Ideally you wouldn't throw away any data above the noise limit just to satisfy arbitrary criteria right? But in practice some refinement programs don't deal with this data all that well and I'm told that for Staraniso, BUSTER is best.
I also vaguely remember being told that the programs substitute Fcalc for missing Fobs when calculating maps, if phenix or refmac applies a spherical limit when doing this then could this lead to spurious map quality/Bias? Perhaps its best to talk to the STARANISO team, but I would have thought that if you both very low spherical completeness AND low elliptical completeness that would indicate that the shape of the ellipse has not been estimated well with ramifications for the accuracy of the anisotropic scaling/correction performed by STARANISO? Best wishes Matthew. ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Wladek Minor <[email protected]> Sent: 06 July 2026 10:13 To: [email protected] <[email protected]> Subject: Re: [ccp4bb] [SPAM] Re: [ccp4bb] Side-chain deletion or zero occupancy for PDB deposition Clemens, You are absolutely right. However common sense is not as common as people believe (Volataire) Wladek On 7/6/2026 1: 49 AM, Clemens Vonrhein wrote: Hi, completeness is a descriptor (of crystal characteristics and experimental setup) and Clemens, You are absolutely right. However common sense is not as common as people believe (Volataire) Wladek On 7/6/2026 1:49 AM, Clemens Vonrhein wrote: 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 [globalphasing.com]<https://urldefense.com/v3/__https://www.globalphasing.com/buster/wiki/plugin/attachments/DepositionMmCifFaq/gphl-diffreso-app.html__;!!PDiH4ENfjr2_Jw!Fx1TwSDTg6N5DIQRvuNOWekPo-dk_IyIRTA_oIcxpYLesOJGT9mrWykvr3B1eo2BLRUW_kay4BmjOQ7l6qXjFYrrmUdyW1CFZBugNpoN8ghmlw$> 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]<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. 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