ci9b01103_si_001.pdf (510.84 kB)
Comparing Cryo-EM Reconstructions and Validating Atomic Model Fit Using Difference Maps
journal contribution
posted on 2020-02-10, 23:43 authored by Agnel Praveen Joseph, Ingvar Lagerstedt, Arjen Jakobi, Tom Burnley, Ardan Patwardhan, Maya Topf, Martyn WinnCryogenic
electron microscopy (cryo-EM) is a powerful technique
for determining structures of multiple conformational or compositional
states of macromolecular assemblies involved in cellular processes.
Recent technological developments have led to a leap in the resolution
of many cryo-EM data sets, making atomic model building more common
for data interpretation. We present a method for calculating differences
between two cryo-EM maps or a map and a fitted atomic model. The proposed
approach works by scaling the maps using amplitude matching in resolution
shells. To account for variability in local resolution of cryo-EM
data, we include a procedure for local amplitude scaling that enables
appropriate scaling of local map contrast. The approach is implemented
as a user-friendly tool in the CCP-EM software package. To obtain
clean and interpretable differences, we propose a protocol involving
steps to process the input maps and output differences. We demonstrate
the utility of the method for identifying conformational and compositional
differences including ligands. We also highlight the use of difference
maps for evaluating atomic model fit in cryo-EM maps.