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Getting Started#

What is SAMSON?#

SAMSON is a software platform for computational nanoscience. Its generic, open architecture makes it suitable for life science, material science, physics, electronics, chemistry, and education. SAMSON stands for Software for Adaptive Modeling and Simulation Of Nanosystems. SAMSON is developed by OneAngstrom.

Simulation of 1PV7 in SAMSON

🌟 SAMSON 2025 webinar#

Register for the upcoming webinar introducing SAMSON 2025.

In this webinar, you will learn in particular:

  • How to create and edit 2D and 3D protein-ligand interaction diagrams using the new Interaction Designer.
  • How to use the new Pattern Builders to rapidly create advanced designs.
  • How to use the updated Protein Aligner, now included by default in SAMSON, to align multiple sequences and structures of proteins.
  • How to use the new Quick Groups to store and control selections.
  • How to use the new colors schemes to rapidly create advanced visualizations.

Date and time: June 17, 2025, 8am PST, 11am EST, 5pm CET.

Visit https://1-a.io/samson2025 to register!

SAMSON 2024 webinar recording#

To learn more about the recent SAMSON 2024 features please check out the webinar recording:

Video chapters
  • 00:00 OneAngstrom and SAMSON
  • 03:16 SAMSON's top six distinctive features
  • 06:55 Documentation and interactive tutorials
  • 09:00 Getting answers and getting things done with SAMSON AI
  • 13:15 Selecting with the Document View and the Context Toolbar
  • 16:29 Selecting with the Viewport and Selection filters
  • 17:37 Selecting with Selection Commands
  • 18:35 Selecting with the Node Specification Language and SAMSON AI
  • 21:26 Selecting with the new Interactive Sequence Viewer
  • 23:47 Producing studio-quality renderings with Cycles, the integrated path tracer from Blender
  • 26:32 Creating new visualizations quickly with the new Visual Preset Editor
  • 31:52 Creating movies with the Animator
  • 33:39 Using the new Cloud Job Manager and predicting protein structures
  • 36:40 Importing and visualization GROMACS simulations
  • 39:39 Creating apps and executable documents with the integrated Python Environment
  • 43:17 Publishing documents securely and privately on SAMSON Connect
  • 45:48 Creating and publishing your social profile on SAMSON Connect
  • 46:26 Creating groups and organizing teams on SAMSON Connect
  • 47:20 Sharing documents with users and groups
  • 50:00 Beginning Q&A
  • 51:10 Using Martinize to create coarse-grained structures
  • 55:35 Importing and sharing cloud jobs
  • 58:07 Contacting the developers

Current version#

The current version of SAMSON is 2025 R1.

Please refer to Versioning for more information about version numbers.

Supported platforms#

This version of SAMSON is supported on the following platforms:

  • Windows 11, Windows 10.
  • Linux: Ubuntu 22.04 and newer, Fedora 42 and newer, CentOS, and other similar Linux OS.
  • macOS (64-bit Intel and ARM): Sequoia (macOS 15), Sonoma (macOS 14), Ventura (macOS 13), Monterey (macOS 12).

This version of SAMSON has not been tested on older OS platforms and might not be supported on them.

Requirements#

Does SAMSON require admin rights?

No admin rights are necessary! SAMSON does not need admin rights to be installed - it installs in the user home. And SAMSON explicitly checks at startup that it's not run in admin mode to encourage users to restrain the rights they give to SAMSON.

For running SAMSON, a 64-bit operating system and a graphics card supporting OpenGL 4.1 are required. For NVIDIA and AMD graphics cards an appropriate driver with an OpenGL support should be installed.

Warning

If you plan on running SAMSON in a virtual machine, then please make sure to give your virtual machine an access to hardware GPU acceleration.

Requirements on Linux#

To run SAMSON, you might need to install some libraries.

On Ubuntu-like Linux, you might first need to install the libxcb-cursor0 and libatomic1 libraries:

sudo apt install libxcb-cursor0 libatomic1

On CentOS-like Linux, you might first need to install xcb-util* packages:

sudo dnf install xcb-util*

If you experience problems with OpenGL libraries, please check the Installing OpenGL drivers on Linux section.

