Discovery Studio Visualizer

Hi Sana, Discovery studio (DS) visualizer is a freeware software. You need not have to procure licence for it. You can use DS visualizer for protein-ligand interaction analysis.

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Discovery Studio is a protein modeling program that contains tools tovisualize, analyse, modify and simulate protein structures. Universityand polytechnic researchers working in Finland can install DiscoveryStudio into their local Windows or Linux computers for academicresearch.

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What is Discovery Studio?. Discovery Studio is a complete modelling and simulations environment for Life Science researchers – Interactive, visual and integrated. DS Visualizer Pro client or Pipeline Pilot client – Requires DS Visualizer Pro – Access to rich Perl scripting language constructs. Objects, Modules, Sub-routines.
Discovery studio visualizer? I have to visualize the interactions (Van der Waals, electrostatic, etc) within a protein. But I don't know how to perform this in discovery research studio.

License

Discover Studio is a commercial program by Biovia Inc. CSC has purchaseda national academic license for Discovery Studio that allows non-profitusage in Finnish universities.

In year 2020 CSC has a national Discovery Studio license which allows unlimited access to all Discovery Studiomodules for 5 simultaneous users.

Available

The following server versions are available on CSC (in Pouta):

Discovery studio DS2019 is available in http://dstudio19.csc.fi:9944
Discovery studio DS2018 is available in http://dstudio18.csc.fi:9944

Usage

To use Discovery Studio you need to install a DiscoveryStudio client on your own computer. Discovery Studio client is available for Windows (Windows 7, 8 and 10) and Linuxoperating systems (Red hat Enterprise linux 6 and 7, Centos7, or SuSE 11 SP4recommended). The license provided by CSC is available only for university researchers working in Finland. Due to that, your computer must bewithin the university network (FUNET) be able to use the license.

You can download the Windows and Linux clients using the links below:* Discovery Studio 2019 client* Discovery Studio 2018 client

Discovery Studio client provides an extensive manual and large set of tutorials thathelp you to get started with the software.

Installing the Discovery Studio client in Windows

DS2019Client.exe starts a graphical installation tool, that will guide you through the Discovery Studio client installation.In most cases you can just accept the default installation settings that the installation tool suggest.

Biovia Discovery Studio Visualizer

If licensing information is not asked during the installation, start the Discovery Studio client, you just installed, and press button Enable additional features in the lower right corner of the interface.This opens a license configuration session where you should apply the license settings listed abowe.

To use Discovery Studio servers of CSC, start the Discovery Studio client normally and select command:

File | Change server...

And set server name to be:

https://dstudio19.csc.fi:9943 (For Discovery Studio 2019)
https://dstudio18.csc.fi:9943 (For Discovery Studio 2018)

Installing the Discovery Studio client in Linux

After the steps detailed in the link above, you should be ready to run (as long as the IP address of your machine is within the FUNET network, i.e. in your university network or in a VPN to it).

To use Discovery Studio servers of CSC, start the Discovery Studio client normally and select command:

File | Change server...

And set server name to be:

https://dstudio19.csc.fi:9943 ( For Discovery Studio 2019)
https://dstudio18.csc.fi:9943 ( For Discovery Studio 2018)

Tricks for installing Discovery Studio client to Ubuntu

Below are some tricks you can try to use to install Discovery Studio Client to an Ubuntu Linux machine.
By default, the sh that Ubuntu is using is actually a command shell called dash that diffters from the sh shell that is in use in e.g. Redhat and Centos linuxes.

In Discovery studio installation this causes problems as the installation process is based on sh scripts.

One way to fix this issue is to redefine sh shell in your Ubuntu server as described e.g. in:

Alternatively you can try following:

Start installation with bash shell and --keep option:

The installation process fails, but provides a temporary installation directory. Go to this direcory and modify the actual installation script a bit and execute the modified version:

This command does most of the installation but the Lincese Pack installtion fails for the same reason as the main instllation process. The fix is also the same:

Now the installation is done and you just need to add the license data as described in the previous example.

References

Please see method descriptions and log files in Discovery Studio for details.

Discovery Studio Visualizer Ubuntu

More information

Discovery Studio client provides an extensive manual and large set of tutorials thathelp you to get started with the software.

Last edited Mon Apr 6 2020

Below are instructions for installing Discovery Studio on Windows systems. For installation on Linux systems, see Installing Discovery Studio on Linux 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.
It is recommended to remove DS Visualizer 1.5 or Discovery Studio 1.5 prior to installing DS Visualizer 1.6 or Discovery Studio 1.6. See Removing Discovery Studio Help topic.
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.)

You must have Administrator privileges to install on Windows systems.

Instructions for the installation wizard

Note. Installation of Discovery Studio may require you to restart your system. To ensure that you do not lose any valuable information, we recommend that you close all other Windows applications and disable antivirus software.

Insert the Discovery Studio media into the drive and double-click setup.exe to start the program.
When the Welcome screen appears, click the Next button.
The Destination Folder screen prompts you to specify the location for the installation. Accept the default location, enter the installation location, or navigate to the desired location by clicking the Change... button. On the Destination Folder screen, click the Next button to proceed with the installation of Discovery Studio.
If you are installing only DS Visualizer, skip to step 5.

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 Profiles-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.
If you have a firewall enabled, a Windows Security Alert dialog displays. Choose Allow to continue with the installation.
Discovery Studio installs and starts a web server. If you see a message informing you that Apache is trying to start, click Yes, allow Apache to start.

On the File Association screen, select whether you want to associate files to automatically open with Discovery Studio.
On the Ready to Install the Program screen, click the Install button to complete the installation.
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.
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 provided in the Windows Start menu.

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.

Discovery Studio Visualizer Manual

Discovery Studio Visualizer 32-bit Free Download

Further information

Discovery Studio Visualizer Free Download

General system requirements and recommendations
Installing Discovery Studio on Linux
Removing Discovery Studio

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