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