From: John Stone (
Date: Fri Dec 15 2006 - 11:13:05 CST

  Are you getting errors or warnings in the VMD text console window
when VMD runs the STRIDE secondary structure prediction program?

  John Stone

On Thu, Dec 14, 2006 at 06:31:09PM -0600, Kenley Barrett wrote:
> 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.
> Kenley

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