VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Dec 10 2013 - 10:06:07 CST

Hi,
  I think that the main issue with your figure is that you have
a color scale range (the math that maps values to colors) that
is showing a lot of "noise" in your data. If you use the min/max
controls in the color scale data range controls within the
"trajectory" tab of the graphical representations window, you
can specifically set the value range that you want mapped to the
color gradient that VMD displays. As others have already mentioned,
you can also use the "Volume" coloring method, which will map the
data values to the active VMD color scale (see the Color window),
starting with the min value and going to the max value, as defined
by the color scale data range controls I mentioned above. Using
that, you can make easy-to-interpret color ramps, and you can also
add a color scale bar to the figure using the color scale bar
plugin found in the Extensions|Visualization menu.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Dec 10, 2013 at 08:55:04AM +0100, Albert wrote:
> Hello:
>
> I am visualizing a .dx map file in VMD as "VolumnSlice". The data it
> self looks good, however the displayed figure looks really bad....Here
> is a screenshot for it:
>
> https://dl.dropboxusercontent.com/u/56271062/density1.jpg
>
> I am just wondering how can we improve the quality? Can we smooth the
> grid so that it doesn't looks like mask. Is it possible to change the
> color? I use the color panel to change it, but it seems doesn't work.....
>
> thank you very much.
>
> Albert 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/