Making measurements in molecular visualization software

Purpose: Some of the most common tasks in molecular visualization and analysis include measuring distances between atoms, and measuring dihedral angles. You should be comfortable doing this in several packages.

Using Rasmol

  1. What is the length of the longest dimension of calmodulin?

  2. Open the file ~/rosetta_workshop/tutorials/day02/sample_files/1CLL.pdb in stick mode

  3. Use Settings --> pick Distance, and choose two atoms from the most distant residues at opposite ends of the protein.

Using Pymol

  1. Open a pregenerated session showing one helix from the potassium channel:
    pymol ~/rosetta_workshop/tutorials/day02/sample_files//alpha_helix.pse

  2. Use Wizard --> Measurement to measure several several (i, i+4) H-bonds (you can hide side chains to simplify the display)

  3. You can change the drop-down box called Distances to Angles or Dihedrals

  4. An alternate method is to ctrl-middle-click on two atoms (producing pk1 and pk2), then type distance. (The Measurements Wizard must be closed.) Ctrl-right-click on the background to clear the picked atoms.

  5. The command-line syntax to do distance and angle measurements looks like this example. This is particularly useful for putting into custom scripts.
    get_dist ///A/102/O, ///A/106/N 
    get_angle ///A/103/N, ///A/103/CA, ///A/103/CB 
    get_dihedral ///A/103/N, ///A/103/CA, ///A/103/C, ///A/104/N

Using Chimera

  1. Measure the dihedral angles of one residue in a helix and one residue from a beta sheet.

  2. Restore the session: chimera ~/rosetta_workshop/tutorials/day02/sample_files/dihedrals.py One segment of helix and one of sheet have been shown in stick mode in this small cytochrome.

  3. Use Tools --> Structure Analysis --> Angles/Torsions (you can do Distances analogously)

  4. Select 4 sequential backbone atoms in the beta strand, then “Create” angle measurement.

    1. Select atoms in order: C, N, CA, C to measure phi

    2. Select atoms in order: N, CA, C, N to measure psi

    3. Select atoms in order: CA, C, N, CA to measure omega

  5. If you have time, you may repeat with a turn of the helix.