VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 14 2006 - 00:27:38 CST

Hi,
  Do you have an example image I can see? It's hard to imagine the
exact scenario you're describing from the description, I can think of
several possible reasons you're seeing a secondary structure representation
that differs from what you expect, depending on whether what you're seeing
is primarily an artifact of the old Cartoon rep, or an issue with Stride,
or something else yet. If you can show me an image (post one on your web site
for example) I can give better feedback.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 13, 2006 at 02:02:53PM -0500, Viswanadham Sridhara wrote:
> I am trying to use cartoon mode to visualize a protein, 1 out of 3 or 4
> times, it looks ok, but the remaining times, it looks kinda mixed newcartoon
> and cartoon, Any reason why?
> I mean, the protein I am visualizaing has 4 helices, so they look like
> perfect tube to me few times(which should be the case), but most of the
> times, it looks like broken tube which some other modes fixed.
> Regards,
> -Vissu
>
> --
> Viswanadham Sridhara,
> Graduate Research Assistant,
> Old Dominion University, "VIRGINIA". 

-- 
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