Note that the elbow formula assumes that the two vectors are normalized.
Remember the dot product <https://en.wikipedia.org/wiki/Dot_product>
equation
<x,y> = |x| * |y| * cos( theta )
-Spencer
On Tue, Dec 1, 2015 at 4:34 AM Sampson, Jared M. <jms2...@cumc.columbia.edu>
wrote:
> Hi Smith -
>
> Check out how I did it in the http://pymolwiki.org/index.php/Elbow_angle
> script.
> As long as you have the vectors, the angle is easy. In particular, have a
> look at this line:
>
> elbow = int(numpy.degrees(numpy.arccos(numpy.dot(direction_v,
> direction_c))))
>
> i.e. the angle (in radians) will be given by the arccos of the dot product
> of the two vectors. For the elbow angle script, I converted to degrees and
> reported an integer value.
>
> Cheers,
> Jared
>
> —
> Jared Sampson
> Graduate Student
> Department of Biochemistry and Molecular Biophysics
> Columbia University
>
> On Nov 30, 2015, at 8:33 PM, Smith Liu <smith_liu...@163.com> wrote:
>
> Thanks Jared, it works.
>
> In addition, if by your way I created 2 vectors for 2 different chains,
> will you please show me how to determine the angle formed by the 2 vectors
> created?
>
> Smith
>
>
>
>
>
>
>
> At 2015-12-01 00:51:46, "Sampson, Jared M." <jms2...@cumc.columbia.edu>
> wrote:
>
> Hi Smith -
>
> I’m not quite sure what you mean by "axis of a subunit." If you mean the
> principal axis of that selection of atoms, `orient my_selection` will get
> it aligned along one of the axes. Then you can create pseudoatoms on that
> axis and create a dash between them with the distance command.
>
> # Get it lined up with the viewport axes.
> select domain, chain A and resi 1-100
> orient domain
>
> # Here I’m assuming this put the long axis of the domain along the
> # x axis. We move the view along the x axis, and place pseudoatoms
> # at the viewport center in two places. You can change the length of the
> # displayed axis based on how far you move.
> move x, -10
> pseudoatom ps1
> move x, 20
> pseudoatom ps2
> move x, -10
> distance axis, ps1, ps2
>
> This is a bit clumsy and not a rigorous approach, but it will work for any
> other kind of vector you want to show, as long as you can get it aligned
> with one of the view axes.
>
> Cheers,
> Jared
>
> —
> Jared Sampson
> Graduate Student
> Department of Biochemistry and Molecular Biophysics
> Columbia University
>
> On Nov 29, 2015, at 7:42 AM, Smith Liu <smith_liu...@163.com> wrote:
>
> Dear All,
>
> Will you please show me how to display an axis of a subunit or a domain by
> pymol?
>
> Smith
>
>
>
>
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