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Worked examples

The examples described below show how to apply STAMP to particular problems. However, by far the most common thing you might want to do with STAMP is to pairwise or multiply align a set of structures. Originally, STAMP was intended to align closely similar structures that you had already collected together - for this reason, we talk first about this way of using STAMP (See section:2.2). We recommend you work through this example as it introduces STAMP concepts and files. However after developing the SCAN option in STAMP we found that the best way to start a multiple struture alignment was to gather structures or structural domains firstly by carrying out a STAMP scan. So, we recommend that unless you already have a set of very similar structures to align, you follow the SCAN example (See section: 2.4) to gather and orientate domains for multiple structure alignment.