Can't burn bootloader with Atmel ICE

Drewski:
Ok, so I'm confused with the talk of using Amtel Studio along with Arduino IDE. Could someone please help me sort this out?

I made a custom board using a SAMD21E17. Using Amtel-ICE & Amtel Studio, I'm able to communicate with the chip and can burn a bootloader to it. Since I followed the design of the Femto USB, I used their bootloader. In Windows 10, I see it pop up on a COM port. I then can see the COM port available in Arduino IDE 1.6.7 but I can't upload anything to it... the IDE hangs on uploading the sketch.

So my question is, with a fresh chip, can I burn the Arduino bootloader directly to the chip from Arduino IDE? Do I need to first convert a bin to hex and use Amtel Studio to burn to the chip before I can use it in the Arduino IDE? Is there any possibility of a clock speed issue? I see the zero is at 48Mhz, and I'm using an external 32Mhz crystal, is that an issue and the crystal needs to be removed? If I understand correctly, the 48MHz is an internal setup?

Thanks in advance for your help.

How did you burn the bootloader in Atmel Studio? I couldn't see the option right away.

Anyway, on my custom J board I used the regular Arduino IDE to drop in the regular Zero bootloader via the Atmel ICE. (Tools | Programmer | Atmel ICE then Tools | Burn Bootloader) It worked fine and I was able to drop in programs directly from the IDE via the Native USB port after that.

The com port assignment in the OS does thrash around a little bit the first fews times and that can spoil the first download attempts but it seems to settle down after a bit.

All that said, I did use a 32kHz xtal on my J board in just the same way that it is used on the Zero. I'm not sure if your 32Mhz xtal will cause issues or not.

Good luck with your E!