Sandbox kinemage

From Proteopedia

BCH222 :: Structure of Biological Macromolecules

(KineMage currently not supported) If you are not already somewhat familiar with polypeptide geometry, please explore the kinemage on the right. Left-drag to move the viewpoint around, and turn on & off the angle and atom labels and the H atoms with buttons on the right-hand button panel. Turn on the "spheres", to get a feeling for the bulk of the atoms and their bonded interpenetration. With spheres off, enable bond rotations under the Tools menu by choosing Specialty -> Suite rotation, which gives you a rotation widget with a choice of possible angles to rotate. Try PHI and PSI, then CHI1 and CHI2. [Don't use the "end" angles, which are a temporary artifact of the current process of updating KiNG to work with these lessons.] Left-button drag around the circle edge changes the angle quickly, right-button drag changes more slowly, and the + and - boxes very slowly.

Finding direction and chain termini

(KineMage currently not supported)

  1. Interact with the kinemage on the right, which shows the mainchain from a crystal structure of oxy-myoglobin refined at 1Å resolution, with color-coded balls for the non-C atoms (O red, N blue). In the overview, drag to rotate the molecule slowly back & forth, to see in 3D the arrangement of helices that enclose the heme group (in pink). Turn on sidechains and sc atoms. The central Fe atom (orange) of the heme has an O2 ligand bound on one side; what is the amino-acid type and the residue number of the sidechain ligand on the other side? [You can click on an atom in the sidechain and read its pointID at bottom left of the graphics window, or figure it out by the shape and atom types of the sidechain.]

Notes

This material is a fragment from BCH222 :: Structure of Biological Macromolecules 1st Graphics Assignment, by David and Jane Richardson, copied here for testing purposes only.