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First, I can't guranatee it is 100% correct, I just took a brief look at the source of xmatrix.
When XPM and GDK_PIXBUF are available (see your warnings), it looks like (can't give 100% gurantee, because didn't check thoroughly) xmatrix uses color from *.xpm images that are compiled into program. So you'll just have to recolor images in gimp and recompile. xmatrix uses matrix1.xpm, matrix2.xpm, matrix1b.xpm, matrix2b.xpm, which are located in xscreensaver-5.07/hacks/images folder. Images are compiled into program, so you'll have to recompile program once you recolor.
If xpm or gdk_pixbuf aren't available, it uses another set of images - matrix1.xbm, matrix2.xbm, matrix1b.xbm, matrix2b.xbm images, which are monochrome. Which means that colormap that makes letters green should be located somewhere inside of program, and you'll have to dig through program logic to find it. I recommend you to get xpm library and gdk_pixbuf, because in this case recoloring should be easier.
The ErV's solution works for me, having changed XPM images with Gimp. Anyway you have to change also the color of the "System Failure" box, which is coded in xmatrix.c. The dive's solution works too, but it is for the GL version of the Matrix screensaver (indeed, much easier in this case).
I can't imagine the face of Tuttle when he wakes up!
Warning: The GTK libraries do not seem to be available; the
`xscreensaver-demo' program requires them.
Warning: The GDK-Pixbuf library was not found.
Warning: The XPM library was not found.
Some of the demos will not use images as much as they could.
You should consider installing GDK-Pixbuf and re-running
configure. (GDK-Pixbuf is recommended over XPM, as it
provides support for more image formats.)
Note: The JPEG library was not found.
This means that it won't be possible for the image-manipulating
display modes to load files from disk; and it also means that
the `webcollage' program will be much slower.
Note: The OpenGL 3D library was not found.
Those demos which use 3D will not be built or installed.
You might want to consider installing OpenGL and
re-running configure. If your vendor doesn't ship
their own implementation of OpenGL, you can get a free
version at <http://www.mesa3d.org/>. For general OpenGL
info, see <http://www.opengl.org/>.
I'm not sure how to install the libraries. I have tried to do so via Synaptic by checking everything that starts with GTK, GDK, XPM and jpeg. Of course something tells me this isn't the right way to go about it.
With regards to the OpenGL 3D library, I had to download and install version 2.3.1 of libdrm as the distro DVDs only have 2.0.2-0.1 included.
You still miss some dependency: in synaptic look for libgdk-pixbuf2, libgdk-pixbuf-dev, libgtk2.0-dev, libjpeg62, libjpeg62-dev, libxpm4, libxpm-dev, libgl1-mesa-dev and accept further dependencies. The last one is the free implementation of the OpenGL libraries. If xscreensaver still complains about the OpenGL 3D library not found, you can always disable the compilation of those screensavers that require it passing the --without-gl option to the configure script.
Since a message that I was getting from './configure' was that I already had xscreensaver 4-.24 installed, I decided to download from the web the source code for that version of xscreensaver. Not sure if that is what made a difference, but I then made the gimp edits of the matrix*.xpm files using filters/colorify and then compiled.
Despite the fact I was having warnings with './configure' and some trouble with 'make', xmatrix.c compiled and I deleted the original xmatrix file and replaced it with the newly compiled one.
Success! Now I just have to play around with the colorify a bit to get exactly the effect I want.
My thanks to Tuttle, colucix, and ErV (you did indeed hit the nail on the head). You folks are wonderful!
P.S. Still not sure what I was doing with the libraries, but at least I have a solid binary 2 Disc (had to burn at a slower speed to ensure image integrity).