There are two ways to tell the virtual train engineer to pass a red signal
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Tell the engineer: If a train is stopped at a signal, the engineer may call you to “remind” you that he is stuck at a red signal. One of the options for you to respond is to tell him to pass the red signal. You can also take the initiative and call the engineer at any time and tell him to pass the next signal on RED. In any case this order is valid only for the signal ahead of the train.
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Set a Signal indicator: If the signal is visible you can move the mouse pointer over the signal, hit the right mouse button, and select the red signal option in the popup menu. The signal will flash in yellow for about two minutes. Of course, the train must be close enough to the signal for the train engineer to see before the flashing stops. If there is more than one train in a block, this signal is valid only for the first train, not for any train that follows right behind. (Note: signal option is not available, if the signal is not displayed)
The system does not do any checks whether the switches are aligned properly or if there are any conflicting movements. Besides of the flashing yellow of the signal symbol, there is nothing else on the display indicating you’ve given the order to pass a red signal. The train engineer will move the train with caution, prepared to stop if the track ahead is occupied by another train, but may run afoul of switches if they are not properly aligned. The track element’s color is changed to red as usual, when the track circuits detect a presence of a train.
If the global option is set to Stop-and-Proceed for invisible or automatic signals, the train may pass such a red signal without needing an order from you to do so. Like above, the engineer will move the train with caution, however, as Stop-and-Proceed is never enabled if there are switches, diamonds and drawbridges on the way, conflicting train movements can occur only on the track ahead.