What’s new in SAMSON 2021

SAMSON 2021 brings numerous new features and improvements throughout the core of SAMSON, so let’s dive right in!   Introducing the SAMSON Animator One of the most exciting features of this new release of SAMSON is the introduction of the SAMSON Animator, which allows you to create presentations, animations, and movies. The Animator, visible below on the bottom part of the SAMSON interface, is composed of two main parts – the Track view on the left, and the Animation panel…

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Proteins: application

This tutorial follows the first one “proteins : secondary structure”. At the end of it, we suggested that SAMSON can be used on a medical purpose. Indeed, as you can modelize any molecule, you can see the structures of different diseases such as HIV or the flu. Now imagine that you are making research on how to fight these diseases, and you’ve developped a medicine for it. The point is : you don’t want to use it directly on a…

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Proteins : visualisation

Now that you’re comfortable with carbon structures, let’s move on to the biological area ! In this tutorial, you will see the main secondary structures of most proteins. Secondary structures First of all, click on the link : http://www.rcsb.org/ . You’ll be redirected on a website that lists different proteins. On the toolbar (top right), write “1EI0” (be careful it’s a capital i and a zero). Download the file and select PDB format.   Now, go back on SAMSON and…

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Programming a path generator

  In this tutorial, we are going to create an editor such that a user can create paths in the viewport. First, use the SAMSON Element Generator to create a new SAMSON Element called Path containing: An Editor class called Editor (full name: SEPathEditor). This class will make it possible for the user to add new nodes to the path. A Visual Model class called VisualModel (full name: SEPathVisualModel). This will be the main class used to represent a path…

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Nanocarbons : Graphene, nanotube and fullerene

For some years now, we have heard a lot more about nanostructures and especially about nanocarbons. You will see here the most famous nanostructures which are the graphene and the carbon nanotube… What’s graphene? You probably already know it, but for the two of you in the back who didn’t pay attention, we will remind you that it’s a plane of multiple six carbon cycles. You might as well know of graphite. So what’s the difference between those two carbon…

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Double, triple bonds

In this tutorial, you will learn more about bonds between atoms, and especially how SAMSON represents bonds, and the differences between a triple, a double and a simple bond…    Create double and triple bonds Go to the “periodic table”  and select two hydrogen atoms that you will put close to each other and link them by creating a bond through « atom creator ». Then do the same with two oxygen atoms and two nitrogens atoms. Now go to “simulator” and « add simulator ». In…

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Open and manipulate bigger molecules

Now that you know how to create your own molecules, you have to know how to save them and reopen them. Open a “.pdb” file Click on “File” then “Open…” or just press “Ctrl+O”, then select “chassis.pdb”. After you have clicked, a window should appear. Tick the boxes as done in this image: Now open the file  “roue.pdb” four times. Moving bigger molecules On the display window you only see one molecule… But still, you opened it four times? Well, as…

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Simulation of stocking different molecules in a nanotube

The carbon nanotube (CNT) has many applications, and we are going to demonstrate some of them in this tutorial.  A CNT is a stable structure, consisting of carbon atoms only, that are twisted into a cylinder and held together by convalent bonds. It has some interesting properties, such as electrical conduction and hydrophobic walls which we are going to discover together in this tutorial. Creating a nanotube: First of all, we create a dihydrogen (H₂) by combining two hydrogen atoms. Be careful not…

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