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For model signals with separate Red/Yellow/Green diodes, the situation is simple: Connect each one to a separate output with the proper polarity, have PanelPro drive those three outputs, and it will Just Work. The "Triple Output" type of Signal handles this type of wiring.
For model signals with just Red and Green diodes, there are two ways of wiring them:
In both cases you wire these to two C/MRI outputs. There are a couple of extra resistors, and perhaps an external power supply involved, so that when one of the C/MRI outputs is activated, power is applied to one diode and it lights, and when the other is activated the other diode gets power. That makes Red and Green. The "Double Output" Signal type handles this.
To get Yellow, you have to power both LEDs. This is easy with wiring (1.) above; the program just activates both of the outputs, both LEDs make light, and the Red and Green combine to make Yellow.
With wiring 2., you can't simultaneously light both LEDs, since current can't flow in two directions at the same time. But "at the same time" is the key; just alternate the direction of the current Very Fast, too fast for the eye to see, and the colors will merge into Yellow. There are two ways to do this:
2.A) Use an external circuit. There's a signal driver board to do this what connects between the C/MRI outputs and the LED leads. When it detects that _both_ outputs are on, it rapidly alternates the voltage to the LEDs, making yellow. This circuit can be used with any C/MRI system type, and you don't have to tell PanelPro anything to make it work.
2.B) Use support built into the SMINI card. An SMINI card can be configured to do a similar thing. When the SMINI detects the two outputs are on, it alternates the voltage. To configure this, you have to go to the PanelPro Preferences, click on "Configure C/MRI nodes" (or select it from the CMRI menu), select an SMINI to configure, and click on one of the little check-boxes to configure a specific output as "two lead oscillating signal". Click "Edit Node" to update, then close that panel, click "Save" and restart the program. Once this is done, a "Double Turnout" signal type will also generate yellow signals on those outputs.
Back to the C/MRI Hardware Support Help page.