1. Assume that you have loaded the base mesh and added some targets. Press the Apply targets button to get a clean mesh. You may need to reload maketarget and/or press the Initialize button first.

2. All shapekeys are applied to the mesh. The mesh is no longer recognized by maketarget. Import base.obj again.

3. With the base mesh active and the morphed mesh selected, press the Load target from mesh button.

4. The morped mesh disappears, but the morph is loaded into the base mesh as a shapekey. Now it should be possible to save the target by pressing Save target as. The target file is saved with the extension .target, irrespective of the extension specified in the file selector.

5. The newly created target can be loaded into maketarget. If you put it in the makehuman/custom folder in your home directory (typically ~/makehuman/custom on Linux and My documents/makehuman/custom on Windows), it should appear under the Modelling > Custom tab.
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