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(Automatic model building step, AMB).
(Automatic model building step, AMB) 4) The phases calculated from auto-built models of step 3 were combined with the step-2 prime-and-switched phases in SIGMAA (Read, 1986) with the appropriate weights between the phases from the above two sources.
Automatic model building for PR72 was performed similarly but used the native data sets.
Density modification and automatic model building were performed using AutoRickshaw and ArpWarp63 and refined using phenix.refine64.refine64
Multiple rounds of manual and automatic model building, followed by molecular refinement, were required for the generation of both PBP2 and PBP2 MreC structures.
The mean phase error in the final cycle dropped to ~45° (Fig. 2B: Cycle 4), with a correlation coefficient of 0.77 (Fig. S1), which is sufficient for automatic model building and structure refinement.
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Cycles of manual building, phase optimization, and automatic model-building were extensively performed with COOT38, PARROT39, and BUCCANNER40.
Registration of multiple range views for automatic 3-D model building.
(1) Model building.
Iterative model building with COOT (Emsley and Cowtan, 2004) and refinement against the anisotropically corrected native data in Buster 2.10 (Bricogne et al., 2011) using automatic NCS and TLS restraints (Smart et al., 2012) yielded the final SAS-5CC model.
LF guided the model building.
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