I have a drawing with a custom coordinate system attached. When I mapimport a shapefile with a different coordinate system it does not transform it to the correct place. The custom coordinate system is a modified state plane with a truncation. Where do I even start to try and figure this out?
The "modified state plane" sort of system isn't actually treated like a "coordinate system". The only way to setup that sort of thing is via the Transformation Tab in Civil 3D. And unfortunately, Map and Civil 3D are actually incompatible software, even though they both reside inside the same executable, and none of the Map commands will honor the Transformation Tab settings.
In order to get your shapefile into your project coordinates, you have to manually scale the linework by the inverse of your scale factor, then move the linework by your "truncation" amount to get it to match your Project.
There is another option, which involves creating an actual Custom Coordinate System that "mimics" your "modified state plane" system. It won't give you exactly the same results, and the difference between the two will increase with distance from your central base point, but the results could very well be within acceptable error limits.
The tricky part about that last option is figuring out the parameters to get the right results. The easiest way to do that would probably be to start with your State Plane coordinate system definition. For Colorado, this would be a Lambert Conformal Conic projection, so you would need to start by playing with the Northern and Southern standard parallels. I suspect you should get good results if you center the parallels on your project, with about 10' of arc difference between the two parallels. Then play with the False Northing and Easting until you get identical coordinates for a point in the middle of your project. Now check the values you get for points on the outer part of your project to see how much difference you have between your new Coordinate System and the "Modified State Plane" system, and if it's within acceptable error limits, you're good to go. You can now configure your drawings to use your newly-defined Coordinate System, instead of using the Transformation Tab, and all the Map tools will work. At least, that's the theory... I've never actually done this.
Actually, on second thought, you'll probably need to switch to a Lambert single-parallel projection, so you can key in a "scale reduction" factor. A good starting point is probably the inverse of the CSF from your "Modified State Plane" system.
You'll probably want to keep the same origin as the State Plane grid, to try and keep the bearings the same.
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