Yuan Cheng wrote:
I am trying to model a S-adenosylmethionine (SAM) molecule into the
active site of a protein using the SAH (exists in the crystal structure)
as the template.
2)Coot: I tried to superpose SAM to SAH in coot. Bot SSM superpose and
LSQ superpose didn't work. when I did SSM superpose, coot said "can't
make graph for SAH structure". when I did LSQ superpose, nothing
happened after I run it. I also tried Extensions> modeling> superpose
ligands, nothing happened too. Does anyone know what's wrong here?
Finger fumble?
AFAICS if you are using Coot, Extensions> Modelling> Superpose
Ligands... is indeed what you want.
I just did it myself, it looks fine.
http://www.biop.ox.ac.uk/coot/screenshots/Screenshot-Coot-SAM-SAH.png
(Using ligands from SBASE and LIBCHECK).
I know that I can probably manually move SAM to the position of SAH and
change the bond angles to make SAM align to SAH.
Bleugh.
(You are not the first to SSM superpose a ligand, I've improved the
dialog to better explain what's needed - thanks.)
Paul.
