From: Kenley Barrett (kenley.barrett_at_gmail.com)
Date: Fri Dec 15 2006 - 12:39:54 CST

I just tried to work with a similar trajectory file, and I found the same
problem, where it wouldn't show secondary structure when I asked for
cartoon. This time, when I asked for cartoon I noticed that the console gave
an "unable to find stride output file" error. Is this the information that
you were asking about before? I hope it helps to clear things up. Please let
me know any thoughts.

Thank you very much for all of your help.

Kenley

On 12/15/06, Kenley Barrett <kenley.barrett_at_gmail.com> wrote:
>
> 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/ <http://www.ks.uiuc.edu/%7Ejohns/> Fax:
> > 217-244-6078
> >
>
>