Generating Ramachandran (phi/psi) plots for Proteins Skip to main content Skip to navigation Sign in Study Research Business Alumni News Engagement Search Warwick Search Molecular Organisation and Assembly in Cells About MOAC Find MOAC MOAC Research Protein Structure Cellular Structure Biological Fibres Intercellular Communication Molecular Interactions Analytical Science Student Publications MOAC Degrees Chemistry with Scientific Writing (MSc)(Restricted permissions) Scientific Research and Communication (MSc)(Restricted permissions) MOAC News MOAC Events Calendar News Graduations Joint DTC Conferences Annual Conferences MOAC Seminars MOAC People MOAC Students Staff How to find and contact MOAC Student Destinations MOAC People MOAC Students Peter Cock Python Programming Ramachandran Plots Other Tools Generating Ramachandran (phi/psi) plots for Proteins On the parent page, I discussed how to load PDB files, calculate phi/psi angles (ϕ,ψ), and thus generate Ramachandran Plots (see references). Now you don't have to use python to do this... If you want to double check the results from python (see calculating the angles), you could use the EMBOSS program psiphi, or Wolfgang Kabsch and Chris Sander's DSSP. Instead of using python to draw the diagram, there are also a selection of online tools to draw Ramachandran Plots for you, including: Ramachandran Server for structures deposited in the PDB, based on MOLEMAN2 by Gerard Kleywegt. STAN Server which will accept any PDB file you provide, also based on MOLEMAN2. MolProbity from the Richardson laboratory at Duke University, which is used on the PDB website itself. RAMPAGE which will accept any PDB file you provide. Using PDB 1HMP as an example, this is the sort of figure MOLEMAN2 produces (cropped for display): MolProbity produces very nice images like this, extracted from this output : This even more beautiful figure is from RAMPAGE, and shows the four plots combined. It was extracted from this output which also contains the data as four separate figures: If you have the angles in a file, then you could draw the diagram yourself using R: Finally, Peter Robinson's Java Program For Drawing Ramachandran Plots does a nice job of visualising the core/noncore regions as originally defined by Kleywegt and Jones (1996), or the Preferred/Allowed but Disfavoured/Forbidden regions introduced by Lovell et al (2003) (see references). Protein Data Bank (PDB) EMBOSS psiphi STAN Server (MOLEMAN2) & Ramachandran Server RAMPAGE Server MOAC DTC, Senate House, University of Warwick, Coventry CV4 7AL Tel: 024 765 75808 Email: moac@warwick.ac.uk MOAC Intranet Page contact: MAS Resource Last revised: Sat 28 Apr 2007 Powered by Sitebuilder © MMXXI Terms Privacy Cookies Accessibility Coronavirus (Covid-19): Latest updates and information Let us know you agree to cookies We use cookies to give you the best online experience. Please let us know if you agree to functional, advertising and performance cookies. You can update your cookie preferences at any time. Cookie policy Essential cookies Functional cookies Advertising cookies Performance cookies Accept all Remember my preference More information
