VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 15 2006 - 11:13:05 CST

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

  John Stone
  vmd_at_ks.uiuc.edu

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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NIH Resource for Macromolecular Modeling and Bioinformatics
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