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. See the pymol wiki for how to select atoms to link with the bond
command. You will have to show sticks to see the bond. Waters are usually
visualized as spheres, and you may want to modify their vdw radius to
0.5-1.0 A to make them small enough.
Cheers,
Roger Rowlett
On Apr 18, 2011 5:48 PM, "Prija Ponnan" <prija.pon...@gmail.com> wrote:
> 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. But using
> Pymol i am not able to visualize the coordinated bonds.
> When I am visualizing the binding site of this protein using Pymol, the
> water molecules are showing multiple hydrogen bonds (6 hydrogen bonds),
> which is not correct according to the valency of oxygen.
>
> Please help me
>
> Thanks
>
>
>
>
> Prija Ponnan
>
> Research Student
> Department of Chemistry
> University of Delhi
> Delhi-110007, India
> &
> Canadian Commonwealth Scholarship Program Scholar
> College of Pharmacy and Nutrition
> University of Saskatchewan
> Saskatoon,SKN5C9,Canada
------------------------------------------------------------------------------
Benefiting from Server Virtualization: Beyond Initial Workload
Consolidation -- Increasing the use of server virtualization is a top
priority.Virtualization can reduce costs, simplify management, and improve
application availability and disaster protection. Learn more about boosting
the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
