TY - JOUR
T1 - Comparing Cryo-EM Reconstructions and Validating Atomic Model Fit Using Difference Maps
AU - Joseph, Agnel Praveen
AU - Lagerstedt, Ingvar
AU - Jakobi, Arjen
AU - Burnley, Tom
AU - Patwardhan, Ardan
AU - Topf, Maya
AU - Winn, Martyn
PY - 2020
Y1 - 2020
N2 - Cryogenic 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.
AB - Cryogenic 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.
UR - http://www.scopus.com/inward/record.url?scp=85085534880&partnerID=8YFLogxK
U2 - 10.1021/acs.jcim.9b01103
DO - 10.1021/acs.jcim.9b01103
M3 - Article
C2 - 32043355
SN - 1549-9596
VL - 60
SP - 2552
EP - 2560
JO - Journal of Chemical Information and Modeling
JF - Journal of Chemical Information and Modeling
IS - 5
ER -