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 | > 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/
