VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 30 2003 - 15:46:30 CDT

Hi Tyler,
  Regarding the cartoon representation, if you want to have it recalculate
for every timestep in your trajectory, you can use the 'ssrecalc'
script in the VMD script library. Alternately you can use the command
  mol ssrecalc top
to force the secondary structure to be recalculated by STRIDE (VMD
uses STRIDE to perform secondary structure determination).

If you're curious how STRIDE decides on structure, check one of
the stride related web sites for docs and info:
  http://www-db.embl-heidelberg.de/jss/servlet/de.embl.bk.wwwTools.GroupLeftEMBL/argos/stride/stride_info.html

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, May 30, 2003 at 02:21:40PM -0600, Tyler Luchko wrote:
> Hi,
>
> I've been trying to use the cartoon representation to look at the results
> of an annealing simulation and I've had some inconsistent results. My
> anneal run is divided up into 4 different trajectories. When I load these
> trajectories into vmd I get different results from the cartoon
> representation (and structure colouring). Notably, several of the beta
> sheets are interpreted as random coil. This is not due to heating as
> they disappear at the beginning of the heating and reappear during the
> following high temperature equilibration phase. In one case, where two
> frames are separated by 2 ps, one has 4 beta sheets shown and the other
> has 2. The tracing of the backbones is almost identical. What might
> cause this?
>
> I have also noted that only the first frame of the dcd file seems to be
> used by the cartoon representation. Is it possible that this might be
> changed?
>
> Thank you,
>
> Tyler
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
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