Dear Ivan,

On Tue, Jun 22, 2010 at 11:06:08AM -0700, xaravich ivan wrote:
> Hi all,
> How can I refine multiple ligands( metall ions and other organic molecules)
> and in the same structure? I guess Refmac automatically generates restraints
> for common metal ions, but how could I put multiple pdbs and cif files of
> molecules in my Refmac cycles other than just metal ions.

you do not need multiple PDB-files. You can put all structures into one file.
You help the programs distinguish them by using a separate chain ID for each
molecule (waters can have all the same one, though).

>
> In my case even Arp ligand can only find one ligand in one of the sites
> (1.15 Angs data). Is there a way to use the partially ligand fitted
> structure to find the second ligand. Or is there a similar thing as
> superpose that would give me the rough coordinates of the ligands in the
> second site.

At 1.15A you should see clear density for the ligand. If you do not, make sure
that you do not fit something you only wish to be there.

To answer you question: You could assign the same chain ID to the ligand and to
the main molecule. Then, upon using this main molecule for superposition, the
ligand is moved, too

Tim

--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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