The Crystal Painter

CP displays crystal structures using Jmol, an open source structure viewer. Like the ProPhylER interface, it is an applet that runs in your browser window.

CP colors each residue in the structure according to the evolutionary constraint calculated on the basis of the ProPhylER alignment.

Unless you search with a PDB ID, ProPhylER's search for a crystal structure that matches your sequence is carried out by Blast. You may therefore get more than one match. The best one is displayed on the results page with a link to the CP. Poorer matches are shown with their PDB IDs.

The PDB structure found by your search may contain more than one peptide ("Chain"), in which case ProPhylER will attempt to find all clusters that match the different PDB chains. The chains that have a corresponding cluster will be colored, but the chains that do not will be grey.

How the Colors are Made

Colors in the crystal correspond to the position-specific evolutionary constraint ProPhylER has calculated for the cluster (alignment) that has the best-matching sequence to the crystal peptide. Mapping colors to the right amino acid in the structure is done via pairwise alignment between the crystal peptide and the best-matching ProPhylER sequence. Blue is high constraint, red is low constraint (below). Constraint is just a better term for "conservation". Section B. on the CP How To Page explains in more detail where the constraint calculations come from.

CP Window Layout

On the right is a small version of the Crystal Painter window. It has several sections with distinct functionalities. A. Title bar with PDB file and ProPhylER cluster descriptions. B. The Jmol applet window. Click and drag in here to zoom, navigate, etc. according to the pointers provided in D. C. Button controls. Pressing those buttons executes Jmol scripts that do useful things. D. Pointers for navigating in the Jmol frame. Read these first! E. Potentially useful downloads.

Last updated 8/25/08