Reply To: Problems in Loop Modeling

[Anonymous]

Does t000.template.pdb contain residues? I’m not trying to be flippant – the obvious answer if you have 0 residues is that you simply don’t have any residues in the protein. You can (and should) try passing a different protein to see if it behaves differently, or manually tweaking the template PDB. You can try deleting atoms from some of the sidechains (or mainchain); this will cause the PDB reader to spit warnings, so you can verify that it’s reading the PDB it’s supposed to read.