MOTIVATION: Cryo electron microscopy (EM) is currently one of the main tools to reveal the structural information of biological macromolecules. The re-construction of three-dimensional (3D) maps is typically carried out following an iterative process that requires an initial estimation of the 3D map to be refined in subsequent steps. Therefore, its determination is key in the quality of the final results, and there are cases in which it is still an open issue in single particle analysis (SPA). Small angle X-ray scattering (SAXS) is a well-known technique applied to structural biology. It is useful from small nanostructures up to macromolecular ensembles for its ability to obtain low resolution information of the biological sample measuring its X-ray scattering curve. These curves, together with further analysis, are able to yield information on the sizes, shapes and structures of the analyzed particles. RESULTS: In this paper, we show how the low resolution structural information revealed by SAXS is very useful for the validation of EM initial 3D models in SPA, helping the following refinement process to obtain more accurate 3D structures. For this purpose, we approximate the initial map by pseudo-atoms and predict the SAXS curve expected for this pseudo-atomic structure. The match between the predicted and experimental SAXS curves is considered as a good sign of the correctness of the EM initial map. AVAILABILITY AND IMPLEMENTATION: The algorithm is freely available as part of the Scipion 1.2 software at http://scipion.i2pc.es/.

This study describes an improved method for Poisson image denoising that is based on a state‐of‐the‐art Poisson denoising approach known as non‐local principal component analysis (NLPCA). The new method is referred to as PieceWise Principal Component Analysis (PWPCA). In PWPCA, the given image is first split into pieces, then NLPCA is run on each image piece, and finally the entire image is reconstituted by a weighted combination of the NLPCA‐processed image pieces. Using standard test images with Poisson noise, the authors show that PWPCA restores images more effectively than state‐of‐the‐art Poisson denoising approaches. In addition, and to the best of their knowledge, they show the first application of such approaches to single‐particle X‐ray free‐electron laser (XFEL) data. They show that the resolution of three‐dimensional reconstruction from XFEL diffraction images is improved when the data are preprocessed with PWPCA. XFELs are currently under rapid development to allow high‐resolution biomolecular structure determination at near‐physiological conditions. Data analysis methods developments follow these technological advances and are expected to have high impact in structural biology and drug design. This study contributes to these developments. As little experimental single‐particle XFEL data is available still, the XFEL experiments shown here were performed with simulated data.

Structural changes are critical for biological functions of proteins and describing conformational changes in large macromolecular complexes is a major challenge. We have recently developed a hybrid method (HEMNMA) combining transmission electron microscopy (EM), normal mode analysis (NMA), and image analysis to study macromolecular dynamics. NMA is traditionally used to study macromolecular motions while HEMNMA provides insight into actual conformational changes seen by EM. HEMNMA uses normal modes to elastically align EM images with a reference structure in order to determine the conformations present in images and evaluate their pertinence. In this paper, we show how HEMNMA can be used with an atomic-resolution reference structure, using as an example the study of the conformational dynamics of Tomato Bushy Stunt Virus.