Hi folks/Jason,


I have been playing with PyMOL again lately for teaching and have noticed that when you run the menu command Action>preset>ligand site >cartoon which looks great... if there are any H-bonds with a protein chain amide carbonyl, then the carbonyl is not displayed. If you use “Show>lines or sticks” this does not then show them. I’m sure there is a background (python) setting to adjust this but is it possible to include the carbonyl’s in question with the initial preset? HIV protease is a good example to show this.





Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand  

Skype: jtyndall

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