Open AccessCrystallographic model quality at a glance
Author(s) -
Urzhumtseva Ludmila,
Afonine Pavel V.,
Adams Paul D.,
Urzhumtsev Alexandre
Publication year - 2009
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s0907444908044296
Subject(s) - polygon (computer graphics) , ideal (ethics) , combinatorics , point (geometry) , set (abstract data type) , mathematics , quality (philosophy) , representation (politics) , ruler , computer science , geometry , algorithm , physics , frame (networking) , telecommunications , philosophy , epistemology , quantum mechanics , politics , political science , law , programming language
A crystallographic macromolecular model is typically characterized by a list of quality criteria, such as R factors, deviations from ideal stereochemistry and average B factors, which are usually provided as tables in publications or in structural databases. In order to facilitate a quick model‐quality evaluation, a graphical representation is proposed. Each key parameter such as R factor or bond‐length deviation from `ideal values' is shown graphically as a point on a `ruler'. These rulers are plotted as a set of lines with the same origin, forming a hub and spokes. Different parts of the rulers are coloured differently to reflect the frequency (red for a low frequency, blue for a high frequency) with which the corresponding values are observed in a reference set of structures determined previously. The points for a given model marked on these lines are connected to form a polygon. A polygon that is strongly compressed or dilated along some axes reveals unusually low or high values of the corresponding characteristics. Polygon vertices in `red zones' indicate parameters which lie outside typical values.