Chart : Ramachandran Plot

Display Protein Backbone Phi & Psi Angles

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

pulldown MolSystem: Selects which molecular system to display data for; from which a structure is selected

pulldown Structure: Selects which structure ensemble to display phi/psi backbone angle data for

pulldown Model: Selects which conformational model(s), from the structure ensemble, to display data for

pulldown Labels: Sets which phi/psi points carry residue labels, e.g. according to whether values are “disallowed” (very uncommon)

button Clone: Clone popup window

button Help: Show popup help document

button Close: Close popup

pulldown Ccp Code: Allows the phi/psi points to be restricted to only those from a particular residue type

pulldown Residue: Allows the display of phi/psi points from only a single residue

pulldown Spot Size: Sets how large to display the circles that indicate the phi/psi points

pulldown Colours: Selects which colour scheme to use to distinguish phi/psi points from different conformational models

Scrollbar: :

button 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

button 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

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