VistaPDB Manual -> Alignments -> Pairwise Alignments

Pairwise Alignments

VistaPDB can align primary 'query' sequences to the primary sequences in a PDB file.

1) To align a primary sequence against an open PDB file, go to Tools -> Align Sequence to Current Model.

2) The current selected chain will be used in the alignment.

3) Enter a sequence into the text box provided. Click Align.

4) Alignment results, based upon the BLOSUM62 matrix, will appear in a new drawer.

5) To import the alignment into the viewer, click Add To Structure.

6) Red indicates mismatches, blue indicates changes to similar resides, and black indicates identical residues.