FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation

In recent years, advances in cryoEM have dramatically increased the resolution of reconstructions and, with it, the number of solved atomic models. It is widely accepted that the quality of cryoEM maps varies locally; therefore, the evaluation of the maps-derived structural models must be done locally as well. In this article, a method for the local analysis of the map-to-model fit is presented. The algorithm uses a comparison of two local resolution maps. The first is the local FSC (Fourier shell correlation) between the full map and the model, while the second is calculated between the half maps normally used in typical single particle analysis workflows. We call the quality measure “FSC-Q”, and it is a quantitative estimation of how much of the model is supported by the signal content of the map. Furthermore, we show that FSC-Q may be helpful to detect overfitting. It can be used to complement other methods, such as the Q-score method that estimates the resolvability of atomsWe thank Prof. David Veesler for providing us the half maps of the spike glycoprotein of SARS-CoV-2. The authors would like to acknowledge financial support from: the Comunidad de Madrid through grant CAM (S2017/BMD-3817), the Spanish National Research Council (PIE/COVID-19 number 202020E079), the Spanish Ministry of Economy and Competitiveness through grants SEV 2017-0712, PID2019-104757RB-I00/AEI/10.13039/501100011033, the Instituto de Salud Carlos III through grant PT17/0009/0010 (ISCIII-GEFI/ERDF-). Instruct-ULTRA (Grant 731005), an EU H2020 project to further develop the services of Instruct-ERIC. UE H2020 grant HighResCells (ERC-2018-SyG, Proposal: 810057). This work was supported by the Intramural Research Program of the National Institute for Arthritis, musculoskeletal, and Skin Diseases, NIH. The authors acknowledge the support and the use of resources of Instruct, a Landmark ESFRI projec

Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures

Using a new consensus-based image-processing approach together with principal component analysis, the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state have been analysed. These studies revealed concerted motions involving the receptor-binding domain (RBD), N-terminal domain, and subdomains 1 and 2 around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations. It is shown that in this data set there are not well defined, stable spike conformations, but virtually a continuum of states. An ensemble map was obtained with minimum bias, from which the extremes of the change along the direction of maximal variance were modeled by flexible fitting. The results provide a warning of the potential image-processing classification instability of these complicated data sets, which has a direct impact on the interpretability of the results.The authors would like to acknowledge financial support from CSIC (PIE/COVID-19 No. 202020E079), the Comunidad de Madrid through grant CAM (S2017/BMD-3817), the Spanish Ministry of Science and Innovation through projects SEV 2017-0712, FPU-2015/264 and PID2019-104757RB-I00/AEI/ FEDER, the Instituto de Salud Carlos III [PT17/0009/0010 (ISCIII-SGEFI/ERDF)], and the European Union and Horizon 2020 through grants INSTRUCT–ULTRA (INFRADEV-03-2016-2017, Proposal 731005), EOSC Life (INFRAEOSC-04-2018, Proposal 824087), HighResCells (ERC-2018-SyG, Proposal 810057), IMpaCT (WIDESPREAD- 03-2018, Proposal 857203), CORBEL (INFRADEV-1-2014-1, Proposal 654248) and EOSC–Synergy (EINFRA-EOSC-5, Proposal 857647). HDT and BF were supported by NIH grant GM125769 and JSM was supported by NIH grant R01-AI12752

Advances in Xmipp for cryo-electron microscopy: from Xmipp to Scipion

Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package

Integration of Cryo-EM Model Building Software in Scipion.

Advances in cryo-electron microscopy (cryoEM have made possible to obtain structures of large biological macromolecules at near-atomic resolution. This "resolution-revolution'' has encouraged the use and development of modeling tools able to produce high-quality atomic models from cryoEM density maps. Unfortunately, many practical problems appear when combining different packages in the same processing workflow, which make difficult the use of these tools by non-experts and, therefore, reduce their utility. We present here a major extension of the image processing framework Scipion that provides inter-package integration in the model building area and full tracking of the complete workflow, from image processing to structure validation.The Spanish Ministry of Economy and Competitiveness through Grants BIO2016-76400-R (AEI/FEDER, UE) and BFU2016-74868-P (AEI/FEDER, UE), the Comunidad Autónoma de Madrid through Grant: S2017/BMD-3817. D. Strelak holds a fellowship from la Caixa Foundation (ID 100010434) with code LCF/B/IN18/11660021. The authors acknowledge the support and the use of resources of Instruct-ERIC.Peer reviewe

Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion

Electron microscopy of macromolecular structures is an approach that is in increasing demand in the field of structural biology. The automation of image acquisition has greatly increased the potential throughput of electron microscopy. Here, the focus is on the possibilities in Scipion to implement flexible and robust image-processing workflows that allow the electron-microscope operator and the user to monitor the quality of image acquisition, assessing very simple acquisition measures or obtaining a first estimate of the initial volume, or the data resolution and heterogeneity, without any need for programming skills. These workflows can implement intelligent automatic decisions and they can warn the user of possible acquisition failures. These concepts are illustrated by analysis of the well known 2.2 angstrom resolution beta-galactosidase data set.Spanish Ministry of Economy and Competitiveness through the BIO2016-76400-R (AEI/FEDER, UE) grant, the Comunidad Auto ´noma de Madrid through grant S2017/BMD3817, the Instituto de Salud Carlos III (PT17/0009/0010), the European Union (EU) and Horizon 2020 through the CORBE