VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Jan 29 2016 - 05:02:16 CST

Using the movie animation system „userani“, you could combnine your custom drawing with comfortable movie generation using the VMD movie maker very easy. This will save you from the trace stuff completely.

 

 <http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/userani/> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/userani/

 

But you’d still need to write your own drawing procedure.

 

Norman Geist

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von Axel Kohlmeyer
Gesendet: Freitag, 29. Januar 2016 00:17
An: Nima Emadi <deeepsky_at_gmail.com>
Cc: Vmd l <vmd-l_at_ks.uiuc.edu>; Josh Vermaas <vermaas2_at_illinois.edu>
Betreff: Re: vmd-l: making a movie in a tcl script using graphics commands

 

On Jan 28, 2016 22:46, "Nima Emadi" <deeepsky_at_gmail.com <mailto:deeepsky_at_gmail.com> > wrote:
>
> 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.

Graphics elements are global and not per-frame. If you want dynamic graphics elements, you need to store the data for it somewhere, and then have a function redraw or update it via tracing the vmd_frame variable. Check out the pdf at the link below for some examples of dynamic graphics etc.

https://sites.google.com/site/akohlmey/redirect/cpmd-vmd.pdf?attredirects=0 <https://sites.google.com/site/akohlmey/redirect/cpmd-vmd.pdf?attredirects=0&d=1> &d=1

Axel

>
> Cheers,
> Nima
>
> On Thu, Jan 28, 2016 at 8:52 PM, Josh Vermaas <vermaas2_at_illinois.edu <mailto:vermaas2_at_illinois.edu> > 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
>>
>>
>