Le 06/04/2011 17:16, Geoffrey Hutchison a écrit : >> translate coordinates, according to the formula introduced in the >> International Tables for Crystallography (2006, Vol. B, chapter 3.3), the >> results are different from those that your program gives. > > Throughout the development of Open Babel, this is one area that has always > made me a little afraid. It always seemed a little arbitrary how you pick the > rotation matrix for fractional to Cartesian. I had even asked a few > crystallographers in the various academic departments and no one could point > me to a standard conversion. > > So if you'd like to suggest a different formula, we'd be happy to use it. I > suspect the difference is simply a difference in orientation.
Yes, there is an arbitrary decision when at least one angle is not equal to 90° - the convention used in OB is an x axis parallel to a, y axis in the (a,b) plane (not necessarily along b if gamma is not 90°), and z parallel to c* to finish the orthonormal reference frame. The OB matrix is : http://vincefn.net/ObjCryst/form_37.png In the IT tables volume B §3.3 there are 3 'usual' conventions listed (the 3rd only for rhomboedral cells) - the one used in OB is the 2nd one listed. Which one did you use ? Could you give us a CIF file, the matrix that you used and the pdb file you generated ? Vincent ------------------------------------------------------------------------------ Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
