VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 26 2021 - 00:14:25 CST

Hi,
  You can draw text labels or other geometry in front of molecular
representations and/or user-drawn geometry, but there is not a
simple "overlay plane" 2-D label compositing scheme like what you're
asking for. Most researchers generate their molecular graphics in
VMD, and then add nice looking labels and diagrams using their favorite
line art tools in Adobe Illustrator or Photoshop, GNU GIMP, or various
other image or vector graphics editing tools.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 12, 2021 at 09:18:16AM -0600, Timothy Leong wrote:
> Greetings all,
> Is there a way to overlay graphics primitives on top of a graphical
> representation of a molecule? My goal is to number the beads of a CG
> system (included in attached zip file as filenames 'CG_15beads.pdb' and
> 'CG_15beads.psf') in similar fashion to that of Figure 1 in this
> paper:Â [1]https://www.pnas.org/content/105/4/1204. However, when I use
> either the draw or the graphics command, I find that the beads of the CG
> system end up occupying the front-most layer of the current view, which
> obscures the numbers that I used to label the beads (as seen in the
> 'Obscured_Numbers.tga' snapshots). I've looked through both the VMD user
> guide and the VMD tutorial and did not find any mentions on how to change
> such a property. The tcl script I use to label the CG file is
> 'Label-CG.tcl'.
> These files I mention can be found at my
> Github:Â [2]https://github.com/TLeong2000/Graphics-Help-Request-VMD
> On a less pressing issue, I find that when I use the coords of the center
> of each CG bead in the draw/graphics command, the command always creates
> the graphics primitive off-center. Is there a way to draw these graphics
> primitives so that they are perfectly aligned on-center within a single
> command and/or a way to reposition their coordinates?
> Sincerely,
> Timothy Leong
>
> References
>
> Visible links
> 1. https://urldefense.com/v3/__https://www.pnas.org/content/105/4/1204__;!!DZ3fjg!tyKHri7lddCYImyIRV3t4w0QnSxLHmFqem0ZqBcJ42GX0LbMIGqyOtsGFLEsG81_1w$
> 2. https://urldefense.com/v3/__https://github.com/TLeong2000/Graphics-Help-Request-VMD__;!!DZ3fjg!tyKHri7lddCYImyIRV3t4w0QnSxLHmFqem0ZqBcJ42GX0LbMIGqyOtsGFLFHSzpfsw$ 

-- 
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/