Hi Jared,
this is a numerical problem. Look in transformations.py for the lines
where values get compared to 1e-8 and change this number to something
like 1e-7.
And in your script the angle calculation missed the arccos:
elbow = 180 - numpy.degrees(numpy.arccos(numpy.dot(direction_v,direction_c)))
Cheers,
Thomas
On Tue, Dec 14, 2010 at 7:57 PM, Sampson, Jared <jared.samp...@nyumc.org> wrote:
> Hello all - I'm trying to calculate the elbow angle of an Fab locally (i.e.
> without uploading to a server) and decided to try it in PyMOL. I got stuck,
> and thought maybe someone much wiser than I might be able to shed some light
> on the error(s) of my ways.
>
> I've been trying to use some of the functions in transformations.py by
> Christoph Gohlke (quite a thorough toolset!); what I have so far is the
> following .pml script:
>
> run transformations.py
>
> import numpy
> import transformations
>
> fetch 3ghe, async=0
>
> # break the fab into 4 pieces
> create vl, chain L and resi 1-107
> create vh, chain H and resi 1-113
> create cl, chain L and !vl
> create ch, chain H and !vh
>
> # align the pieces
> super vl,vh
> super cl,ch
>
> python
>
> # get the transformation matrices
> mat_v = cmd.get_object_matrix("vl")
> mat_c = cmd.get_object_matrix("cl")
>
> # turns Pymol's output into a 4x4 python array
> def mat_to_R(mat):
> R = [[mat[0],mat[1],mat[2],mat[3]],
> [mat[4],mat[5],mat[6],mat[7]],
> [mat[8],mat[9],mat[10],mat[11]],
> [mat[12],mat[13],mat[14],mat[15]]]
> return R
>
> Rv = mat_to_R(mat_v)
> Rc = mat_to_R(mat_c)
>
> # calculate the axis & angle
> angle_v,direction_v,point_v = transformations.rotation_from_matrix(Rv)
> angle_c,direction_c,point_c = transformations.rotation_from_matrix(Rc)
>
> # calculate the elbow angle
> elbow = numpy.degrees(numpy.dot(direction_v,direction_c))
> print "Elbow angle:",elbow
>
> python end
>
> I'm getting the following error, but I'm not sure how to address it:
>
> Traceback (most recent call last):
> File "/sw64/lib/pymol-py26/modules/pymol/parser.py", line 155, in parse
> exec(py_block,self.pymol_names,self.pymol_names)
> File "<string>", line 19, in <module>
> File "transformations.py", line 348, in rotation_from_matrix
> raise ValueError("no unit eigenvector corresponding to eigenvalue 1")
> ValueError: no unit eigenvector corresponding to eigenvalue 1
>
> Any help would be greatly appreciated!
>
> Thanks,
>
> Jared
>
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> New York, NY 10016
> 212-263-7898
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