From: John Stone (
Date: Fri Jan 13 2017 - 23:18:08 CST


On Sat, Jan 14, 2017 at 04:57:34AM +0000, Amit Gupta wrote:
> Hi, I would like to know if anyone can shed any light on how these two figures were rendered in VMD/Tachyon
> 1.

This was drawn using the NewRibbons representation in combination with
the Licorice representation. The PaperChain representation was not used
at all in that figure, so the rest of the questions/comments for 1) below
are not relevant to that image.

> No matter what i do i cannot change color of paperchain in vmd. Similar thing is discussed here :
> however I cannot change color by selecting color type color-id. All my rings are red.

PaperChain is really meant to be used for carbohydrate, not DNA...

> 2.
> the 'glow' that yellow spheres are emitting, is it possible in vmd or
> its very impressive photoshop? If possible, then how to make it in VMD?

While I didn't help make that image, I expect that Prof. Onufriev's
team used the "glowlights" script I had previously made available
on the VMD-L list to make that figure. In essence, the glowlights
script adds extra lights into a VMD scene that can be rendered by Tachyon.
Unlike the normal infinite directional lights in VMD, the glow lights can
be positioned within the molecule, and they can have an arbitrary
set of quadratic distance attenuation coefficients, yielding the very
localized lighting such as is shown in that figure. It is possible
that they did this by hand, editing a Tachyon scene file themselves,
or that they might have used a version of the glowlights script I've
previously made available.

Here is a rendering by some of the people in our Center that used the
glowlights to add extra local lighting in various places, albeit with
some photoshop in a couple of places too:

You might also get other ideas from the VMD images produced here as well:

  John Stone

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349