Dear Ian, thank you for enlightening my ignorance! So George, maybe PDB coordinates will be accepted by chemical crystallographers? Doing this also them will develop something as nice as bioinformatics! :-) FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jan 6, 2013, at 15:01 , Ian Tickle <ianj...@gmail.com> wrote: > > ... anyhow all calculations during refinement are in fractional coordinates > > ... > > Not necessarily: I can only speak for the RESTRAIN program for restrained > refinement that I was involved in developing (the first use of TLS in > macromolecular refinement), and at no point were co-ordinates converted to > fractional or fractional co-ordinates ever used. All structure factor > calculations (and of course the geometric restraints) were done with the > original orthogonal co-ordinates read from the PDB file, using the classical > structure factor equations (of course more modern programs use FFT for this). > > Essentially, you can express the phase factor as exp(2 pi i h.(Sr + t)) = > exp(2 pi i (H.R + h.t)) where h is the index vector in integers as read from > the MTZ file, r is the fractional co-ordinate vector (not needed in the > calculation), S and t represent the real-space symmetry operator, H is the > orthogonalised rotated reciprocal lattice vector (H~ = h~SB^-1), and R is the > orthogonal co-ordinate vector (R = Br). I think this is the most efficient > way of organising the calculation provided the outer loops are over symmetry > operators and reflections (so H is calculated once) and the inner loop is > over co-ordinates. Of course I accept that using FFT via the electron > density is a much more efficient way but I think even then no conversion to > fractional is necessary. > > Cheers > > -- Ian
