Category: User tips and tutorials

Using the SMILES Manager

In this tutorial, you will learn how to use the SMILES Manager extension of SAMSON. This extension is based on RDKit. RDKit is a widely used open-source toolkit for cheminformatics. One of its features is the conversion of molecules SMILES strings to 2D and 3D structures. The extension interface presents three tabs: Manage SMILES, Replace fragments, and Positional Analogue Scanning. In this tutorial, we will present the first two sections one by one as they are totally independent. For the…

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Building carbon nanotube models with SAMSON

In this quick tutorial, we will show you how to easily generate carbon nanotube (CNT) models within SAMSON. Nanotube creator First, make sure you have the Nanotube creator SAMSON Extension that you can find on the SAMSON Extensions web page. If you need help with installing new SAMSON Extensions to your SAMSON installation, please visit User guide: Adding Extensions from SAMSON Connect. If you need help with installing SAMSON itself, please visit User guide: Installing SAMSON. Note: you can check whether you have…

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Generating crystal models

The Crystal Creator SAMSON Extension contains the basic tools to write and manipulate crystals. I will show you here how to use it. Read a crystal structure To have your first crystal, you can import one. With the Crystal Creator App, you can load CIF (Crystallographic Information File) files. First, go fetch some nice crystals on those 2 websites : The American Mineralogist Crystal Structure Database : http://rruff.geo.arizona.edu/AMS/amcsd.php The RRUFF Project Database : http://rruff.info/ I personally advise you to test…

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Calculating non-linear normal modes

In this tutorial, we will present you the functionalities of the Normal Modes Advanced (NMA) SAMSON Extension. This SAMSON Extension is an advanced version of the Normal Modes Analysis SAMSON Extension also available on SAMSON Connect. This SAMSON Extension computes 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). First, you have to import a structure. For this…

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Aligning proteins

In this tutorial, we will show you how to use the Protein Aligner SAMSON extension. First, go to SAMSON Extensions web page, log in, and add the Protein Aligner SAMSON extension. This Protein Aligner extension can align both sequences and structures of proteins. Open SAMSON and use the Protein Data Bank Downloader to fetch two proteins: 1DLW and 1RTX. Those two are hemoglobin proteins from different organisms. Now, click twice on the protein aligner editor to open the GUI. Click on “Align Sequences”…

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Simulating small molecules, graphene and proteins

For more information please refer to User guide: Modeling and Simulation. Note: this tutorial has been made for an older version of SAMSON. Introduction This tutorial will make you perform different types of simulations using various force fields and integrators. In SAMSON, force fields are named Interactive Models and integrators state updaters. Simulations are interactive in the sense that users can still act on the atoms while the simulation is running. First, you need to download the benchmarks available at the…

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Snapping, cloning and extracting with selection editors

Please refer to the updated documentation: User guide: Selecting and User guide: Moving objects. The guide below is for the SAMSON version older than 0.8.0. 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):  …

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Fast geometry optimization with the FIRE minimizer

Geometry optimization is a fundamental step in many molecular modeling applications, used to produce stable, realistic structures which correspond to energy minima. Many algorithms have been developed for energy minimization, and we have just released a new SAMSON Extension that implements the FIRE minimizer described by Bitzek et al.: Erik Bitzek, Pekka Koskinen, Franz Gähler, Michael Moseler, and Peter Gumbsch, Structural Relaxation Made Simple. Physical Review Letters, Vol. 97, 170201 (2006) FIRE, which stands for Fast Inertial Relaxation Engine, is…

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Making nano-batarangs (and more)

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. Content Simple Script Extension Atoms Selector Extension…

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Computing axes of symmetry of biological assemblies

The Symmetry Detection Extension computes the axes of symmetry of biological assemblies. Here with 1CHP, just start the Symmetry Detection 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 symmetry of order 3:   Another possibility is to provide the…

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