Hi,
completeness is a descriptor (of crystal characteristics and
experimental setup) and not necessarily a quality indicator. If you
have a crystal that diffracts anisotropically, computing a spherical
completeness value makes no sense: you can't pretend that one could
have observed all those reflections within a sphere ... that would
just be wishful thinking.
Think about a crystal diffracting isotropically to say 3A and you
collected data with an over-ambitious crystal-detector distance. Just
because the detector surface could have caught reflections to 1A
resolution doesn't mean that we are computing a completeness value of
our significant data to 1A. We are rather defining a cut-off surface
(here: sphere to 3A) that tells us what reflections we realistically
could have observed because they are assumed significant. Completeness
is then the fraction of reflections we actually did observe
(i.e. completeness = observed / observable).
If we had a crystal diffracting to 1A and our crystal-detector
distance was too large (catching only 3A diffraction), we would never
compute our completeness to the theoretical 1A diffraction limit of
the crystal (which would give us abysmal completeness).
A sphere is a good cut-off surface when dealing with isotropically
diffracting crystals. If your crystal diffracts anisotropically you
should use an anisotropic cut-off surface - but the computation of
completeness is the same: observed / observable (both within that
anisotropic cut-off surface).
I don't see how there could be any "policy" regarding "ranges of
spherical vs ellipsoidal completeness (that) are typically acceptable
for deposition". An anisotropically diffracting crystal with 90%
ellipsoidal completeness (and 60% spherical completeness) can be
deposited in the same way as a virus structure with 60% spherical
completeness ... right? If you observed 90% of the observable
reflections it should not matter what shape the cut-off surface has.
Cheers
Clemens
PS: of course the best is to deposit a multi-datablock reflection data
(as produced e.g. by autoPROC+STARANISO) that contains the data at
various stages, i.e. with/withut cutoff and right down to the
initial scaled+unmerged reflection data.
PPS: we tried to design an interactive jiffy about those topics at
https://www.globalphasing.com/buster/wiki/plugin/attachments/DepositionMmCifFaq/gphl-diffreso-app.html
which might help.
On Fri, Jul 03, 2026 at 09:22:36AM +0100, srikannathasan velupillai wrote:
> Hi All,
>
> In addition, I have a related question regarding data processing. I have
> similar datasets (3.6A) and would like to know what is generally considered
> acceptable for completeness when using anisotropic data processing
> (Staraniso). In particular, what ranges of spherical vs ellipsoidal
> completeness are typically acceptable for deposition? The other statistics
> (Rfree Rfactor, CC1/2, RMSD for bonds and angles) look good.
>
> I would appreciate any guidance or experience you can share, especially for
> structures around this resolution.
>
> Many thanks in advance.
>
> Kannan
>
> On Fri, 3 Jul 2026 at 08:53, Italo Carugo Oliviero <
> [email protected]> wrote:
>
> > Dear Martin,
> >
> > in my opinion, it would be preferable not to deposit the coordinates of
> > atoms with (extremely) high B-factors (or "invisible" atoms) in PDB files.
> > Many users of the database, including statisticians and biologists, may not
> > be familiar with the concept of B-factor. When visualizing the structure
> > with tools like ChimeraX or PyMOL, or whenorming statistical surveys, they
> > might mistakenly interpret the position of these atoms as experimentally
> > determined.
> >
> > Unfortunately, I have noticed that even some crystallographers do not
> > fully understand the role of B-factors, which could lead to misleading
> > interpretations of the data.
> >
> > Best regards,
> >
> > Oliviero Carugo
> >
> >
> >
> > PS I published, years ago, something on this topic. You will find it, if
> > you need it.
> >
> > Il giorno ven 3 lug 2026 alle ore 09:31 Alexandre Ourjoumtsev <
> > [email protected]> ha scritto:
> >
> >> Dear all,
> >>
> >> B-factors, as well as occupancy values, are "physical" characteristics of
> >> a structure.
