[phenixbb] map deposition strategy after density modification

[Pavel Afonine]

Hi Daniel,

> 1) Which map should I refine against (most importantly, do the final minimization using phenix.real_space_refine)? The DM map is the most clear one, so I’m favoring to do it against this one (as long as the geometry/validation is also best for this one).

I think one should refine the model against the original least 
"massaged" map. However, I'm aware of strong arguments for and against 
this. So may be this is an opportunity to re-discuss this topic again, 
if there is interest! Think of B factor refinement using original vs 
sharpened maps, just to prime the conversation!

> 2) Which map should I deposit as my main map? Is it the autosharpened one or the DM one? Since the DM map looks the best, I want the user who only downloads one map to see this one, so again I favoring this map.

I fully agree with Tom's answer on this topi.

> 3) Which nominal resolution should I quote for my reconstruction? Since the procedure seems to introduce correlation between the two maps (see point 4 below), it does not seem to be possible to obtain a gold-standard FSC value between two truly independent half-maps. As the DM procedure supposedly actually improves the map (by leveraging knowledge about what solvent and macromolecular maps usually looks like and thereby improves the Fourier coefficients), it feels like it would be misrepresenting the data by quoting the FSC_0.143 from the original reconstruction. Should I use the FSC_0.5 estimated value that phenix.resolve_cryo_em outputs?

Given the lack of strict and clear requirements, I believe it does not 
matter as long as you clearly specify what method and maps you used to 
calculate it, and also as long as you deposit all relevant maps so that 
others can re-evaluate your analyses if needed. There are multiple ways 
to estimate the resolution, each one having its pros and cons, and 
so-called "gold standard" is just a name for one of them (see more here: 
https://doi.org/10.1107/S2059798318009324).

> 4) Which FSC curve should I deposit? When I calculate the FSC between the two density modified half-maps, I get a funny (or rather not so funny) looking curve with a bump at around 3Å and it does not go to zero at Nyquist (which does not agree with the map quality). This must again be due to the induced correlation between the maps, presumably during the masking of solvent and macromolecule density. Phenix.resolve_cryo_em calculates a FSC curve to calculate the FSC_0.5 value, which according to the manual page corrects for the correlation induced between the two maps:
>
> "Density modification introduces some correlations between half-maps due to solvent flattening. This can have a small effect on the resolution estimates obtained with half-map FSC. The resolution estimates provided by the program are corrected for this effect."
>
> But is this curve good enough? I think OneDeposit wants to have the gold-standard FSC curve, right?

Similarly to previous point, I believe it does not matter. Why? It is 
because FSC curve is hardly reproducible anyway (exactly or even within 
some tolerance) across different software. Reasons for this are: 
resolution binning schemes are different across programs or can be 
different even within the program due to numeric uncertainties, formula 
to compute CC (there are two at least and do we know which one is used 
in software you use?), and maps used.

> 5) Which (nowadays mandatory) half-maps should one deposit? Here I would say that the original half-maps before DM makes more sense, since these are less processed. But if one specify these as the half-maps, there will be inconsistencies during validation, since the DM map will look quite different from the average between the two original half-maps. Also the automatic FSC curve will be very different from the deposited one.

I fully agree with Tom on what to deposit and why! And see above re 
differences in values deposited vs recomputed.

Pavel