Thank you Tim and Partha, The reason I do not have clear density of my ligands ( at 1.15 Angs) is that I have a native-active enzyme complexed with substrate and product forming at the active site. We have reason to believe from our enzyme kinetics data that we would be able to capture both the states. The structure shows the overall density of a substrate forming a product but the distinction is not clear before any refinement of the individual ligands. I am sure that correct refinement with partial occupation of substrate and product should do it. Hence my question.
Thanks, Ivan On Tue, Jun 22, 2010 at 11:10 PM, Tim Gruene <[email protected]>wrote: > 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 > > GPG Key ID = A46BEE1A > > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.9 (GNU/Linux) > > iD8DBQFMIaVQUxlJ7aRr7hoRAmJnAJ9GJMVdDpq+6AjVCpcgEjC6SZVKKgCeN46X > MbXcANyz66SLxlrC4PI4Ie0= > =/Sa9 > -----END PGP SIGNATURE----- > >
