On 02/17/2010 06:11 AM, Offord, Victoria wrote: > I couldn’t find anything on this but was wondering if anyone else had > come across asterisks in the pdb output file?

Where in the output file are you seeing asterisks? Can you post an example? Typically this happens with really large models, since PDB is a fixed-width format and has only 5 digits for the atom serial number and 4 for the residue number, so if you have 100,000 or more atoms in your system PDB format is not sufficient to represent the atom numbers (and Modeller will just 'give up' and write ***** instead). There's unfortunately nothing we can do about that, short of writing invalid PDB files, splitting the output into multiple files, or writing the coordinates out in a non-PDB format (e.g. PDBML, CHARMM, MMCIF).

Ben Webb, Modeller Caretaker