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I often need to make maps that match the projection used on USGS topo maps and others. Many newer maps use UTM projections but older ones often use a conic projection such as Albers or Lambert. UTM and Pseudo Mercator projections work fine in Manifold 9 but I have not found a conic projection that works except for "polyconic." If I try to apply an Albers Conic or Lambert Conformal Conic nothing happens. All of these worked correctly in Manifold 8. Unfortunately, a UTM projection won't register with an Albers Conic topo map.
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Details? What projection, specifically, do you want to use? Can you post an example of the original, source data?
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It is possible that you are trying to apply a conic projection without setting the values of the latitude parameters -- some have center lat, others two standard lats, these should be set to the values you want, the default 0 is not going to work.
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