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Ramachandran plot. Introduction. This server will display a Ramachandran plot, against a background of phi-psi probabilities. Methods. This server will display a coloured Ramachandran plot. Blue means helix, red means strand and green means turn and loop according to DSSP. The lines in the plot indicate prefered areas.
RAMPAGE is a CCP4 program that generates Ramachandran plots for protein structures based on the Richardsons’ data. It can be used to validate the phi and psi angles of each residue in the input pdb file.
The Ramachandran plot is probably the very best indicator of the quality of the experimental determination of three dimesional protein coordinates. This server analyses the Ramachandran plot of a PDB file and compares it with the Ramachandran plots of about 400 representative structures solved at high resolution.
Learn how to use python, online tools and R to create Ramachandran plots for proteins from PDB files. Compare different programs and see examples of plots with different features and styles.
RAMPAGE is a consequence of RAPPER which generates a Ramachandran plot by data derivative by the Richardsons and coworkers. RAPPER performs conformer modelling through sampling residue-specific phi / psi propensity tables and rotameric states with given a set of restraints.
Drawing Ramachandran (phi/psi) plots for Proteins with R. These pages shows how to use R to draw a protein backbone's psi/phi torsion angles (ϕ,ψ) from a supplied file as a scatter plot overlayed on a filled contour plot showing the favoured and allowed regions, for example:
The Ramachandran plot for p27 SJ using RAMPAGE software revealed that among the 263 residues, 259 (99.2%) were in favoured region, 2 (0.8%) were in allowed region and 0 (0.0%) were in...
