Re: [ccp4bb]: Ligand on symmetry axis

["Garib N. Murshudov" <garib@ysbl.york.ac.uk>]

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Maneesh Yadav wrote:

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>
> Hi all,
> I am in the final stages of refinment (ignoring arp/warp warning etc., I
> have finally got my 2.17A dataset down to (24%,29%), waters added).
>
> Now I have to add my iodobenzene ligand whose C-I bond sits on a two fold
> symmtery axis, which makes it "run into" itself.  Refmac keeps adjusting
> the conformation out of the density as to prevent the copies from
> overlapping.
>
> Does anyone know how to turn of specific VdW interactions of ligands with
> themselves?  I know that CNS has the igroup mechanism, but things finally
> came together for me in refmac and I would like to stay here ;)...

If your ligand is on two fold axis then only thing you need to do is to put
occupancy 0.5. Then
There will be no VDW repulsion between atoms.


Garib