@adtaheri There is an argument for forcing convering in Relion (I can’t remember exactly, should be in the expert section if you run
relion_refine with no arguments). Usually this is used to run a final iteration on CPUs when the GPU doesn’t have enough memory for the converging iteration.
@apunjani and @olibclarke are correct that you should also be able to use the half-maps directly via the command line. The GUI and some command-line options in Relion do only accept a seed name that’s used to automatically find files with different endings, and some other operations like polishing etc. now require optimiser files, so sometimes it’s useful to create something that looks like a Relion job structure.