<div>FYI, for anyone inclined to write their own programs, there is a similar Python function for this in CCTBX:</div><div><br></div><div>from mmtbx.refinement.fit_rotamers import rotate_point_around_axis</div><div>xyz_new = rotate_point_around_axis(axis_start, axis_end, xyz, angle_degrees)</div>
<div><br></div><div>I'm not posting the code here because Paul's version is clearer, but it's in $PHENIX/cctbx_project/mmtbx/refinement/fit_rotamers.py. (It wouldn't surprise me if this duplicates a more general function in one of the lower-level math modules, but I'm not sure where to look.)</div>
<div><br></div><div>-Nat</div><div><br></div>On Wed, May 25, 2011 at 12:11 PM, Paul Emsley <span dir="ltr"><<a href="mailto:paul.emsley@bioch.ox.ac.uk">paul.emsley@bioch.ox.ac.uk</a>></span> wrote:<br><div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">On 25/05/11 19:41, Hena Dutta wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Dear Members,<div class="im"><br>
<br>
<br>
I want to know the mathematical relations between 2 sets of co-ordinates, one before and one after the rotation. I used COOT to rotate the side chain (containing atoms N1, C2, N3, C4, C5, C6, N6, N7 and C8) of Adenine by 180 degree about the glycosidic bond (C1’-N9). How the initial co-ordinates (Xi, Yi, Zi) and final co-ordinates (Xf, Yf, Zf) are mathematically related? I shall be very grateful if someone can tell me the equations.<br>
<br>
<br>
</div></blockquote>
<br>
I got it from the matrix from the Amore documentation.<br>
<br>
Coord_orth<br>
rotate_round_vector(direction, // vector of the bond about which we are rotating<br>
position, // of the moving atom<br>
origin_shift, // typically the position of the B atom (e.g. N9)<br>
angle) {<br>
<br>
unit_vec = direction.unit();<br>
<br>
l = unit_vec[0];<br>
m = unit_vec[1];<br>
n = unit_vec[2];<br>
<br>
ll = l*l;<br>
mm = m*m;<br>
nn = n*n;<br>
cosk = cos(angle);<br>
sink = sin(angle);<br>
I_cosk = 1.0 - cosk;<br>
<br>
// The Rotation matrix angle w about vector with direction cosines l,m,n.<br>
//<br>
// ( l**2+(m**2+n**2)cos k lm(1-cos k)-nsin k nl(1-cos k)+msin k )<br>
// ( lm(1-cos k)+nsin k m**2+(l**2+n**2)cos k mn(1-cos k)-lsin k )<br>
// ( nl(1-cos k)-msin k mn(1-cos k)+lsin k n*2+(l**2+m**2)cos k )<br>
//<br>
// Thanks for that pointer EJD :).<br>
<br>
<br>
<br>
Paul.<br>
<br>
<br>
<br>
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</blockquote></div><br>