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Figure 1
Flowchart for Namdinator. As input, the user must provide an initial model and a target map with its corresponding resolution. A number of settings can be set or default values can be used. Namdinator then modifies the initial model and runs a NAMD2 simulation using MDFF. After the run, phenix.real_space_refine will be run on the output to either calculate group ADP only or to perform a real-space refinement and group ADP calculation. The latter, in particular, will help improve Ramachandran plot outliers (backbone/secondary structure improvements), and rotamer outliers.

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