What are SAMSON Extensions?#

SAMSON has an open architecture which allows you to extend it, and adapt it to your needs, by downloading SAMSON Extensions (modules) from the SAMSON Connect website. SAMSON Extensions come in many flavors: apps, editors, controllers, models, parsers, etc., and are adapted to different application domains. They help users build new models, perform calculations, run interactive or offline simulations, visualize and interpret results, and more.

Installing SAMSON#

Please, check the Requirements first.

To install SAMSON, download the SAMSON installer from this page on SAMSON Connect. You will be asked to sign in, or create an account if you don't have one. When you download the installer, a key will be sent to the email address you used for registration. You can also access your keys in your account on SAMSON Connect.

If you want to install an older version of SAMSON, please check How to install an older version of SAMSON.

Note

SAMSON Extensions are updated only for the latest version of SAMSON and they are updated automatically when you launch SAMSON. So, we encorage you to update SAMSON when its new version is available. SAMSON regularly checks for updates. The update can also be invoked manually directly from SAMSON via Interface menu > Update SAMSON.

Start the SAMSON installer you just downloaded.

Note

On Linux, open a terminal in the folder where you downloaded the SAMSON installer and execute the following commands (make the installer executable and launch it):

cd ~/Downloads
chmod +x ./SAMSON-Setup.run
QT_QPA_PLATFORM=xcb ./SAMSON-Setup.run

Once the installer has started, you should see the following window:

The SAMSON installer

Note

Intel graphics cards may currently cause issues. If you have one, the SAMSON installer will generate a warning. You may choose to ignore the warning, especially if you also have a non-Intel graphics card (NVIDIA or AMD).

After accepting the license agreement, you reach a page that allows you to configure a proxy, if necessary:

Enter proxy parameters if necessary

At this point, the SAMSON installer checks that it can reach SAMSON Connect - the installer needs to download SAMSON and SAMSON Extensions. If it can, this page shows the message "SAMSON Connect reached successfully". Else, you might have to enter proxy parameters (you may have to ask your system administrator for information). Use the Test connection button to check that the proxy parameters you entered are valid.

Next, the installer asks you to enter the email address you used to register on SAMSON Connect, and the SAMSON key that was sent to you at that address when you downloaded the installer (you can also access your keys in your account on SAMSON Connect).

Enter your email address and the SAMSON key you received at that address

If you want, you may check the Advanced mode box to choose a custom installation path and specify which version of SAMSON you want to install (by default, the latest version is installed).

Then, the installer downloads SAMSON from SAMSON Connect, and installs it:

SAMSON is being downloaded from SAMSON Connect

Finally, the last page of the installer gives you the possibility to start SAMSON and visit SAMSON Connect:

SAMSON has been installed successfully

Post-installation steps on macOS:

It might be necessary to provide a full disk access on macOS for SAMSON. Please see Full Disk Access In MacOS.

Starting SAMSON#

Here is how you start SAMSON depending on your operating system.

Windows#

On Windows, start SAMSON from the Start menu. Typing SAMSON in the search box might just lead you there. Else, SAMSON executable can be found in the following folder:

C:/Users/%USERNAME%/OneAngstrom/SAMSON-Application/7.0.0/Binaries/SAMSON-Core.exe

Mac#

On Mac, start SAMSON from the launchpad or from the Applications folder. The most recently SAMSON version will be launched.

SAMSON is installed in the following folder:

$HOME/Applications/SAMSON.app/

Linux#

You can launch SAMSON as other apps via the Apps dashboard.

You can also directly launch the SAMSON-Core.sh script from the SAMSON installation folder path (it should be ~/OneAngstrom/SAMSON-Application/7.0.0/Binaries):

./SAMSON-Core.sh

You may create an alias in your ~/.bashrc or ~/.zprofile:

alias samson='$HOME/OneAngstrom/SAMSON-Application/7.0.0/Binaries/SAMSON-Core.sh'

Now, open a new terminal and execute samson.

In case you have issues on Linux with AMD/ATI graphics cards, please refer to the Troubleshooting section.

Extending SAMSON#

The first time you start SAMSON, it downloads a set of default SAMSON Extensions from SAMSON Connect. To customize your SAMSON installation from SAMSON Connect, simply sign in to your account, then go to the Marketplace to choose the SAMSON Extensions you need. Please refer to this page for more information.

Quick Start Guide#

For a very brief introduction in SAMSON, you can check out the Quick Start Guide in PDF format.