Aligning proteins

In this tutorial, we will show you how to use the Protein Aligner SAMSON extension. First, go to SAMSON Extensions web page, log in, and add the Protein Aligner SAMSON extension. This Protein Aligner extension 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 two are hemoglobin proteins from different organisms. Now, click twice on the protein aligner editor to open the GUI. Click on “Align Sequences”…

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Computing axes of symmetry of biological assemblies

The Symmetry Detection Extension 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 which has a dihedral symmetry of order 3:   Another possibility is to provide 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 Symmetry Mate Editor Extension helps to generate symmetric replicas of a protein based on the information contained in a PDB file. You can add the Symmetry Mate Editor Extension by clicking the ‘Add’ button. When this editor is selected, control nodes appear in…

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