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Figure 4
ProSMART structural comparison of macromolecules during crystallographic refinement. Comparative analysis of the 3.5 Å model 1ryx of ovotransferrin, before and after re-refinement with external restraints from the sequence-identical 2.15 Å model 2d3i , which adopts a different global conformation. For clarity, the reference model 2d3i is not shown. Details of the re-refinement of 1ryx using 2d3i as a reference structure are detailed elsewhere (Nicholls et al., 2013BB66). The models are superposed and colored according to (a) local backbone dissimilarity and (b) side-chain dissimilarity using a color gradient (yellow implies similarity, red relative dissimilarity), displayed using PyMOL. These representations allow a quick visual identification of which regions of the backbone and side chains have dramatically changed conformation during refinement. In this case, it is evident that there were substantial changes to the local structure but no changes to the global conformation during refinement. (c) Using Coot (Emsley et al., 2010BB29) to visualize the external restraints used during refinement provides information regarding the nature of the external restraints, which are represented as interatomic lines colored gray to red, indicating the similarity of the restraint target values to the current interatomic distances. The prevalence of restraints colored red between domains is due to differences in global conformation between the target and reference models; these restraints would have little effect during refinement due to being down-weighted by REFMAC5.

IUCrJ
Volume 2| Part 1| January 2015| Pages 45-58
ISSN: 2052-2525
doi:10.1107/S2052252514023306