Scoring conservation and variability. The crystal structure of two domains of the photosensory core of DrBphP, the bacteriophytochrome from Deinococcus radiodurans , is shown colored by conservation and variability relative to a published alignment of 122 phytochromes and phytochrome-related proteins  using a charge scoring scheme. Conservation of net charge [A] is shown colored from red (conserved negative charge) to blue (conserved positive charge). The standard deviation of charges at each position [B] is shown colored from white (0.0) to black (0.7). The combination of the two outputs permits the user to distinguish between conserved uncharged positions (regions that are white in both panels) and variable positions with no net charge enrichment (regions that are white in [A] but black in [B]). Both panels were prepared from a single output file by coloring using values reported in occupancy [A] or B-factor [B]. Figure prepared with VMD , Stride , and homolmapper.