Retouching Transparent Pixels

[kevponce]

Greetings

I have been retouching since Photoshop 2.0 but man I am going nuts trying to resolve this issue. 

I have posted three photos.  The first shows a "Y" Chromosome that I am trying to retouch out of the gray drop shadow, but the pixels here are transparent.  On the second photo I have turned on a white background just so you could see that there is a gray drop shadow behind the "Y". The gray drop sahdow normally sits over a blue background, The third photo show when I try to retouch out the "Y" it is multiplying in the transparent pixels.  I can't seem to understand why it just won't clone the transparent pixels and leave them transparent.  I mean I get it in some regards; "They are transparent" so duh, they will automatically multiply, but is there NO way for me to just clone them over, deleting the "Y", leaving me with just gray drop shadow, and without them multiplying? 

Help.

[Mylenium]

That's what cahnnel operations do (Image --> Calculations). You generate an opaque mask e.g. using the red and green channel for your orange and yellow chromosome, then apply it to the layer as a layer mask, ideally also on a fully opaque layer. Then you can clone ahead without ever having to worry about unwanted blending because the masks can always be converted to selections, inverted, modified and opacities tweaked.

Mylenium

[c.pfaffenbichler]

One can also edit a Layer’s transparency by turning it into a Layer Mask first (Layer > Layer Mask > From Transparency). 

[Earth Oliver]

Yes, it's because you're cloning transparency on top of transparency which is multiplicative.
Unfortunately, after 30 years of development, the clone tool still doesn't have a Preserve Transparency option.

[c.pfaffenbichler]

The Layer itself has one, though. 

[kevponce]

The Layers transparency doesn't matter.

It's the pixels temselves.  Unfortunately I think Earth Oliver is reight.  The clone tool has to have the abilty to replicate transparent pixels while overwritng the pixels that are already there. 

[c.pfaffenbichler]

Then I guess I misinterpreted @Earth Oliver ’s point, sorry. 

[Earth Oliver]

yeah, but locking the layer transparency still doesn't allow the clone tool to work as wanted on a partially transparent layer.