Shamshad Zarina wrote: > I am trying to superpose two models using superpose > command. The command runs okay and it creates a .fit > file. Although the fit file looks fine but it has an > unusual line connecting the last and first residues of > both models. Any ideas why this is happening?
It's hard to say without seeing your input files and the generated fit file, but PDB files generated by Modeller only contain ATOM and HETATM records; there is no connectivity information, and thus no 'lines'. Any such information must therefore be guessed by your PDB viewer (usually based on simple criteria such as atom-atom distance, and some knowledge of standard amino acid connectivity), and it's probably just guessing incorrectly in your case. If the model looks OK otherwise, this is probably nothing to worry about.
Ben Webb, Modeller Caretaker