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Section: New Software and Platforms
SAMSON-Various-tools
SAMSON-Various-toolsrere
Keywords: 3D - 3D modeling - Chemistry - Algorithm - Bioinformatics - Nanosystems - Structural Biology
Functional Description: Cluster Game : This element has been made in order to help students discover the Lennard Jones interactions. It is a game in which the goal is to optimize the atoms' placement. Contains eight levels and five tutorial levels.
Atoms Selector : This SAMSON element allows selection of atoms in the active document according to a user-provided expression with the usage of NSL-like variables (NSL - Node Specification Language), standard mathematical and logical operations. Parsing and evaluation of expressions is done with the usage of C++ Mathematical Expression Parsing And Evaluation Library 'exprtk' by Arash Partow (https://github.com/ArashPartow/exprtk)
Simple Script : This SAMSON element allows modification of some parameters of atoms using scripting language, standard mathematical and logical operations, and NSL-like variables (NSL - Node Specification Language). The script is applied to each atom independently. Parsing and evaluation of the script is done with the usage of C++ Mathematical Expression Parsing And Evaluation Library 'exprtk' by Arash Partow (https://github.com/ArashPartow/exprtk)
Bond Angle Distribution : This App will compute the bond angle distribution of the selected atoms. The result and its image can then be exported.
Bond Distortion Visualisation : This App permits to visualize with colors the distortion of a molecular or crystalic structure. The angle distortion, the bond distortion and the projected bond distortion can be represented with colors on bonds and atoms.
Frame axis : Basic visual model to show cartesian axis. Open a new visual model and select "Frame axis" to see the frame axis as arrows, lines or both.
Radial Distribution Function : This app computes and draws the radial distribution function of a selection. - Compute the crossed-RDF by selecting 2 different sets of atoms. - Follow the evolution of the RDF by selecting a simulator.
Adaptive Lennard-Jones : An interaction model to compute the forces with an adaptive version of Lennard-Jones potential. The update of forces is done by storing all the position, and at each position update, subtracting previous pair forces, then adding new ones. If both pair particles were frozen by restraining dynamical model, the update is useless and so not done.
STL File Importer : Reads Stereolithography ( .stl ) binary and ASCII files. Spawns carbon atoms at the intersections of vertices to create quickly new original atomic configurations. Many STL files are avalaible online to generate thousands of new configurations.
StyleSheet Viewer : An app for internal developers to test their skin/styles ...
Animation Player : Create animation from a list of conformations in SAMSON Document view There are 3 play modes: loop, only 1 time, or continuous back-forth. The user can change the frame order by drag and drop in the frame list.
Internal Coordinate Editor : This editor rotate the molecule by defining rotation axis and rotation angle. The user define the rotation axis (represented by an arrow in the view) by clicking on one atom and drag it to the second atom. The rotation angle is defined by the small GUI windows. The editor will try to rotate all the atoms after the head of the arrow and in between the tail and head of the arrow
RMSD : This app calculates RMSD between 2 structures. If it is an amino acid chains, a sequence alignment of the structures is needed (in fasta format). The fasta format has to be obtained from external sources. If it is not a protein, the app will try to match atoms one by one in both structures.
Trajectory Importer : This app import selected pdb files (hold Ctrl + Mouse click for multiple selection) as a trajectory. The result is one single structural model and a list of conformations in SAMSON Document View
Open Babel connector : This app allows users to use Open Babel from inside SAMSON
ARPS demo : This SAMSON Element features a demonstration of ARPS: Adaptively Restrained Particle Simulations, an adaptive simulation technique able to focus computations on the most mobile degrees of freedom. In this demo, a collision cascade may be simulated with various degrees of precision by changing the restrained dynamics threshold and the full dynamics threshold. For example, 0 0 produces a classical, non-adaptive simulation, while 0.625 and 0.7 result in a 10 times speedup in this example (without the graphics overhead). Click on 2D Shock to generate the example, enter the simplification parameters, and press start to simulate the collision cascade. Undo and redo make it possible to zoom on and compare simulations. Please refer to "S. Artemova and S. Redon. Adaptively restrained particle simulations. Physical review letters, 2012" for more details.
Hydrogen bond finder : Find hydrogen bonds in a given structure. The bonds is detected by specifying a threshold distance. Bonds are displayed by yellow lines.
Lennard-Jones model : This SAMSON Element contains a Lennard-Jones interaction model that may be used for several purposes: teaching, learning about van der Waals interactions, developing optimization algorithms, looking for minimum energy Lennard-Jones clusters through interactive simulation, etc. Add this force field to a group of atoms (the atom types do not matter) via the 'Simulation' menu.
Catalogue : BETA version. Bunch of structures easy to load, with images.
Catalogue Generator : BETA. Generator for the Catalogue module.
SAMSON Basic Tutorial : Tutorial for SAMSON : Basic functionnalities. Learn how to create, move and delete an atom, and then create a basic molecule thanks to a step-by-step guide. Experiment in sandbox mode. Test your mastery of SAMSON's tools with 4 speed challenges. The following elements are required : SAMSON Editors, Periodic table, Basic importers. Currently only available in french.
SAMSON Courses : BETA. Module with a custom display, depending on the entry files
SAMSON Courses Creator : BETA. Generator for SAMSON Course module
Charts : A SAMSON Element to allow user plotting something from SAMSON datas interactively
Leap : A driver to control SAMSON with the Leap motion controller