VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 13 2020 - 12:13:49 CST

Francesco,
  It sounds to me like you're experiencing trouble that relates to
so-called "gamma correction" of your images. The "snapshot" rendering
mode in VMD takes the exact image data you're seeing on the screen
and writes it to a file. There is no difference in the color content
vs. what you saw in VMD itself, therefore I suspect an issue with your
image viewer.

The renderings that VMD and Tachyon create use a linear color space
without any gamma correction factor (a gamma value of 1.0).
If you load the images that VMD or Tachyon generate into a viewer
program that assumes a monitor gamma of 2.2, it will have a tendency
to wash out your image somewhat compared to the way they are shown
in VMD itself (gamma 1.0).

You can usually overcome this problem by telling the image viewer to
either disable automatic gamma correction, or to change its assumed
gamma value from 1.8 or 2.2 to 1.0, or worst case, if such controls
aren't available, you can tell it to apply the inverse gamma correction,
e.g. 0.5 and then the images should look the way they do in VMD itself.

If you're not familiar with gamma correction or the problems it
creates when creating images for printed or online manuscripts,
this is probably a good time for you to read about it:
  https://en.wikipedia.org/wiki/Gamma_correction

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Feb 13, 2020 at 06:28:10PM +0100, Francesco Pietra wrote:
> Hello
> With VMD 1.9.4a12 I am trying to obtain images, on a black background, of
> a RNA-protein complex displayed in color by chain (new carton). As you can
> imagine, there are so many chains. In this system, pathways of a ligand
> are illustrated by highlighting RNA residues, as colored wdw, that lie at
> a few Angstrom from the traveling ligand.
> Using Snapshot or Tachyon, the variety of colors for the new carton
> assembly (both RNA and proteins) in poorly reproduced, actually nearly
> uniform color, while colors of wdw residues is correctly reproduced. All
> that by opening the .tga file with various tools, including GIMP.
> Can that be a problem of using the correct tool instead of Snapshot or
> Tachyon? Are there any better?
> Thanks for advice
> francesco pietra 

-- 
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/