From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 15 2006 - 14:08:59 CST

Kenley,
  Yes, this is what I was referring to. STRIDE expects atom names
to follow the PDB atom naming conventions, and so it may not like the
names used in your AMBER files and this may be the reason it is not
giving a secondary structure prediction to VMD. (VMD automatically
runs STRIDE to calculate secondary structure on-the-fly)
If you send me a PDB or Parm/CRD files, I would be happy to take a look
and determine what the source of your trouble is.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Dec 15, 2006 at 12:39:54PM -0600, Kenley Barrett wrote:
> 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
> >>
> >
> >

-- 
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