We use a similar work flow to that described by Scott Pegan, except we use
the Dundee PROGDR server to generate the ligand PDB and cif file. I would
add that you should double check your cif file and make sure it has all the
proper restraints, and also double check your stereochemistry. If you are
not used to this, it could take some time, but it is easy to make mistakes
here (at least for me).
If the ligand density in not clear, try to finish as much of the structure
as possible before adding ligand, but beware amino acid side chains drifting
into ligand density.
We sometimes see more than one possible orientation of the ligand, or parts
of it. Most of the time this can be resolved by docking both ligand binding
orientations and doing a round of refinement.
Best,
Kendall Nettles
The Scripps Research Institute
On 2/5/09 10:27 AM, "ANDY DODDS" <[log in to unmask]> wrote:
> Hello,
>
> does anyone know of a tutorial which lays out some sort of pipeline,
> hopefully using CCP4 packages, to fit and refine a small molecule
> ligand please?
>
> cheers
>
> andy
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