display DSSP with MSA

Hi all, is there anyway to display DSSP with MSA if one of the seq has a known structure (pdb from RCSB or customized pdb)? I tried Jpred 2nd structure, but it’s way off from the real structure.

Also if there a way to highlight or “box” certain range (saying, alignment position 50-100)?


Hi Jim,


Hi Fei.

I’m still not absolutely sure what you are after - groups are temporary in that they’re alignment annotation, and the user can delete any annotation on an alignment view, if they want (of course, you could hack jalview to disable the ‘remove groups’ menu option, …).

What do you need ? Are you interested in highlighting ranges based on alignment coordinates or according to ranges on specific sequences (e.g. conserved secondary structure), for instance. Some example data would help here :slight_smile:

On 11/08/2012 18:46, Fei Cai wrote: