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Pronterface + Makerbot issues

Ok here is the thing .

Im trying to get my makerbot thing-0-matic mk6 work with the pronterface printing software .

I found out that pronterface communicates in raw gcode something replicatorg doesn't do .

So I assumed that different firmware will be needed .

And found out that teacup or scribblej firmware would work with the tom .

Though I have some questions .

Why there is only firmware for the motherboard while in the replicatorg there is firmware not only for the motherboard but also 

for the extruder controller ?

Why when I tried to upload the same firmware to the extruder controller I couldn't do it ?(meaning it didnt write to the chip and stucked on the process)

Is there actually a firmware for the extruder controller and if not how the whole thing will work together ?

Also when I only uploaded the firmware to the motherboard and tried to connect to the pronterface ,I got an error on

the command line saying couldn't connect to port 7(motherboards usb driver )though I have installed ftdi drivers succesfully ...

What is going on here ,can someone help to figure out everything and get it working ?

Thanks anyway for your time .

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One by one here are the answers:

Q: "Why there is only firmware for the motherboard while in the replicatorg there is firmware not only for the motherboard but also 

for the extruder controller ?" 

A: because the Makebot dudes created their hardware based on the original reprap hardware where the extruder board has it own MCU and it runs it own firmware. This has been long obsoleted by the comunity, the current electronics are all in one.

Q: "Why when I tried to upload the same firmware to the extruder controller I couldn't do it ?(meaning it didnt write to the chip and stucked on the process)" 

A: It's a different chip and you do not need to change the firmware on it except updating it with what ever the Makerbot guys update. The firmware on the mother board you can change, do not mess with the extruder.

Q: "Is there actually a firmware for the extruder controller and if not how the whole thing will work together ?"

A: there is the makerbot one use that on the extruder. The extruder is controlled by the motherboard trough RS485 I think (did not dig into the specs so anyone knowing better correct me on this)

Q: "Also when I only uploaded the firmware to the motherboard and tried to connect to the pronterface ,I got an error on ..."

A: most likely you uploaded a firmware which is not compiled for the chip on the motherboard, they made many versions you need the correct one 

I would recommend you to stick to the stuff makerbot provides until you are totally clear with how all this works, and since you paid a "shitload" (sorry for the term) of money for something that should work out of the box, you should make use of their support site. I would think their own ReplicatorG should have anything needed to support their own machines and thing-o-matic is supported.

What's the arduino you have the mother board running on?

I'm afraid changing to another firmware and host will require modifications to the firmware to adadpt it to the electronics of the makerbot.