> >> Defining non-identified atoms with zero occupancy or with huge B-values
> >> (up to 10^4, as for some cryoEM models available in EMDB) has no physical
> >> meaning, as discussed multiple times in CCP4. Moreover (while this is not
> >> fully true), in overall, values of these parameters, similarly to atomic
> >> positions, are expected to be independent of a particular experiment.
> >>
> >> On the other hand, atoms missed in a given model are a feature of a
> >> particular map and not of the structure, this depends on how well this part
> >> of the model can be distinguished, recognized in this map (let's put aside
> >> not-realistic situations when one simply did not build a model within a
> >> clear density).
> >>
> >> Recently, we have proposed to complete a model description by one more
> >> parameter, a "local resolution", which is not a characteristic of the
> >> "physically existing, universal structure" but of the "map from which the
> >> deposited model was obtained". At my knowledge, this parameter has been
> >> formally accepted by Phenix and can be used right now.
> >> This parameter allows one:
> >> 1) to reproduce an (experimental) variable-resolution map from an atomic
> >> model
> >> 2) for a given atom, to characterize the confidence of its parameters
> >> (coordinates, occupancy and ADP) obtained from a particular map
> >>
> >> Some large value (100 A?) of this parameter seems to be a better
> >> description of the situation that Martin reminds, and which, unfortunately,
> >> is frequent enough. Unless, when one, in purpose, wishes to characterize a
> >> highly mobile residues by large B.
> >>
> >> I understand that this would change the traditions (actually, not well
> >> established, as Mark and Robert confirm) but it seems to be more
> >> appropriate using this parameter and neither huge ADP nor zero occupancy to
> >> characterize the model parts poorly distinguished (totally missed) in the
> >> map.
> >>
> >> With best regards,
> >>
> >> Sacha Urzhumtsev
> >>
> >>
> >> ----- Le 2 Juil 26, à 17:13, Mark J. van Raaij <
> >> [email protected]> a écrit :
> >>
> >> have a look in the ccp4bb archives, this has been discussed multiple
> >> times without a clear conclusion
> >> my approach would be to keep them and let the B-factors refine to high
> >> values, the reason is that you know the side-chains are there and with full
> >> occupancy
> >> (the validation statistics may be worse but that is normal for low-res
> >> structures)
> >>
> >>
> >> Mark van Raaij
> >> Dpto de Estructura de Macromoleculas, lab B5B
> >> Centro Nacional de Biotecnologia - CSIC
> >> calle Darwin 3
> >> E-28049 Madrid, Spain
> >> tel. +34 91 585 4616 (internal 432092)
> >>
> >>
> >>
> >> On 2 Jul 2026, at 16:47, Martin Hu <
> >> [email protected]> wrote:
> >>
> >> Dear all,
> >>
> >> I would like to ask for some advice on the best way to handle poorly
> >> defined side chains for deposition of a low-resolution (~3.6 Å) X-ray
> >> structure.
> >>
> >> For a number of residues in my structure, there is little or no
> >> side-chain density, so I do not feel confident modelling the full side
> >> chains. At the moment, I have deleted the residues that are not supported
> >> by the electron density, which also gives better geometry and refinement
> >> statistics.
> >>
> >> I asked the PDBe deposition team whether they had any preference between
> >> deleting the unsupported side-chain atoms or keeping them with zero
> >> occupancy. They replied that they do not have any specific requirements, as
> >> long as the deposited model is appropriate.
> >>
> >> I was therefore wondering how people here would normally deal with this
> >> situation for PDB deposition. Would you generally:
> >>
> >> * delete the unsupported side-chain atoms,
> >> * keep the full side chains but set the unsupported atoms to zero
> >> occupancy,
> >> * or use another approach?
> >>
> >> I’d be interested to hear what people usually do for structures around
> >> this resolution.
> >>
> >> Many thanks in advance.
> >>
> >> Best regards,
> >>
> >> Martin Hu
> >>
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