Interesting...
Has this got onto the radar (or critical path) of the PDB's mmCIF
working group (or whatever it's called?)
I'm assuming that's where this would go to next, if the downstream
developers are ever going to take it seriously.
Frank
On 04/03/2025 12:21, Alexandre Ourjoumtsev wrote:
Dear all,
Fully relevant to this discussion, you might noted that a couple of
years ago, we (Vladimir Lunin and myself) argued
https://journals.iucr.org/m/issues/2022/06/00/tf5001/
that, when describing an atomic model, each atom should have one more
parameter, namely a local resolution with which it contributes to the
map from which it has been identified - or, in other words, with which
value its image should be calculated to reproduce the experimental map
(and NOT the density / potential itself) as a sum of atomic
contributions (different atoms may have different local resolution).
Indicating the local resolution large (and neither B-factors
large nor occupancy small) means exactly that one cannot localize it
in this given map; again in other words, that the map from which this
part of the model was constructed had not enough information.
Naturally, cif-format has no obstacle to complete the model
description by the local resolution value associated to each
individual atom. Moreover, even the old good PDB format has a space
for this; positions 67-72 have been reserved :-)
Going behind the current discussion, as you perfectly know, both
B-factors and resolution cut-off blur atomic images; however they do
it in a different way (Ezra already mentioned Fourier ripples).
Considering this new parameter allows one distingushing these two
effects and even to identify (fix?) some errors occured when using the
current, conventional procedures : see, for example, Lunin et al. in
Current Research in Structural Biology (2023) :
https://doi.org/10.1016/j.crstbi.2023.100102
<https://doi.org/10.1016/j.crstbi.2023.100102>
There is a couple more of relevant articles, in Acta D and
J.Appl.Cryst, and there are works in progress.
I hope, this helps...
Have a nice day
Sacha Urzhumtsev
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