VMD-L Mailing List

From: Barry Isralewitz (barryi_at_ks.uiuc.edu)
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
Timeline!

          Cheers,

          Barry 

-- 
Barry Isralewitz, Ph. D.
Theoretical and Computational Biophysics Group
3043 Beckman, University of Illinois at Urbana-Champaign
Office Phone: (217) 244-1612 
email: barryi_at_ks.uiuc.edu   http://www.ks.uiuc.edu/~barryi