Explanations of external program features

* WHATIF

See Protein structure verification and A crystallographer's guide to interpreting WHATIF output.

* Procheck_NMR

See AQUA and PROCHECK-NMR - Operating manual.
CING Plots

Ramachandran and Janin plots

  • The background shading is for the probability derived from What If’s internal database of high-resolution structures on a 10 by 10 degree grid. The color coding refers to one of three states the secondary structure (by DSSP) was assigned to be in. Blue, yellow, and green are respectively for helix, sheet, and other. The coloring changes linearly from white to e.g. yellow for densities 2 to 20%. They are consequently put on top of each other (blue on top) with some alpha blending. More details in code at dihedralComboPlot.
  • The CHI 1 and 2 combination plot is named after Janin
  • For angles PHI, PSI, CHI 1 and 2, if a dihedral restraint involves one or more of these angles, a transluced orange rectangle or square will be drawn evidencing the limits of this particular dihedral

Symbols

o (blue) circular averaged value
+ (green) non-proline/glycine
▴ (green) non-cacheable-glycine
■ (green) non-cacheable-proline
| (blue) a line indicates the circular averaged value for a given angle