This graphical display allow the user to display phi and psi protein backbone
dihedral angles on a Ramachandran plot that indicates the likelihood (database
abundance) of those angles. This can be used as a form of structure quality
control to detect residues in a calculated three dimensional structure that
are distorted away from regular protein-like conformations. Although a few
atypical angles may truly occur in a given protein structure the presence of
many unusual angles and abnormal distributions of angles over a structure
ensemble with many models may indicate a poor quality structure.
With this popup window the user selects a molecular system and then a
structure ensemble that relates to that system. Th e user can choose to display
dihedral angle information for all models (conformations) in the structure ensemble
or just one model, by changing the “Model” pulldown menu. The user can control which
residues are considered by selecting either a particular type of residue via
“Ccp Code” or a specific residue in the sequence. Other options control how the
phi & psi angle information is presented on screen. The “Labels” options
control which angle spots on the Ramachandran chart have residue sequence number and
type displayed; by default only the “disallowed” angles in unusual (white) regions of the
plot are labelled. The “Spot Size” dictates how large the angle markers are and
the “Colours” is a colour scheme to differentiate the different models
from within the selected ensemble.
The [Previous Residue] and [Next Residue] buttons allow the user to quickly
scan though all of the residues in the structure, to check for
unusual/disallowed backbone angles or unlikely distributions of within the
ensemble. In the Ramachandran matrix plot the wite areas represent phi & psi
angle combinations that are very unusual and thus usually indicative of a poor
structure at that point. The grey and red areas represent the more common, and
thus more expected, angle combinations. The more red the colour of a square
the greater the likelihood of the phi & psi angles. It should be noted that
when displaying angle points for only a single residue or residue type, the
Ramachandran chart in the background is at residue-specific version, i.e. it
shows angle likelihoods for only that one kind of residue. This is particularly
important for Pro and Gly residues that have notably different distributions
(and hence angle expectations) to other residues.
Main Panel
MolSystem: Selects which molecular system to display data for; from which a structure is selected
Structure: Selects which structure ensemble to display phi/psi backbone angle data for
Model: Selects which conformational model(s), from the structure ensemble, to display data for
Labels: Sets which phi/psi points carry residue labels, e.g. according to whether values are “disallowed” (very uncommon)
Clone: Clone popup window
Help: Show popup help document
Close: Close popup
Ccp Code: Allows the phi/psi points to be restricted to only those from a particular residue type
Residue: Allows the display of phi/psi points from only a single residue
Spot Size: Sets how large to display the circles that indicate the phi/psi points
Colours: Selects which colour scheme to use to distinguish phi/psi points from different conformational models
Scrollbar: :
Previous Residue: Show phi/spi spots for the previous residue in the sequence; when there is no current residue, starts fron the first in sequence there is data for
Next Residue: Show phi/spi spots for the next residue in the sequence; when there is no current residue, starts fron the first in sequence there is data for