Hi Mojie,

In the current daily build there is a new command named "define" that allows you to define axes (and planes) from the command line.  The "distance" and "angle" commands have been enhanced to accept "object IDs" (which is what "define" defines) to allow measurements between axes/planes/atoms.  The documentation for the define command and the enhanced angle command are here (and are in the daily build as well):

So, one approach would be for you to build a script that generally goes like this:

open noprefs (conformation 1)

sel (residues in first helix) & backbone.minimal

define axis [options you want] number 1

sel (residues in second helix) & backbone.minimal

define axis [options] number 2

angle a1 a2

close all

open noprefs (conformation 2)

etc.

When the script is finished all the angles will be in the reply log.  Obviously you wouldn't write this script by hand, but instead would use any programming language you are familiar with to generate it.  The 'noprefs' keyword to 'open' will speed things up since then Chimera will skip all the fancy computations it does to show the initial "smart" representation with various side chains hidden, backbone ribboned, etc.

Alternatively, you could write a Chimera Python script which could do the looping directly.  Assuming that you already had all the structures open in Chimera, a script something like this:

from chimera import openModels, Molecule, runCommand

for m in openModels.list(modelTypes=[Molecule]):