Although the doom ray and plasma III weapons look the same on your ship, they do fire different animations when using them. Blacksaber, try moving the black place-holder thumbnail out of the /thumbnails folder, and see if that helps. I renamed the file extension to .OLDpng and now there's
Blacksaber
As far as I can tell from poking around the models folder, the S0_DoomRay.X file references TextureFilename { "s0_Plasma.png" so it seems to just load the plasma texture by design. Ugh....surely this is something that will be changed in a patch. If you look in the thumbnails folder, you'll also notice that there is only a black place holder file for the Doom Ray instead of an actual pic. <img src="http://images.stardock.com/gc2/T_DL/smiles/
Doom Ray beam weapon has no thumbnail picture in the Shipyard builder, and when placed on a ship, has the same graphics as a Plasma 3 weapon. Pretty disappointing.
I too just researched and outfitted my ship with the Doom Ray. Needless to say, I was sorely disappointed in it's graphic (it's using the Plasma 3 model). The disruptor and phasor models were gratifying. Somebody slipped up here. We need a patch here.