There might be a simpler way. Please remember, I basically followed what I think Mike did with the 6131 2K and 1K, and other than that, I'm clueless about Atlas.
How about we take this path initially.
1. Go to KM or RM and using at least two upgrades, perhaps TV and one other such as the receiver or DVD, make sure you select the correct remote and select extended. If you use RM, before all this put the RDF file where your other RDFs are. Review the files and save them.
2. Open the .IR file (has "blank" in name or something similar) from the zip file. Bring in the upgrades and protocols (if needed) into IR.
Please add few notes.
3. If you're up to it, make several keymoves in IR and try to make a special protocol or two (DSM, LKP), use any old buttons, even if they don't make sense at the time. this is just to check you can build at all.
4. Zip it all up, the IR file and the upgrades from KM/RM, and we'll take it from there.
Please, do NOT use extinstall to merge old IR file with new. Just start from scratch. It's simpler, based on my work with the 6131.
I'll pm you, and yes, it you really want me to play with it, please do put in the 2K eeprom (I find even opening a remote challenging
), but I think the initial work above would be a better way to start and if you run into building problems, well... maybe Mike will help if I get lost.
