If you want to make your crappy EM map look better( with look being the operative word, as the quality of the map is unchanged) when using e.g. coot, you might want to consider increasing the grid spacing, that is the number of sampling divisions along any of the axis. It is basically the same process you use in PyMol when generating figures with a very fine mesh density, there it is just called map double .
And this how it looked after I doubled the grid points from 360 to 720 on all three axis (1.4 gb map).
Programs like USF’s mapman and others are able to do this fast and without any problems, but if you want/need a GUI I would use FFT from the CCP4 suite. When I say GUI it is more of an ugly advanced text editor to be honest, but it works.
Load in your mtz file, under “Infrequently Used Options” fill in the desired grid number for x,y and z (e.g. 2x the current values), choose a name for the output map and hit run.
It should be noted that the map will increase 8 fold in memory if you double the grid spacing. but it is often worth it (as the above example shows).