WebThe program used to refine atomic models in real space is phenix.real_space_refine. The algorithm uses a simplified refinement target function that speeds up calculations, so … WebThen, refinement is performed using the remaining 90%. The R-free value is then calculated by seeing how well the model predicts the 10% that were not used in refinement. For an ideal model that is not over-interpreting the data, the R-free will be similar to the R-value. Typically, it is a little higher, with a value of about 0.26.
(IUCr) Real-space refinement in PHENIX for cryo-EM and …
WebJan 10, 2024 · In this paper, we describe the implementation of the phenix.real_space_refine program and demonstrate its performance by applications to simulated data and to cryo … WebJun 1, 2024 · This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified … ftx ip3
[phenixbb] on B-factor refine of the phenix.real_space_refine
Webachieving a reasonable model from which to start full-model refinement. There are a variety of tools in Coot that can help with this (e.g. Rotate Translate Molecule, Jiggle Fit “J”, Morph Fit, real space refinement with self-restraints, etc.), … WebMay 30, 2024 · To address the emerging structure-refinement needs of the rapidly growing field of cryo-EM, the phenix.real_space_refine program (Afonine et al., 2013), which is capable of the refinement of atomic models against maps, has been introduced into the PHENIX suite. It is not limited to cryo-EM and can also be used in crystallographic … WebNov 1, 2024 · The real space refinement command in Phenix (Afonine et al., 2013) was applied to all models after manual refinement. Ramachandran plot outliers, allowed, and favored regions, rotamer outliers, EMRinger Score ( Barad et al., 2015 ), and Molprobity ( Chen et al., 2010 ) Clash Score were validation tools provided in addition to the refined … gilles planted box