Docked with Metal complex by using Autodock vina. vina results visualized by using pymol software but Complex(M-L) bonds are missed. what is the reason for the metal-ligand bond is missed. kindly help me.
PyMol doesn't really know which atoms are bonded. It draws bonds (normally) on the basis of the distance between the atoms, i.e. when the distance is below a certain threshold, it displays a bond.
Bonds to metals are usually relatively long, so I could imagine that the distances are above the threshold. You can add bonds manually with the "bond" command.
Hi, I once also had such a problem when visualizing a structure with an iron/sulfer cluster, initially there was no bond between Fe and S when loaded in pymol. But when I use the pymol preset 'pretty', the iron/sulfer cluster was shown perfectly with all the bonds needed. Maybe you can try this method.
If a bond is not recognized automatically by PyMOL, you can draw it explicitly using the "bond" command:
https://pymolwiki.org/index.php/Bond
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