PT  - JOURNAL ARTICLE
AU  - Sjors H.W. Scheres
TI  - Amyloid structure determination in RELION-3.1
AID  - 10.1101/823310
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 823310
4099  - http://biorxiv.org/content/early/2019/10/29/823310.short
4100  - http://biorxiv.org/content/early/2019/10/29/823310.full
AB  - Helical reconstruction in RELION is increasingly used to determine atomic structures of amyloid filaments from electron cryo-microscopy (cryo-EM) images. However, because the energy landscape of amyloid refinements is typically fraught with local optima, amyloid structure determination is often difficult. This paper aims to help RELION users in this process. It discusses aspects of helical reconstruction that are specific to amyloids; it illustrates the problem of local optima in refinement and how to detect these; and it introduces a new method to calculate 3D initial models from reference-free 2D class averages. By providing starting models that are closer to the global optimum, this method makes amyloid structure determination easier. All methods described are open-source and distributed within RELION-3.1. Their use is illustrated using a publicly available data set on tau filaments from the brain of an individual with Alzheimer’s disease.