without the density score the scripts are distorting the shape, for example the scorpion tail is getting pulled into the rest of the fold.
The chain you can see in the electron density is longer than the given chain of amino acids. If you directly start to fit one end of the chain into the density, the residues won't fit properly.
It looks like that there are about 5-6 residues missing after residue 114 (C-terminus) and about 4 residues missing before the first residue (N-terminus).
Thanks Batz I think I saved the first one I did...
There is also something odd about residu 114. It cannot be changed. It will remain a loop. Residu 1 does not have this limitation. Is this intentional or an artifact ?
Sorry, but I really dislike ED puzzles, and this one is no exception. There is always too much clutter. If it were possible to toggle sidechains on/off on the cloud it would probably be easier. This cloud is better than most of the previous EDs, but I might do as well or better working it as a denovo.
I know that seeing the sidechains can occasionally give extra clues, but when trying to determine the SS/backbone, they're more a hindrance than help.