VMD-L Mailing List

From: Kenley Barrett (kenley.barrett_at_gmail.com)
Date: Fri Dec 15 2006 - 11:27:30 CST

John,

Thank you very much for your reply. I'm sorry, I'm ignorant and I don't know
what you mean by the "STRIDE secondary structure prediction program". How do
I make this program run so that I can check for errors?

Thanks,
Kenley

On 12/15/06, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>
> 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
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>