Subject: Re: predict protein side-chain conformations
From: Andras Fiser <andras@tuba>
Date: Tue, 06 Nov 2001 12:23:49 -0500
Cc: modeller_usage
Organization: The Rockefeller University
Reply-to:
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