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5. Some PDB files have multiple RNA chains. For instance, 1s72.pdb contains a 5S chain and a 23S
chain, and both chains have some of the same nucleotide numbers. If there is any ambiguity in the
chain for the Query nucleotides, the user must specify the chain which contains the Query motif. This
may be selected using the drop-down menu labeled Query Chains. The order of the drop-down menus
corresponds to the order of the nucleotides supplied by the user. In this case we are using chain ‘0’.
6. Once the chains have been selected the user should press the Generate Interaction Matrix button. The
Interaction Matrix allows the user to impose certain types of constraints on the search. A purely
geometric search makes no such constraints. Below we describe mixed geometric and symbolic
searches and purely symbolic searches.
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