From: Kenley Barrett (
Date: Thu Dec 14 2006 - 18:31:09 CST

Dear VMD users,

I am viewing an AMBER trajectory in VMD 1.8.4, and when I ask VMD to show a
"cartoon" representation, it gives me a picture similar to the "ribbon"
format in which the backbone is just shown as a tube. There are no cylinders
to represent helices or anything. However, just looking at the ribbon
representation reveals that there is SOME secondary structure; even if my
protein is a complete mess, there are still some clear helices, so I am not
sure why VMD is not detecting secondary structure. Does anyone have any
suggestions on what the problem might be?

I would be very grateful for any advice. Thank you in advance.