This is a demonstration using a user-provided pymol script to measure the angles between two helices. The original post and script can be found and downloaded at PyMOLWiki.

I am using a coiled-coil homodimer crystal structure (PDB: 2E7S) to show the results at here. The crystal structure has multiple copies of coiled-coil dimer and I used “extract” to display chains A + B at here. There is a cross-over point around residues 67-70 presenting an X-shaped coiled-coil dimer (the left panel). The right panel below highlights light yellow and orange colors for two helices from residue 31 (tip point) to residue 67 (cross point).

I downloaded the “anglebetweenhelces.py”, executed it (File -> Run script) to provide external commands for measuring the angles between two helices in PyMOL.

We need to select our target first! “select” command can do it.

select H1, 2E7S and chain A and resi 31-67
select H2, 2E7S and chain B and resi 31-67

Then, run the command “angle_between_helices”. Users can use “tab” to auto fill the command in the command line input box.

angle_between_helices H1, H2, method=0 

The script provides four methods to measure angles.

• method =0 (helix_orientation), the default
• method =1 (helix_orientation_hbond)
• method =2 (loop_orientation)
• method =3 (cafit_orientation)

The angles I got from the 4 methods are: 24.71, 22,26, 22.22 and 22.68 degree.

The script will generate two “arrowed vectors” based on user’s selections to calculate the angles. The vectors are also drew in PyMOL for visualization, shown in the two panels below (left: method=0, right: method=1)

This script can be used for measuring angles between two beta sheets. method=3 (fit C_alpha atom) is suggested.

Note: PyMOL 2.3.5 running in MacOS 10.14.1 was used for this demonstration.