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.
What is the length of the longest dimension of calmodulin?
Open
the file ~/rosetta_workshop/tutorials/day02/sample_files
/1CLL.pdb
in
stick mode
Use Settings --> pick Distance, and choose two atoms from the most distant residues at opposite ends of the protein.
Open
a pregenerated session showing one helix from the potassium
channel:pymol
~/rosetta_workshop/tutorials/day02/sample_files/
/alpha_helix.pse
Use Wizard --> Measurement to measure several several (i, i+4) H-bonds (you can hide side chains to simplify the display)
You can change the drop-down box called Distances to Angles or Dihedrals
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.
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
Measure the dihedral angles of one residue in a helix and one residue from a beta sheet.
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.
Use Tools --> Structure Analysis --> Angles/Torsions (you can do Distances analogously)
Select 4 sequential backbone atoms in the beta strand, then “Create” angle measurement.
Select atoms in order: C, N, CA, C to measure phi
Select atoms in order: N, CA, C, N to measure psi
Select atoms in order: CA, C, N, CA to measure omega
If you have time, you may repeat with a turn of the helix.