VMD-L Mailing List

From: Timothy Leong (tleong4_at_uic.edu)
Date: Tue Jan 12 2021 - 09:18:16 CST

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:
https://urldefense.com/v3/__https://www.pnas.org/content/105/4/1204__;!!DZ3fjg!tyKHri7lddCYImyIRV3t4w0QnSxLHmFqem0ZqBcJ42GX0LbMIGqyOtsGFLEsG81_1w$ . 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:
https://urldefense.com/v3/__https://github.com/TLeong2000/Graphics-Help-Request-VMD__;!!DZ3fjg!tyKHri7lddCYImyIRV3t4w0QnSxLHmFqem0ZqBcJ42GX0LbMIGqyOtsGFLFHSzpfsw$

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