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How can I automatically break contour lines when they cross a fault, but keep the faults a single polyline?
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You can do this in Didger by creating line intersections and then reconnecting the fault polylines:

1. Digitize the fault and all the contours as whole polylines, using a unique Primary ID for each fault polyline such as "fault1", "fault 2", etc.

2. Use the Tools | Create Line Intersections command in Didger. That will break the polylines at every junction. 

3. Now to join the fault polylines back together, the first thing would be select all the polyline segments for one fault using Edit | Criteria Select and selecting all objects with a Primary ID = fault1

4.Connect all the selected polyline segments by using the Tools | Connect Polylines command.

5. Repeat steps 3-4 for each fault you have.

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