糖心TV

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 program , or Wolfgang Kabsch and Chris Sander's .

Instead of using python to draw the diagram, there are also a selection of online tools to draw Ramachandran Plots for you, including:

• for structures deposited in the , based on by .
• which will accept any PDB file you provide, also based on MOLEMAN2.
• from the Richardson laboratory at Duke University, which is used on the PDB website itself.
• which will accept any PDB file you provide.

Using PDB as an example, this is the sort of figure MOLEMAN2 produces (cropped for display):

produces very nice images like this, extracted from this output :

This even more beautiful figure is from , 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, 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).

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