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…

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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…

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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…

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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…

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