HI 6327 Session 3

1. Lecture 1: Visualization of Biomolecular Structures (PDF file)
2. VMD Tutorial
3. Lecture 2: Introduction to UNIX Pt. 2 (PDF file)
4. Homework Assignment 1

Resources and Assignments:

VMD Tutorial

The VMD classroom tutorial covers the following topics. For more information please consult the VMD user's guide.

• File menu:
  • loading files, types (pdb, psf, dcd)
  • single-frame pdb, multi-frame pdb, trajectories (dcd)
  • saving / loading state
  • Save Trajectory: saving pdb and dcd files
  • creating snapshots

• Molecule menu (top, display, active, fixed)
• Graphics menu:
  • Representations (selection synthax, coloring, drawing)
  • Colors (background, definitions)
  • Materials (use with Representations)

• Display menu:
  • reset view / stop rotation
  • perspective
  • lighting
  • axes and stages
  • stereo
  • settings
• Mouse menu:
  • set up mouse functionality
  • rotate, translate, scale (hotkeys)
  • pick (measure) atom, bond length, angles
  • move (rotate: shift) changes actual coords!

• Extension menu:
  • sequence monitor
  • Ramachandran plot
  • least-squares fitting structures
  • contact map
  • making movies
  • solvating structures for MD simulations

• Command shell
  • everything that can be done on menus can be done with commands
  • shell supports Tcl and Python scripting languages
  • core text commands
  • draw triangle {0 0 1} {0 1 0} {0 0 1}   (reset view)
    
  • scripting library

Homework Assignment 1

Due @ beginning of session 5.

1. Find the expected net charge of the polypeptide AAVLITSQNKRDEHFYWMCPGAA at pH 2.0, 7.3, and 13.0. Assume that all residues are exposed and are in the most favored ionization state. Use the pKa values given in the first session. Also, consider the ionization state of the N- and C-termini.
   
2. Use the hard-sphere model to find 2 sets of limiting angles phi and psi for a Gly-Gly dipeptide in the special cases phi = +/- psi. First, sketch the 2D structure of the dipeptide with the proper C- and N-terminus (at pH 7), indicating the angles phi and psi closest to the carboxy terminal, and the planar groups of atoms. Next, indicate the atoms in contact for the two cases (look first at the corners of the Ramachandran plot at +/- 180 degrees, then consider intermediate values of phi and psi). After identifying the limiting angles using the rotation matrix calculus, sketch the Ramachandran plot for the Gly-Gly case. Hints: Assume that the angle phi = 0 is sterically forbidden and focus only on the oxygens (we are only looking at nonbonded interactions, i.e. you can ignore atoms connected by fewer than four covalent bonds in between). You can learn about rotation matrices here and here.

   Definitions: The angle phi (i) corresponding to residue (i) in a general polypeptide chain is defined as the dihedral angle C(i-1) - N (i) - C_alpha (i) - C (i), with phi = 0 for the cis (U shape) configuration, i.e. C(i-1) and C(i) are on the same side of the bond N (i) - C_alpha (i), and phi = 180 degrees for the trans (zig-zag) configuration. Likewise, the angle psi (i) in a polypeptide is defined for the dihedral angle N (i) - C_alpha (i) - C (i) - N (i+1), with psi = 0 for the cis form and psi = 180 for the trans form. Note: what is special in the case of a dipeptide? Adapt these definitions to Gly-Gly considered here. Handedness: Dihedral angles A-B-C-D are positive, if D is clockwise from A when looking down the B-C axis (right-handed rotation). Negative dihedral angles correspond to left-handed rotations.

   Use the following polypeptide chain geometry.

   Atomic radii (for hard sphere model):

   • H: 0.70 A (1 A = 0.1 nm)
   • C: 1.50 A
   • N: 1.30 A
   • O: 1.35 A

   Distances (for covalent bonds):

   • C_alpha - C: 1.53 A
   • C - N: 1.32 A
   • N - C_alpha: 1.47 A
   • C - O: 1.24 A
   • N - H: 1.00 A

   Angles:

   • Idealize the trigonal bond angles to 120 degrees and the tetrahedral angle to 109.5 degrees (see slides).

3. Adapt any existing VMD graphics script to draw a ring torus surface given by the parametric torus equations:

   x (u,v) = (c + a cos v) cos u
   y (u,v) = (c + a cos v) sin u
   z (u,v) = a sin v

   where c > a are constants. Note that the range of angular variables u and v is the interval [0, 2π]. To draw the surface, triangulate the (u, v) space and render the resulting triangles in (x, y, z) space with VMD (fill the triangles).