Dear Pavel,
Your comment has been made many times, especially in discussions
that eventually led to the official decision to make room for these
coefficients in the mmCIF dictionary. The idea behind granting them an
independent status and recommending that they should accompany the
deposition of a model is that they provide a means of recomputing
precisely the map that the investigators had in front of them as
supporting evidence at the time when they proposed an interpretation
of that map in terms of their final model.
The argument that "maps are derived information that can be
trivially computed using source data" misses that point: if that
trivial recomputation is done with software versions significantly
more recent than those originally used, questions about controversial
interpretations of certain features of the original map can no longer
be asked. In other words the notion of "derived information" is not
time-invariant. These coefficients therefore owe their potentially
usefulness to the fact that they capture something one could describe
as "a backup of the evidence available at the time".
Doesn't this make sense?
With best wishes,
Gerard.
--
On Tue, Jan 14, 2025 at 12:52:14PM -0800, Pavel Afonine wrote:
> Hi all,
> maps are derived information that can be trivially computed using source
> data, like reflection data and the atomic model, so there isn’t much point
> in keeping them around and maintaining an accession service (which costs
> something). If that disappeared, I’d totally understand the reasons!
> You can get these maps in seconds, for example, using:
> phenix.maps model.cif data.cif
> or the usual mtz and pdb files.
> I'm sure other software packages should be able to do the same.
> Pavel
>
> On Tue, Jan 14, 2025 at 6:39 AM Yong Tang <liutan...@gmail.com> wrote:
>
> > Dear all,
> >
> >
> > Taking a random PDB entry 8hbk as an example, at one point of time, we
> > have access to a phase file called 8hbk_phases.mtz under the download
> > section in https://www.rcsb.org/structure/8hbk However that option
> > doesn't seem to be available anymore in general.
> >
> >
> > I do understand PDBe offers electron density maps (8hbk.ccp4 and
> > 8hbk_diff.ccp4 separately)- is that our go-to nowadays when we would like
> > to inspect the maps of any particular PDB entry
> > https://www.ebi.ac.uk/pdbe/entry/pdb/8hbk
> >
> >
> > Please help – maybe I have missed something obvious?
> >
> >
> > Thank you! -yong
> >
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