On Apr 16, 2009, at 2:29 AM, James Stroud wrote:
> On Apr 16, 2009, at 1:18 AM, Leiman Petr wrote:
>> I am not sure if it possible to understand _anything_ in
>> crystallography if it is not clear how to calculate an angle
>> between two vectors!
>
> More difficult is deciding exactly how to define said vectors in the
> first place, especially when one is attempting to define said
> vectors for helices "of different subunit[s] in different
> orientation[s]".
On second thought it's only slightly less trivial than the angle
calculation: (1) decide the C-alphas of the helix (e.g. DSSP) (2) do
PCA on their coordinates (3) the first principle component defines the
direction of the helix.
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