From: Barry Isralewitz (
Date: Thu Oct 27 2011 - 13:25:08 CDT

Hi Bryan,

On Thu, Oct 27, 2011 at 11:34:40AM -0500, Bryan Roessler wrote:
> Hello,
> Due to the size of my system, I am forced to break my rmsd analysis into
> chunks, run the script on our high-throughput cluster, and finally recombine
> the data into a formatted tml file. However, due to the requirements of the
> timeline plugin, I am forced to load all of the analyzed frames of my
> trajectory before I can load my pre-rendered tml file. Due to memory
> limitations, this is impossible. I am only interested in visualizing the
> data using the "heat map" featured in the timeline plugin and do not care if
> my residue selections are passed to the structure viewer.
> Is there anyway to visualize the data in VMD without having to load the
> corresponding trajectory files first? If not, does anyone have any
> recommendations for programs that will be able to generate a good visual
> representation of the change in rmsd values by residue over simulation time?
> I can obviously tweak my script to generate the appropriate formatting so
> that the file can be natively imported into the recommended program.
> Thanks,
> Bryan Roessler
> The University of Alabama at Birmingham

  The current VMD release, VMD 1.9, should be able to load your entire
.tml file with as little as 1 frame of the original trajectory loaded.
When you select a frame on the Timeline plot that references a frame
number beyond than what has been loaded (e.g. click on frame 500 when
only 3 frames are loaded) the final frame (in this example, frame 2,
since zero-counting) of the loaded structure trajectory will be displayed
in the OpenGL view, but the correct Timeline/.tml data will still be
displayed through the Timeline GUI. (Apologies if this tip too obvious,
but: to load just a few frames (or even 1 frame) from your large file,
you can use the normal VMD GUI controls or text commands at load time,
or make a 1-frame version of the file.)

  Let me know if this doesn't work for your file. Thanks for using



Barry Isralewitz, Ph. D.
Theoretical and Computational Biophysics Group
3043 Beckman, University of Illinois at Urbana-Champaign
Office Phone: (217) 244-1612