Analyzing molecular trajectories with MDAnalysis in SAMSON

MDAnalysis is a well-known Python library for analyzing molecular dynamics trajectories. In this tutorial, we demonstrate how it can be used to analyze trajectories saved in Path nodes in SAMSON and superimpose structures. Analyzing trajectories Let us, for example, compute the radius of gyration and the RMSD for a protein with trajectories saved in Path in SAMSON. To use the functionality of MDAnalysis, we need to export trajectories we would like to analyze from SAMSON into a format supported by…

More…

RDKit – SMILES Manager

Hello everyone, In this post I will present you the new version of the RDKit-SMILES Manager module that I integrated in the SAMSON platform. As some of you know, RDKit is an open source toolkit for cheminformatics which is widely used in the bioinformatics research. One of its features is the conversion of molecules SMILES strings to a 2D and 3D structures. The module interface presents two tabulations: Manage SMILES and Replace fragments. I will present these two sections one by one…

More…

Building nanotubes models with SAMSON

In this quick tutorial, you will learn how to easily generate nanotube models within SAMSON. Nanotube creator First, make sure you have the Nanotube creator SAMSON Element that you can find on SAMSON Connect: If you need help with installing new SAMSON Elements to your SAMSON installation, please visit this page. If you need help with installing SAMSON itself, please visit this page. Note: you can check whether you have this SAMSON Element in at least three different ways: In…

More…

Sixteen step-by-step tutorials from SAMSON School 2017

SAMSON School 2017 is now over, and this year sixteen lectures had accompanying written step-by-step tutorials! Feel free to follow the links below to learn how to install and use SAMSON, as well as develop your own SAMSON Elements and share them on SAMSON Connect: Users program Installing SAMSON We introduce the Users program of the SAMSON School and SAMSON, the software platform for computational nanoscience. We highlight the need for an integrated platform able to combine diverse domains of…

More…

Making nano-batarangs (and more)

Graphene batarang

Have you ever thought about how you could create the Batman’s batarang at the nanoscale? Maybe it won’t fight cancer or viruses, but every scientist, like a hero, needs tools to work on their cause. In this post, we introduce two such tools that can be used for creating nano-batarangs and other complex-shaped objects at the atomic level by selecting atoms and modifying some of their properties using mathematical expressions and scripting language. The Simple Script App allows you to…

More…

Snapping, cloning and extracting with selection editors

The new version of selection editors now includes the possibility of snapping to atoms and nodes, as well as cloning and extracting structural nodes. Selection editors (point, lasso and rectangle selection) can be found in the editors toolbar and the Edit menu:   Activate snapping by clicking twice a selection editor (or use the corresponding shortcut twice):   Snapping to atoms helps achieve precise positioning:   You may also snap to entire nodes:   For example, choose the “Structural models”…

More…

Computing axes of symmetry of biological assemblies

Hi all, Second post about symmetry, this time, we will focus on symmetry detection. This new App computes the axes of symmetry of biological assemblies. Here with 1CHP, just start the App and compute the symmetry:   For large assemblies, automatic symmetry detection may detect several different symmetries. Click on the one that is interesting (typically the one with the higher order and a small RMSD) to visualize the axis. In this example, we use 1B4B which has a dihedral…

More…

Computing non-linear normal modes of biomolecules

Hello all, Welcome to this tutorial. Here, I will present you the functionalities of the Normal Modes Analysis Lite (NMAL) SAMSON Element. This SAMSON Element computes the nonlinear normal modes of a biomolecular system (protein, RNA, DNA) very quickly using the NOLB algorithm developed by Alexandre Hoffmann and Sergei Grudinin (J. Chem. Theory Comput., 2017, 13 (5), pp 2123-2134, DOI: 10.1021 / acs.jctc.7b00197.). First, you have to import a structure. For this tutorial I used the 1vpk PDB entry. Then, you launch the…

More…

Generating symmetry mates in SAMSON

PDB files often provide very interesting information on how proteins are organized in their crystal structure and biological assembly. Here we present a new SAMSON editor that will let you use this information in a few clicks. The so-called “Symmetry Mate Generator” element helps generate symmetric replicas of a protein based on the information contained in the pdb file. When this editor is selected, widgets appear. Use the mouse wheel to see more or fewer of these widgets. Here is an example…

More…

  • Subscribe

    Subscribe to make sure you receive all our updates, tips and tutorials