Hi Daniel,
Finally taking time to answer this message (I saved it when it came up; I know we discussed this a few times since then, but I figured I should also post this publicly).
1) I prefer refining against the least "massaged" map, so the one fresh out of the 3D refinement I consider "final". This simplifies many decisions down the line, as you will see in my answers to your other points.
I also use sharpened or otherwise post-processed maps, but only during manual model building/refinement. My favorite tools these days are ISOLDE for manual model building/refinement and deepEMhancer for map post-processing (very easy to use, and almost no parameters to tweak, so less user bias). I use the "final" map to guide MDFF (= pull on the atoms) in ISOLDE, and the deepEMhanced map on top of it, but only used as a visual guide (it doesn’t guide MDFF). Many times, I found that locations with poor or no side-chain density are more easily interpretable in the deepEMhanced map, and that the side-chain conformation suggested by this map ends up nicely stable in the combined pull of the "final" map and the MD force field (without the hint from the deepEMhanced map, it is sometimes a big headache to find such a stable conformation). When I think I can’t improve the model any further in ISOLDE, I use the parameter file it generates for phenix.real_space_refine (this parameter file essentially turns off most things except B-factor refinement) and run a refinement, and the output model is the one I deposit.
2) I always deposit the "final" map (the one fresh out of my final 3D refinement, see 1) as "main map" in the deposition system. I believe this is the most honest thing to do, because it is whatever I saw in this map that convinced me to deposit it and write a paper about it. So, this is the map I want people to see when they simply run "open emdb:xyz" in ChimeraX, even if it’s not the prettiest map and not necessarily the one I use to make figures. I also deposit the deepEMhanced map as "additional map", because I used it to guide model building, and because I most likely used it for the figures (I sometimes use both maps in figures; in any case, I always clearly indicate which map is shown in which figure).
3) I quote the global resolution from the "final" 3D refinement (see 1). It depends on the mask used, so of course I also deposit this mask along with the mandatory half-maps. Unless the particle under study is very rigid and stable, a single global resolution number is pretty much meaningless (in most cases, the location in the reconstruction where the interesting things are has much worse resolution than the global number suggests), so I choose to spend the least amount of time possible coming up with this number. What matters to me is only that people can use the deposited half-maps and mask to recalculate this number, and find something in the same ballpark as I reported.
4) I deposit the FSC curve I obtain from the two half-maps from the "final" 3D refinement (see 1). Same as for the global resolution number: I simply want people to know where this comes from and be able to recalculate it from the deposited data.
5) I deposit the half-maps from the "final" 3D refinement (see 1). I make sure to deposit the mask used in refinement and the mask used to calculate the masked FSC curve (sometimes they differ, for instance cryoSPARC comes up with a tighter mask to give a more optimistic global resolution number because it looks nicer in a title or abstract).
So, you could sum up my approach like this, independently of the programs used: "deposit as main map the least massaged map that convinced me something interesting is here to see; deposit the corresponding half-maps, masks and FSC curve so they agree with this map; deposit as additional map any other map that was helpful along the way; clearly explain in the paper which map was used for what".
I try to go for the simplest possible process from "final" map to deposited files and figures, because I think it is more transparent this way, and I want readers of my papers to see the same evidence that convinced me in the first place to write a paper about it.
I admit this is very opinionated, and mostly originates from my own experience of what was helpful in my hands, but hopefully this is helpful to others as well. :-)
Happy to learn from other opinionated people if their approach differs.
Cheers,
Guillaume
On 2 Dec 2022, at 14:22, Daniel Larsson