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RAMPAGE is a web-based tool that allows you to generate and display Ramachandran plots for any protein structure from a PDB file. You can also compare the plots with different definitions of allowed and disallowed regions, and download the data as images or text files.
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.
Ramachandran plot evaluation. Introduction. Determines the quality of a Ramachandran plot. Methods. The Ramachandran plot is probably the very best indicator of the quality of the experimental determination of three dimesional protein coordinates.
- Loading The Phi/Psi Angles For Your Protein
- Loading The Phi/Psi Density Profile
- Combining Scatter & Contour Plots
- Downloads
My code assumes you will have an input file where each line contains one (ϕ,ψ) angle pair (between -180 and 180 degrees) with the associated "Ramachandran Type" - i.e. Glycine, Proline, Pre-Proline or General. The example input file (1HMP_mmtk.tsv, tab separated variable file created in python) looks like this: We can read this into R using the fir...
The following code is written to load the rama500-*.data files from Lovell et al. 2003 (see references, and downloads). For example, their file rama500-general.datalooks like this: I wrote an R function to load this data format, and turn it into an array suitable for use with R's contour functions (see downloads). It assumesthat the grid is 180 by ...
One of the nice things about R is that you can look at the source code to most of the built in functions - just try typing filled.contour at the R command prompt. I started with a copy of this code, removed the bits to draw the key, and added code to overlay a scatter plot to make my own function, ramachandran.plot (see downloads). This preample co...
You might want the following files: 1. 1hmp_mmtk.tsv- Example phi/psi angle input file, tab separated variables 2. draw_rama.r- Example R script with all the above code 3. Expected occupancy files top500-angles/pct/rama/rama500-*.data from one of the following archives: 3.1. top500-angles.050606.zip (80MB) (newer, 2005-06-06) 3.2. top500-angles.040...
Nov 27, 2019 · A collection of web tools and databases for assessing the reliability of structural models (crystallographic, NMR, or homology based models). Includes RAMPAGE, a tool for Ramachandran plot analysis, and other programs such as PROCHECK, ERRAT, WHAT CHECK, and more.
RAMPAGE is a CCP4 program that generates a Ramachandran plot using data from 500 high-resolution protein structures. It can be used to validate the phi and psi angles of each residue in an input pdb file.
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