is ready for use. Start the application using the shortcut placed on the desktop or via the command line.

If you installed the server, you can connect to it using the hostname and the port number specified during installation.

To learn more about working with Discovery Studio, see the Help topics available from the Help menu in the Discovery Studio client.

Further information

General system requirements and recommendations
Installing Discovery Studio on Windows systems
Removing Discovery Studio