Thank you Eleanor for your reply. I am actually considering how to describe a pseudo-NCS with an arbitrary rotational and translational relationship. I don't have to do this but I am just curious. It is more straightforward if I say how the two molecules are related by a rotation around unit cell axis than around orthogonal coordinate axis, which does not have an absolute physical meaning.
The command line output after coot superpose prints out the rotational and translational matrices for both the orthogonal and fractional coordinate system. For using coordconv, my concern is that if I deal with a low-symmetry unit cell, which is not orthogonal by itself, the Euler angles for the fractional coordinate system and the orthogonal coordinate system should be different. If I just feed some numbers into coordconv, will it consider them as orthogonal coordinates? Thank you, Chen On Fri, Sep 5, 2014 at 6:24 AM, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > Rotation matrices are rarely specified in a fractional coordinate system? > The criteria for checking such a matrix is "Is the determinant 1?" and this > only holds for orthogonal matrices. > > > > I guess the way I would do this though. > > You presumably have two sets of fractional coordinates, before and after > rotation? > > There is a ccp4 program - coordconv which will read the fractional > coordinates and generate pdb format with the convention ncode = 1 (You may > need to fudge the fractional format I suppose..) > > You can then use superpose to match the two sets of coordinates and the > output will tell you the Eulerian angles used for the rotation! > > Lots of ways to kill cats! > Eleanor > > > > > > On 4 September 2014 21:21, Phil Jeffrey <pjeff...@princeton.edu> wrote: > >> The orthogonal/fractional matrix is outlined here: >> http://www.iucr.org/__data/assets/pdf_file/0009/7011/19_ >> 06_cowtan_coordinate_frames.pdf >> >> Sorry to say I apparently ditched my old Fortran o2f and f2o programs to >> do that. >> >> Bear in mind, however, that orthogonal has no fixed orientation with >> respect to fractional - for most space groups "ncode 1" is often used but >> for primitive monoclinic "ncode 3" is sometimes used, and I think the >> matrix shown in Kevin Cowtan's document above corresponds to "ncode 1". >> >> Phil Jeffrey >> Princeton >> >> >> On 9/4/14 3:55 PM, Chen Zhao wrote: >> >>> I am sorry, just to clarify, the fractional coordinate matrix I referred >>> to is a rotational matrix in the fractional coordinate system. >>> >>> >>> On Thu, Sep 4, 2014 at 3:52 PM, Chen Zhao <c.z...@yale.edu >>> <mailto:c.z...@yale.edu>> wrote: >>> >>> Hi all, >>> >>> I am just curious whether there are some tools extracting the Euler >>> angles from a fractional coordinate matrix. I have no luck searching >>> it online. >>> >>> Alternatively, I found the analytical solution for the Euler angles >>> from an orthogonal coordinate matrix. So in the worst case, my >>> problem reduces to calculating the transformation matrix between the >>> fractional and orthogonal coordinate system. I feel a little bit at >>> a loss because it is 6 years since I last studied linear algebra. >>> How can I calculate this for a specific unit cell? >>> >>> Thanks a lot in advance! >>> >>> Sincerely, >>> Chen >>> >>> >>> >
