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 > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
