Run macro "PDB_GapFromAlig" to transfer the gapping and labelling information to the vertical alignment. Check worksheets "Insert", "Chain","Label" and "Seq" to make sure everything is correct. The vertical alignment serves as a template for relabelling the PDB files.

For sequence alignments which are too long to convert to a horizontal alignment, the vertical alignment can be gapped directly. The three-letter code can be changed to one-letter code using the macro "AA_Convert_3to1", and fill the gaps using "AA_Empty". Chain labels, residue rabels and insertion code have to be entered in the first three columns of the worksheet. Run "PDB_GapFromSeq" to transfer the information to the other three worksheets.