3motif

http://fold.stanford.edu/3motif/
a tool can let you see pattern in 3D structure.
input pattern in prosite format.

advantage of this one to prosite's is, prosite's colored the whole regien, this one colors matched residues only.

I've used this tool one year ago, but I didn't see it in my blog, so I add it in.

our alignment and SSM's, what's the difference?

What's the difference between our alignment and SSM?
they align secondary structure first, then align the sequences.
I think the result will be pretty similar.