This protocol wraps e2initialmodel.py EMAN2 program.
It will take a set of class-averages/projections and build a set of 3-D models suitable for use as initial models in single particle reconstruction. The output set is theoretically sorted in order of quality (best one is numbered 1), though it’s best to look at the other answers as well.
See more details in: http://blake.bcm.edu/emanwiki/EMAN2/Programs/e2initialmodel
Run the EMAN program to create the initial model.