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Figure 1
Example output of the PDB_REDO web server. (a) The table of global structure model quality indicators for the starting model and the final PDB_REDO model. Significant improvements are marked in green and deteriorations in red. See the main text for a description of the significance levels. The blue question marks are hyperlinks to the PDB_REDO FAQ. (b) Box-and-whisker plots of global model quality indicators. The plots represent quality scores of at least 1000 structure models (from the PDB or their PDB_REDO data bank counterparts) that have a resolution close to that of the user's model. The whiskers extend to 1.5 times the inter-quartile range. The quality of the starting model is indicated as a blue line and that of the final model as an orange line. (c) Changes in real-space correlation coefficient per residue (for the N-terminal part of a study case). Significant improvements are coloured green and deteriorations red, while grey denotes no significant change and white denotes undefined significance; the dotted line denotes the average change across the whole protein. This plot also demonstrates that the significance of a change depends on the magnitude but also on the size of the residue and the resolution of the diffraction data. (d) A Coot (Emsley et al., 2010BB10) window with a button list that highlights the structural changes made by the PDB_REDO pipeline.

Volume 1| Part 4| May 2014| Pages 213-220
ISSN: 2052-2525