Why can't I draw with my Apple Pencil?

Please double-check the opacity of the tool you're using. Sometimes it is set to 0% which gives the impression the tool is not working. To verify:

1. Select the tool (for example, the Scribble Tool)
2. Tap the color selection menu.
3. Tap the right pane and verify that the opacity is not 0%

Additionally, make sure Apple Pencil is connected to your iPad (Settings > Bluetooth). Also in PDFpen, check Tools > Settings > Stylus. If the problem persists, quit PDFpen and launch it again. 

As of PDFpen 6 for iOS, the Apple Pencil automatically connects to PDFpen so it is no longer listed among the stylus options.