How to make a shader's alpha editable in script?

I need a shader that loads an image alpha as transparency, and is also self illuminated, this shader works for that:

Shader "Self-Illumin/Transparent" {
Properties {
_Color ("Color Tint", Color) = (1,1,1,1)
_MainTex ("SelfIllum Color (RGB) Alpha (A)", 2D) = "white"
}
Category {
Lighting On
ZWrite Off
Cull Back
Blend SrcAlpha OneMinusSrcAlpha
Tags {Queue=Transparent}
SubShader {
Material {
Emission [_Color]
}
Pass {
SetTexture [_MainTex] {
Combine Texture * Primary, Texture * Primary
}
}
}
}
}

But now I also need to be able to tweak the whole texture's transparency in runtime in script, like this:

nuColor.a = Time.time*0.001;
renderer.material.color = nuColor;

I've noticed that the scipt works with some Unity's built-in shaders, and doesn't work on others, sadly, it doesn't work with my trasparent/self-illum shader, why is that?, what parameter(s) control that?

 

Please use the code tags.

http://unity3d.com/support/documentation/ScriptReference/Material.SetColor.html

You have to incorporate the alpha channel of _Color somewhere in your shader. Sadly, it doesn't come through the Material block, for any term, as far as I remember, anyway. Just multiply by the constant instead of primary, on the last line, for the alpha channel. Also, realize that you do not need to write a separate alpha function if it's the same thing as the RGB calculation.

Some of Unity's shaders use something other than "_Color", like "_TintColor". There's no good reason for it, aside from compatibility with old code.