Re: predict protein side-chain conformations

[Andras Fiser <andras@tuba>]

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:
New York, NY 10021-6399, USA # http://salilab.org/~andras