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