I would like to get a nicer view of the sequence alignment that shows the secondary structure elements in top of the alignment rather than below the sequence. In addition to this, the helix number and the beta-strand number with the secondary structure is even more important to intrepret the alignment in report. I had found one nice tool for this purpose (ESPript). However, the files created by discovery studio create some problem as it complains about the secondary structure. Could anyone please help me either working with new program or managing with ESPript.

Thanking you in advance!

Kisun