if you wish transparent textures you need to model inside the biodomes...so there is something to see in it...and transparent texture isnt a problem...
i make windows like this:
open Photoshop, make 256x256 image with no background, make simple rectangle of desired color same size of image, apply texture overlay for better feeling, but apply it lightly blending not more then 40%, merge all layers and blend that layer to 30-40%, save as DDS and apply it in Milkshape...
there are few other tricks to make only part of textures transparent, but this will do for start
on second thought, its not really needed for biodomes on a ship. - i was rather thinking of some grill or so that protected the domes, - but the greenish ( slightly cartoonish ) look is OK. - its not perfect. - but the fragile look of the station domes might look a bit out of place there, considering the ship is still meant to be used in combat.
but, doom, if you haven t submitted that one yet and you have an idea for them, don t hesitate to apply it, - i tried quite some skins on the domes, and there wasn t one that i really liked. - the only other one i liked very much was one that looked like heavy armour plates with slits that went around the whole dome. - looked nice, ... just not like a biodome, but rather like some strange reactor case.
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*pictures very small nomad bomber attempting to Nova the armour plating of the reactors to find tomatoes inside*
That is one of the best looking battleships I have ever seen! Beats all of the Vanillias. I just hope they won't see to much combat, being Zoner 'n all that.