There are many ways to do this. You can also try Action>preset>ligands. This will show the ligands (hetatms) and their interactions. Unfortunately this doesn’t highlight metal ions everytime (unless it interacts with the ligands). You can usually view this using the sequence option. [show the sequence – S button bottom right, move the slider to the end of the protein (usually) and select the metal(s) show spheres of selection]
Hope this helps
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Ph / Waea +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034
Jhon Thomas [mailto:firstname.lastname@example.org]
Sent: Thursday, 26 March 2009 5:30 a.m.
Subject: [PyMOL] depiction of ligands
I would like to know, how we can show the ligands in pymol. Although i can see the non-bonded atoms ( HOH) automatically, eacept other nonbonded atoms l;ike sulphate and metal ions. I will appreciate the suggestions.
Thanks in advance