Basic Setup
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If you are a first time user, you will find there are lots of features in NaP3 that are explained in this Help file. You can choose among these once you have the program running with the core settings.

When you run NaP3 for the first time - not an update - the windows below will appear on your desktop for a minute or so while a 'wisdom' generation routine is run.

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The 'wisdom' routine is storing some frequently-used math routine results which are used as a reference to make the program run faster. The windows will never appear again unless you delete 'wisdom', which is stored in a hidden User file whose location depends upon your OS.
For Windows 7 this is "C:\Users\your_user_name\AppData\Roaming\NaP3". This location is also used to store a database with your settings.

With the CAT connected via the appropriate hardware and leads, and NaP3 opened but not yet RUNning, go to Configure and a tabbed Setup dialog will appear, partly shown below. In the Rig tab select your Rig Type, in the Rig Serial Connection group choose the COM Port connected to the rig, and in Baud the connection speed. For most rigs the other entries will now auto-fill but you may come back to fine tune some later.
 
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Now click on RUN in the NaP3 menu and, if you have a rig connected and decent signals at your card input, some form of display may appear, but the exact display does not matter at this point. Your rig should now tune the NaP3 VFOs, confirming that the CAT connection is working..
You can now STOP NaP3 and continue in the Menu/Configure/Input sections of this Help file according to your input device. For some rigs you may also need to enter some settings in the Menu/Configure/Rig section.