You need to use a transparency map. When making a transparency map one thing to remember is that 100% black is complete transparency and any lighter shade (usually greys)gives less transparency. The lighter the grey the more visible an object becomes. To have part of an object transparent while keeping parts visible your trans map would be black where you want the transparency and white where you want to see parts. I would suggest a shade of grey to make glass. Trial and error really until you get the look you want. You still set your transparency dial to 100% Helen

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