Setting parameters for Multiple Structure Alignments

Before you align the molecules you may want to set certain parameters for the alignment.

1 Go to the in the MultiSeq window and select Alignment in the top pull-down menu. 2 Then click on Alignment Parameters. A new window entitled Alignment Parameters will appear with four setting options (see Figure 5).

Figure 5: STAMP Parameters

This tutorial will use these settings. If you would like more information about STAMP parameters, please refer to the STAMP manual.¹ To proceed with the tutorial, close the Alignment Parameters window.