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Artoria2e5 (talk | contribs) →In cryo-EM: Fo-Fc, more likely than you think |
Artoria2e5 (talk | contribs) →In cryo-EM: Eh, good enough. Now we are hearing from PHENIX and CCP/RELION/REFMAC, two of the big players on this sort of software. |
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Geometry-based validation tools similar to those used in X-ray crystallography can be used to highlight implausible modeling choices and guide modeler toward more native-like structures. The CaBLAM method, which only uses Cα atoms,<ref>{{cite web |title=CaBLAM Validation in Phenix |url=https://phenix-online.org/documentation/reference/cablam_validation.html |website=phenix-online.org}}</ref> is suitable for low-resolution structures from cyro-EM.<ref>{{cite journal |last1=Rohou |first1=Alexis |title=Improving cryo-EM structure validation |journal=Nature Methods |date=February 2021 |volume=18 |issue=2 |pages=130–131 |doi=10.1038/s41592-021-01062-1}}</ref>
A way to compute the [[difference density map]] has been formulated for cyro-EM.<ref>{{cite journal |last1=Yamashita |first1=Keitaro |last2=Palmer |first2=Colin M. |last3=Burnley |first3=Tom |last4=Murshudov |first4=Garib N. |title=Cryo-EM single-particle structure refinement and map calculation using Servalcat |journal=Acta Crystallographica Section D Structural Biology |date=1 October 2021 |volume=77 |issue=10 |pages=1282–1291 |doi=10.1107/S2059798321009475 |doi-access=free |quote=}}</ref><ref name="Winn"/> Cross-validation using a "free" map, comparable to the use of a free [[R-factor]], is also available.<ref>{{cite journal |last1=Falkner |first1=B |last2=Schröder |first2=GF |title=Cross-validation in cryo-EM-based structural modeling. |journal=Proceedings of the National Academy of Sciences of the United States of America |date=28 May 2013 |volume=110 |issue=22 |pages=8930-5 |doi=10.1073/pnas.1119041110 |pmid=23674685}}</ref><ref>{{cite journal |last1=Beckers |first1=Maximilian |last2=Mann |first2=Daniel |last3=Sachse |first3=Carsten |title=Structural interpretation of cryo-EM image reconstructions |journal=Progress in Biophysics and Molecular Biology |date=March 2021 |volume=160 |pages=26–36 |doi=10.1016/j.pbiomolbio.2020.07.004 |doi-access=free}}</ref> Other methods for checking model-map fit include correlation coefficients, model-map FSC,<ref>{{cite web |title=Cryo-EM Validation tools in Phenix |url=https://phenix-online.org/documentation/reference/validation_cryo_em.html |website=phenix-online.org |language=en}}</ref> confidence maps, CryoEF (orientation bias check), and TEMPy SMOC.<ref name="Winn">{{cite web |last1=Winn |first1=Martyn |title=Cryo-EM validation tools in CCP-EM |url=https://www.ccpem.ac.uk/training/validation_symposium_2020/Winn_validation_in_CCP-EM_201120.pdf |publisher=www.ccpem.ac.uk/ |access-date=22 November 2023 |date=20 November 2020}}</ref>
== In SAXS ==
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