From: Norman Geist (
Date: Wed Nov 15 2017 - 01:24:53 CST

You'd need to use the trace procedure in order to update the drawing every
frame. See this example:


It should be easy to adapt it. One hint from my side. Save the return values
of the draw command (handles) so that you can easily delete them before
drawing the new ones every frame. In case of having multiple drawings per
frame, it more smooth that "draw delete all"


Additionally the atoms you want to overlay with the cylinder can be aligned
using e.g. the Extension->Analysis->RMSD Trajectory Tool so they move less
between frames.


Good luck


Von: [] Im Auftrag von
Nuno Sousa Cerqueira
Gesendet: Dienstag, 14. November 2017 19:21
An: VMD <>
Betreff: vmd-l: graphics in VMD and overlay


Hello vmd community.,


Is it possible to draw a graphic, e.g. a cylinder, that stays all the time
above the structure that is displayed.


Here is an example of what is happening :


I have two molecules loaded in the VMD interface.

Molecule 1: any protein

Molecule 2: a cylinder or the type of graphic.


The problem is that every time I move molecule 1 (the protein), the atoms
it get above the cylinder that is in the molecule 2.


Is there any way to get this working ?



Thanks for the help.










Nuno M. F. Sousa A. Cerqueira

Chemistry Department

Faculty of Sciences

University of Porto

Rua do Campo Alegre, s/n

4169-007 Porto


Tel: +351 220402501

Fax: +351 220 402 009

email: <>