## Friday, May 23, 2008

### ramaplot

http://boscoh.com/ramaplot/

MacOSX Universal binary

The Ramachandran Plot Explorer is designed to make it easy to examine the conformation of a polypeptide - through the interactive Ramachandran plot (φ-ψ angles) and χ-angle tool. Simply click on a residue, then drag the marker on the Ramachandran plot.

To see how conformational changes might affect the energetics, I've included real-time calculation of H-bonds, weak H-bonds and steric clashes. This makes it easy to see why (i) certain regions of the Ramachandran plot (what is this?) are forbidden, and (ii) certain sidechain chi angles are favoured, (iii) the core is packed so tightly.

You can also edit (cut/paste/insert) protein sequences and mutate residues, with a simple click of the mouse.

I've worked hard to make an intuitive interface with lots of visual cues and feedback, and I've included what, I think, is a necessary set of navigating tools (sequence-bar, z-slab-bar, snake-measure tool). The program uses native widgets (standard file open/save dialogs!) and you can resize the window to your heart's content.

There is a 3-point-clamp function, that (i) explores discrete solutions of a loop with fixed anchors and 3 hinge-residues, and (ii) allows the exploration of the phi/psi angles of residues inside the clamp without disturbing the rest of the protein.

Limited to a single chain.