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![[Figure 4]](rr5162fig4mag.jpg)
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Figure 4
External restraint visualization and usage during parallelized full-chain real-space atomic model refinement in Coot. In order to mimic a `typical' stage of the model-building and refinement process in which the model is complete yet the conformational geometry is suboptimal, the atomic model corresponding to the RAD51 filament (PDB entry 5jzc, EMDB entry EMD-8183; Short et al., 2016  ) was subjected to simple re-refinement, causing overfitting into the map. External restraints were generated by ProSMART using a homologous structural model derived using MX (PDB entry 1n0w; Pellegrini et al., 2002) as a reference. In Coot, the colouring of interatomic vectors representing restraints indicates local structural conservation; consistent interatomic distances are coloured grey, whilst those that are substantially longer/shorter in the target than in the reference model are coloured red/blue. (a) The re-refined model of 5jzc is shown, along with the interatomic distance restraints that were generated using 1n0w. From observing the restraint colouring it is evident that there are substantial local conformational differences between the two structural models despite the sequence homology. (b) Performing full-chain real-space refinement of the model in Coot results in the local conformation of the model becoming much closer to that of the high-resolution homologue, as indicated by the increased quantity of interatomic vectors coloured grey. Regions containing restraints coloured red/blue indicate persisting differences between the target and reference models. Such regions are indicative of either true differences between the target and reference structures (as is the case in Fig. 5), suboptimal restraint weighting parameters or errors in the model that require manual resolution. Regardless, the presence of any such regions would warrant closer inspection. |
![[Figure 4]](rr5162fig4.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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