From: Barry Isralewitz (
Date: Tue Jan 02 2007 - 12:21:16 CST

Hi Ana,

On Tue, Jan 02, 2007 at 12:21:31PM -0500, ANA DAMJANOVIC wrote:
> Hi Barry,
> In case you have an easy answer about VMD, and you are not on
> vacation and swamped, could you please let me know ASAP,
> as my paper cannot go out until I redo the figures, and
> basically that's all I'm waiting for.
> Many thanks in advance!!!
> ANa

   Happy New Year Ana, and thanks for the beautiful pictures!

  Sorry for the delay with the VMD response. Here is the easy answer on
how to output giant pictures from VMD:

1. Get your figure displayed nicely in the VMD OpenGL window. Make sure you have
cranked up "resolution" settings for appropriate represenations.

2. Render out the geometry to a plot.dat file. That is, render with with
"File:Render..."; Render using: Tachyon External

This is will put a plot.dat file in the same directory as your output
bitmap file. (The default format is Targa (.tga), a non-lossy

Now that you have the geometry rendered to a plot.dat file, you can re-render from the
command line multiple times for different resolutions, anti-aliasing
settings, and more.

3. The default command for TachyonExternal is

 /Projects/vmd/pub/linux/lib/vmd186a14/tachyon_LINUX -aasamples 4 -trans_vmd -mediumshade -format TARGA plot.dat -o plot.dat.orig.tga
(you vmd executable path will vary)
 ..but since we want higher resolution we can ask for
a) more anti-aliasing samples (smoother appearance), just increase the number on the command

 /Projects/vmd/pub/linux/lib/vmd186a14/tachyon_LINUX -aasamples 16 -trans_vmd -mediumshade -format TARGA plot.dat -o plot.dat.the_antialias_setting_is_16.tga

b) a larger size render. The output render size is determined
in the second line of the plot.dat program. Simplest to just multiply
both by the same integer.

For instance, copy plot.dat to plot.bigger.dat, then edit
plot.bigger.dat, and change

Resolution 669 834


Resolution 2676 3336

and save plot.bigger.dat.

then render. In the below, think I'll combine a) and b), I'll render plot.bigger.dat, and raise the anti-aliasing from the
default 4 to 8.

 /Projects/vmd/pub/linux/lib/vmd186a14/tachyon_LINUX -aasamples 8 -trans_vmd -mediumshade -format TARGA plot.bigger.dat -o plot.bigger.dat.aa_8.tga

  For really big pictures, it can be faster to work in /tmp (especially
if files are in a network directory).

4. For an extra level of smoothing, render the image a twice the
final required pixel dimensions, then use convert -resize 50%.

5. Of course, stay with .tga or .tif files (or non-lossy .pgn formats)
continously. Only use jpg or gif for web-only preview images.

6. Type /Projects/vmd/pub/linux/lib/vmd186a14/tachyon_LINUX (or local
equivalent) by itself to see more rendering options.

   Hope that does it! Let me know if you have any questions or problems!



Barry Isralewitz   Theoretical and Computational Biophysics Group, UIUC  
Beckman 3043   Office Phone: (217) 244-1612  Home Phone: (217) 337-6364