Hi Simon,
I tried phoenix.model_map and it successfully generates ccp4 and xplor files.
note, this generates a model-calculated exact map (infinite resolution). I'm not sure this is what you want, thinking of practical applications. You can always FT this map to get an image of it at particular resolution, but this is a separate step. Just making sure you are aware of all of this.
However, I fail to understand the xplor file format for further analysis. Is there any suggested documentation on xplor (ccp4) format?
While X-plor is old format (yet much easier to understand and deal with at low-level than ccp4), ccp4 is pretty much the standard these days with most software being able to deal with it. So I'd say some web search should get you up to speed!
Visualization on pymol also suggests that my electron density was truncated by the box boundary. Is there any way to first centralize the box at the core of the protein, then create a box with a defined (sub)region of the PDB?
Perhaps you want to calculate the map in the entire unit cell and then choose how to crop it for your convenience. Does this answer your questions? Do you still have more? Please feel free to let us know and we will follow up! Pavel