Fasta formatted input file must have the fasta extension

[jonblack]

This isn't clear at all. Either the documentation should be updated, or the code should determine the file type by checking for the fasta header.

The error message displayed is also silly:

empty protein, or no valid complete residues

I assume this is because by default files are assumes to be in PDB format.

[touwwouter]

Let's update the documentation