Skip to main content Skip to navigation

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:

Using PDB 1HMP as an example, this is the sort of figure MOLEMAN2 produces (cropped for display):
[Ramachandran Plot by MOLEMAN2]

MolProbity produces very nice images like this, extracted from this output [PDF]:
[Ramachandran Plot by MolProbity]

This even more beautiful figure is from RAMPAGE, and shows the four plots combined. It was extracted from this output [PDF] which also contains the data as four separate figures:
[Ramachandran Plot by RAMPAGE]

If you have the angles in a file, then you could draw the diagram yourself using R:
[Ramachandran Plot 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).