predict protein side-chain conformations

[Evers Andreas <evers AT mailer.uni-marburg.de>]

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