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When you're working on a model that has both poly groups and subtools you can run into a few strange conflicts when using certain hot key combinations. I have the demo soldier. This is one of the models that comes with ZBrush. He's loaded on the canvas here and I have him in Edit mode. I turned on the wire frame so that you can see the poly groups. These are the different regions of color here. So there's a poly group for each leg. The torso, each arm and the head. I can isolate the leg poly group by holding Ctrl and Shift and clicking on it.
And now it's isolated. To bring everything back, I hold Ctrl and Shift and click on the canvas. The problem arises when I'm working with subtools at the same time. I'm going to make all the subtools visible by clicking on the eyeball icon. The hotkey combination to interactively switch between one of subtool for the other is also Ctrl+Shift. So if I want to switch to the kneepad here, I can press Ctrl+Shift and click on that and now I'm changed subtools to the kneepad subtool. So I'm no longer working on the torso, just the subtools, and you can tell because the wireframe display is only active for the current subtool that I'm working on.
The problem is if you have the subtools visible and you want to switch from one poly group to another, it's very easy to accidentally switch subtools instead of switching poly groups. So by Ctrl+Shift-clicking on his leg, I have switched back to the main body subtool. So the other problem that occurs when you do this, let's say I want to isolate the leg here, but I accidently click on the boot. Notice in the Subtool palette it looks like I deleted all of my subtools. They're here on the canvas, but I can't see them in the palette.
This is actually a bug is Zbrush. To fix this you just need to click on the up arrow key to bring back the visibility of those subtools. And now it's filled the palette and it's a little more obvious what's going on. So the solution to this problem is to change the way that you work. In other words, be careful not to switch poly groups while you have other subtools visible. If you just want to work on the body and you're switching between the poly groups, hide everything but the body.
And now I can easily switch between the various poly groups without warring about switching between the various subtools.
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