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The most useful approach in many cases is to start with coordinates representing the desired final deflected shape of the structure. After running the staged-construction analysis, use the command Analyze > Modify Undeformed Geometry to change the joint coordinates so that the deflected shape at the end of the staged construction case matches the originally specified geometry. Iterate a few times until the coordinates converge to the desired shape.
This approach automatically gives you the desired location of joint at the time it is added to the structure, and the deflected shape is meaningful. It also has the benefit of calculating camber for you.
The Concept of "Ghost Structure"
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Both options are discussed in the CSI Analysis Reference Manual, chapter "Nonlinear Static Analysis".
Manually Modifying Joint Coordinates
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Start with a model having preliminary joint coordinates, and run the first stage of construction. Modify the coordinates of the joints that will be added in the second stage so that they have the correct location with respect to the deflected shape of the first stage. Re-run the analysis for two stages, locate the joints for the third stage, and continue this process recursively until all joints in the model have been located.