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Figure 4
Large-scale movements of models into density. (a). Fitting of E. coli adenylate kinase transition-state conformation (1ake) into a 5 Å simulated density of the adenylate kinase in the apo-state conformation (4ake) using Namdinator with a plot of the CC_mask values and clash score for every 1000th step from Namdinator. Default settings were used, except the simulation steps which were increased from 20 000 to 60 000 to reach convergence. (b) Fitting the open conformation of the magnesium channel CorA into the density (EMD-6553) of its closed state using Namdinator. The initial model (red cartoon) rigid-fitted to EMD-6553 (grey surface), that was used as input for a two-step Namdinator procedure. A plot of the CC_mask values for every 1000th step from both sequential Namdinator runs are shown.

IUCrJ
Volume 6| Part 4| July 2019| Pages 526-531
ISSN: 2052-2525
https://doi.org/10.1107/S2052252519007619