Hello Andreas, in the manual FAQ 2 question explains it. Select only the sidechains like: PICK_ATOMS ATOM_TYPES = 'SDCH' Andras Evers Andreas wrote: > > Hallo Modellers! > > I would like to use Modeller to predict Side-Chain conformations of > proteins (and subsequently compare the orientations with the original > crystal structure). For this purpose I want to take a protein and align > the sequence with itself, i.e. the alignment would look like this: > > ------------------------ > >P1;1dlw > structureX:1dlw: : : : : : : : > SLFEQLGGQAAVQAVTAQFYANIQADATVATFFNGIDMPNQTNKTAAFLCAALGGPNAWTGRNLKEVHANMGVSN > AQFTTVIGHLRSALTGAGVAAALVEQTVAVAETVRGDVVTV* > >P1;seq > unknown:seq: : : : : : : : > SLFEQLGGQAAVQAVTAQFYANIQADATVATFFNGIDMPNQTNKTAAFLCAALGGPNAWTGRNLKEVHANMGVSN > AQFTTVIGHLRSALTGAGVAAALVEQTVAVAETVRGDVVTV* > ----------------------- > > To predict side chain conformation I somehow have to keep the backbone fixed and tell > Modeller to model (only) the side-chains (without taking any information > from the template protein). > > How can I do that? > > Thank you for your answer, > > Andreas -- , Andras Fiser, PhD # phone: (212) 327 7216 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras