Visualizing the coordinated bonds are easy, e.g.,
select zn, resn zn (this would select the metal)
show sticks, zn (this will show bonds to any atoms withing bonding distance
of zn that are also shown as sticks)
Additional bonds to heteroatoms may have to be manually added using the bond
command.
Hi Prija,
PyMOL does have trouble with heteroatoms every now and then. Is the
structure public--if so, can we please have the PDB ID? It'll be
easier for us to hunt for a solution if we have the data.
Cheers,
-- Jason
On Mon, Apr 18, 2011 at 5:45 PM, Prija Ponnan wrote:
> Hello
> I am trying
Hello
I am trying to visualize a protein-ligand complex of a metalloprotein using
Pymol.
The ligand and certain amino acids are coordinated with the metal ions in
the binding site.The binding site also have some water molecules which are
also making interactions with amino acids and the metal ions.
