Hi James,
start Coot, and read in your cif file plus a coordinate file containing
your ligand. Read in your structure and read in your mtz file as Auto,
then you end up with two maps FWTxPHWT and DELFWTxPHDELWT.
Next go to Calculate / Other Modelling Tools and select Fit Ligand.
Since you should have some nice extra density in you difference map
select this map to search your ligand in that map. Let Coot do the rest.
You can also select flexible ligand docking etc.
Should work as advertised. Once your ligand is in the position you
expect it to be you can run real space refinement using the difference
density map at this point. Then go to Calculate/Merge Molecules and
select which one you want to merge, save the new coordinates including
your found ligand.
Good luck,
Juergen
P.S. this is assuming Coot 0.31, and there's also a Coot BB :-)
James Pauff wrote:
>Good day all,
>
>I have what may be a very simple question. I am
>trying to insert a substrate/ligand into the active
>site of my enzyme using COOT, into electron density
>that I have already utilized in "O" for this purpose.
>I've created the substrate library file (*.cif) using
>a pdb file from PRODRG in the ccp4 sketcher. In COOT,
>I went to File->Get Monomer..., but when I type the 3
>letter code, I get nothing.
>
>Further, I have imported the substrate as a separate
>pdb file, and can move it close to the active site,
>but I have no idea how to orient/manipulate the ligand
>into the electron density. If I can eventually get
>the ligand as a monomer into the screen, I still don't
>know how to manipulate it's orientation prior to
>writing it into the enzyme's pdb, so I guess that I'm
>just generally stuck here.
>
>Any help/suggestions/advice would be appreciated.
>Thank you all for your time here.
>
>
>
>
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>
--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
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