Aligning sequences with MUSCLE – Interactive Ramachandran plots

This tutorial will teach you how to use two SAMSON elements related to structural biology: Protein Aligner and Interactive Ramachandran Plot. First, if it’s not done yet, go to SAMSON Elements web-page. From here, add the two elements to your SAMSON. The first element we are going to play with is Protein Aligner. This element can align both sequences and structures of proteins. Open SAMSON and use the Protein Data Bank Downloader to fetch two proteins: 1DLW and 1RTX. Those…

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Computing axes of symmetry of biological assemblies

Hi all, The second post about symmetry, this time, we will focus on symmetry detection. The Symmetry Detection Element computes the axes of symmetry of biological assemblies. Here with 1CHP, just start the Symmetry Detection 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…

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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 Symmetry Mate Editor Element helps to generate symmetric replicas of a protein based on the information contained in the pdb file. You can add the Symmetry Mate Editor Element by clicking the ‘Add’ button. When this editor is selected, control nodes appear in…

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