When starting out in the field of cryo-EM it is often the small annoying problems that you waste a lot of time on. These problems are often very difficult to Google as the experienced Cryo-em scientist often take the solutions to them for granted.
One such problem I found difficult in the beginning was how to generate an initial reference map from a PDB model. As always there are more than one way of solving this problem, but what I have found to be the best approach for people new in the field, is using Chimera for it. Chimera have implemented a EMAN program called pdb2mrc and called it molmap. By going through Chimera instead of generating the map via pdb2mrc in a linux terminal, you get to visualize the map and the pdb file, which I think is general easier for people new to cryo-EM. That being said I think pdb2.mrc is better as it has more options and it is the one I use now.