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…

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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”…

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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…

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Two weeks left before SAMSON School 2017

There are only two weeks left before SAMSON School 2017, which will take place next to Lyon, France’s third largest city, from June 19 to June 23. The SAMSON School is split into two independent parts, and you can register to either part, or both of them: The Users program from Monday 19 at 10:30 am to Wednesday 21 at 2pm The Developers program from Wednesday 21 at 10:30 am to Friday 23 at 2pm The Full program from Monday 19…

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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…

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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…

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SAMSON 0.6.0 is available on Windows, Linux and Mac!

Dear all, After almost a year of hard work since the previous release, we are proud to announce that SAMSON 0.6.0 is now available for Windows, Linux and Mac, and can be obtained from SAMSON Connect at https://www.samson-connect.net ! Here’s an overview of some of the most prominent new features of the core of SAMSON (separate posts will cover new SAMSON Elements): Proxy configuration SAMSON needs to reach the SAMSON Connect website during installation, and when installing and removing SAMSON Elements.…

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New functions for memory management

Memory management is an important issue in an application such as SAMSON, where developers independently write modules, and users may use these modules in combination – and in any order. Moreover, since users may undo and redo actions, SAMSON has to ensure that any allocated memory is properly freed when it cannot be used anymore. To help developers achieve this, the SAMSON SDK now contains new functions to manage memory. Assume for example a function adds a new structural model…

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Cite your research in SAMSON Elements

If a SAMSON Element corresponds to one or more research papers, you now have the possibility of letting users know about them. First, add the SBGWindow::Citable tag in the getFormat function of your GUI (for example, the GUI of the app, or the property window of an interaction model): int SEEMyModelProperties::getFormat() const {   return (SBGWindow::Savable | SBGWindow::Lockable | SBGWindow::Citable);   }int SEEMyModelProperties::getFormat() const { return (SBGWindow::Savable | SBGWindow::Lockable | SBGWindow::Citable); } This adds a question mark to the window…

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