From: Nima Emadi (
Date: Thu Jan 28 2016 - 15:37:23 CST

Thanks Josh

Using bond representation is a good idea that can work for simple
cylindrical particles. However, In my case, the actual particle is much
more complicated than jus a single cylinder. I have a tripod like rigid
particle which I can draw easily using a collection graphics commands with
a help of a script which reads the trajectory and generates a tcl output
for each snapshots of the trajectory. I just need to combine all these
snapshots in VMD to make a movie.

Note that I want to be able to play and/or change the viewing angle of the
movie in the vmd GUI, just like a normal trajectory which is loaded in vmd.
Is this possible without so much effort? Would be great, If you could point
me to a similar script that can do this.


On Thu, Jan 28, 2016 at 8:52 PM, Josh Vermaas <> wrote:

> Hi Nima,
> Its a bit unclear as to what you will be doing, which might impact how
> easy it is to get setup. If your real cylinders are atoms connected by
> bonds that merely look cylindrical, the "bonds" representation is probably
> what you want, and gets around using the graphics commands at all. The
> reason the graphics commands sound like they might be alot of work is that
> they don't vary if you add more frames. So in order to make a movie using
> graphics objects alone, you'd need to draw a frame, render the frame, clear
> the frame, draw the next frame, render the frame, clear it, and so on and
> on until you've drawn everything. Luckily this can all be scripted, but
> animate dup 0 won't do anything for you unfortunately.
> -Josh Vermaas
> On 01/28/2016 02:10 PM, Nima Emadi wrote:
>> Dear all,
>> I want to make a movie from a given MD trajectory of some cylindrical
>> rigid
>> particles.
>> Using graphics command in tcl, I'm able to produce a single snapshot.
>> However I am stuck when I want to add a new frame to my molecule.
>> Simplified version of what I have in my tcl script (for just one particle
>> which moves along z axis) is:
>> color Display Background white
>> mol new
>> graphics 0 color 7
>> graphics 0 cylinder {0 0 0} {0 0 1} radius 0.4 resolution 30 filled yes
>> animate dup 0
>> graphics 0 delete all
>> graphics 0 cylinder {0 0 0.5} {0 0 1.5} radius 0.4 resolution 30 filled
>> yes