Hi there,


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
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand                   


Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054

Ph / Waea               +64 3 4797293
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From: Jhon Thomas [mailto:jhon1.thomas@gmail.com]
Sent: Thursday, 26 March 2009 5:30 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] depiction of ligands


Hi all

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