To see a tridimensional view of the alignment:

1- start pymol in the directory where you have done the extract with tar.
2- on the menu "File" use the option "Run" on the script "showall.pml"
3- Here you can see the alignment of the three domains: 
   The one in red is the first domain you uploaded, it is not changed.
   The one in blue is the second domain you uploaded, not deformed and aligned to the first one.
   The one in green is the second domain deformed; the dotted lines mark sites that were adjacent, and
   the black ribbons show ribbons not aligned (gaps).
4- On the panel on the right
   you can see the objects. There on the menu "H"ide, with the option "everything", you make the
   selected structure disappear and see better the others. 
5- If you want to see the structures again, on the panel on right, on the top, in the object "all", on
   the menu "S"how with the option "cartoon" you will see everything again.

Thanks for using ProtDeform.
