Category: What’s new

What’s coming up next

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As SAMSON 0.7.0 is approaching, we would like to highlight a few upcoming features that we feel are bringing us a little closer to our vision of a federating platform for computational nanoscience. Python scripting Python scripting is coming to SAMSON 0.7.0, and we are (very) excited about it. Most of the SAMSON API is now exposed in Python, and this will allow you to create models and run simulations, generate movies, perform analysis and reporting, etc., directly from scripts.…

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Making nano-batarangs (and more)

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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…

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Snapping, cloning and extracting with selection editors

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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”…

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Computing axes of symmetry of biological assemblies

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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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Computing non-linear normal modes of biomolecules

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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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Generating symmetry mates in SAMSON

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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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Welcome!

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Welcome to the SAMSON Connect blog! Here, we will post updates about development, tips and tutorials for users and developers of SAMSON, and announce releases. Feel free to comment posts and tell us what you’d like us to discuss!

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