Hi Kannan,
I always use CC1/2 > 0.5 and I/sigma > 1. The R numbers should sit somewhere
close to your resolution. Personally, I always aim for > 90% completeness,
ideally 100%. Sidechain and Ramachandran outliers depend on your protein size,
but I would say < 5% is acceptable. But all of these are personal preferences
based on what people generally. The most important question is if your model
supports or not your hypothesis.
Best wishes
______________________________________________________
Rafael Marques da Silva
PhD Student – Structural Biology
University of Leicester
Mestre em Física Biomolecular
Universidade de São Paulo
Bacharel em Ciências Biológicas
Universidade Federal de São Carlos
phone: +44 07861 273773
"A sorte acompanha uma mente bem treinada"
________________________________________________
________________________________
De: CCP4 bulletin board <[email protected]> em nome de srikannathasan
velupillai <[email protected]>
Enviado: sexta-feira, 3 de julho de 2026 09:22
Para: [email protected] <[email protected]>
Assunto: Re: [ccp4bb] Side-chain deletion or zero occupancy for PDB deposition
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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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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