Hey guys, I think Kannan is specifically asking about Staraniso datasets, which might come with 20% or so completeness of the highest resolution shell, depending on the anisotropy of the data.
I usually check the refinement stats per resolution shell. Buster gives a plot of map-to-model cross-correlation versus resolution that you can use to base your decision. Actually the latest versions of Buster automatically cut the resolution based on that – and/or maybe other stats. R-Rfree vs resolution is also an indication. Essentially you are looking for the resolution where the data is still properly guiding the refinement. Very often I prefer to cut more conservatively, to get a very nice model for 2.5 angstroms, instead of a nominal 2.2 angstroms with bad PDB grades and noisy map. One alternative is to start with the staraniso dataset, do as much as you can, then switch to the isotropic dataset for refinement, using the first model as target. Of course, the quality of the map is still the best parameter, you can compare different refinement runs and decide. Upon deposition you might get warnings for some stats. They just ask you to confirm that you are aware of those, but this doesn't usually block deposition. You might get reviewer #3 pulling your ear, you'd better know how to defend yourself. Cheers --------------------------------------------------- Carlos KIKUTI, PhD Structural Motility Team UMR144 - CNRS - Institut Curie 12 rue Lhomond - 75005 Paris, France [email protected]<mailto:[email protected]> De : CCP4 bulletin board <[email protected]> au nom de Rafael Marques <[email protected]> Répondre à : Rafael Marques <[email protected]> Date : vendredi 3 juillet 2026 à 17:13 À : "[email protected]" <[email protected]> Objet : [SUSPECTED SPAM] Re: [ccp4bb] Side-chain deletion or zero occupancy for PDB deposition 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 ######################################################################## 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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://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 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/
