wondering how to change the effects of water, to make it LESS transparent? I tried .50 (default for holodeck_temple is .25) but no noticeable difference. Do I go to the negative scale?

You're probably just adjusting the transparency in Radiant.
You'd have to edit the .tga file to change the transparency in-game.

I think...

Can't you 'cheat'? I mean, make the alphagen a wave, choose as base the transparency you want (will take some experimenting), and give it an amplitude of 0. It will probably make the shader a little more difficult to calculate for the game, but I doubt this will be noticable.

Since when you can put a wave on a blending option?

I remember seeing in a map the use of a fog brush inside water to give it that murky look. Try that and see how it works.

Why he cant just edit the alpha channel?

yeah on waterzone map he used fog texture with the water texture to create misty water. good for sneaking (shoudl that be sweaking a mix of sneaking and swimming????lmao)

i dunno if that is the effect that u want but personally seens as i have no idea what your talking about with alpha channels and crap i woudl just do the fog thing.

keep it simple when u don't no what your doing thast what i say. otherwsie u may get some crappy errors and it may mess stuff up. but there are far more expericned mappers out there then me . but i reckon i can produce same amount of good stuff as them hehehehehehe

good luck with it though  

Alphagen can have a wave, just like rgbgen. This will darken/lighten the alpha channel, so this will only have effect on textures with an alphachannel.