SSM tutorial (explain the algorithm and output format)

for align sequence by using 2D/3D structures info
this paper is interesting, and they use this tool.
here's lots of software doing this.
and I also find a newer version here, which have POSA, which provide align distance tree, and also 3D superimpose structures in chime, and you can easily select common sse by click the POSA graph.

You can use http://proteinexplorer.org/ to enter Chime command interactively.
You can use Chime to Calculate Secondary Structure by using command "structure", then "si".
When I'm playing it,
I have an idea to align all the properties, like hydrophobic, polar, charged, sheet, bonded, etc.
then apply data mining tech on it to categorize if the residue is one of the 6 residues on interlock.

HB info missed in 1akp.hb2

in 49328 1akp, strand 6,7,8,9 missed.
to fix it, we have to use
hbplus -d 3.95 -h 2.97 1akp.pdb
in order to generate 1akp.hb2 contants strand 6 7 8 9
so you'll get
1-3
2-10
4-5
6-7
8-9
and if you increase the -d and -h, you might be able to get 5-4-8-9 connected.