(I think) these matrices are roughly 180 degrees apart, so they may just correspond to different signs of the axes Phil
On 28 Dec 2014, at 21:37, Igor Petrik <petr...@illinois.edu> wrote: > I am working on a small project which requires me to obtain the proper > orientation of a crystal lattice with respect to the gonistat and source. I > have until now successfully used the matrices from Mosflm and DENZO, which > are consistent with each other and define the orientation of the reciprocal > lattice in the lab space when the spindle is at 0deg. > > I am trying to use the orientation computed by XDS, but this seems to not be > consistent with the others. Here is an example: > > mosflm .mat file: > -0.00458796 -0.01054146 -0.01052990 > 0.00600652 0.01617284 -0.00696834 > 0.02352343 -0.00618559 -0.00027442 > 0.000 0.000 0.000 > -0.1856881 -0.5200068 -0.8337343 > 0.2431015 0.7978011 -0.5517381 > 0.9520617 -0.3051332 -0.0217278 > 39.6412 48.3160 77.5507 90.0000 90.0000 90.0000 > 0.000 0.000 0.000 > SYMM P222 > > (top part is reciprocal matrix in the format: > a*x b*x c*x > a*y b*y c*y > a*z b*z c*z > where x is the x-ray beam axis and z is the spindle axis) > > DENZO (HKL2000) gives an equivalent matrix. > > XDS orientation parameters: > CORRECT.LP > ... > REFINED VALUES OF DIFFRACTION PARAMETERS DERIVED FROM 30955 INDEXED SPOTS > REFINED PARAMETERS: DISTANCE BEAM ORIENTATION CELL AXIS > STANDARD DEVIATION OF SPOT POSITION (PIXELS) 0.70 > STANDARD DEVIATION OF SPINDLE POSITION (DEGREES) 0.08 > SPACE GROUP NUMBER 16 > UNIT CELL PARAMETERS 39.528 48.153 77.542 90.000 90.000 90.000 > E.S.D. OF CELL PARAMETERS 4.0E-02 3.3E-02 3.8E-02 0.0E+00 0.0E+00 0.0E+00 > REC. CELL PARAMETERS 0.025299 0.020767 0.012896 90.000 90.000 90.000 > COORDINATES OF UNIT CELL A-AXIS -37.650 11.269 -4.236 > COORDINATES OF UNIT CELL B-AXIS 14.624 41.546 -19.461 > COORDINATES OF UNIT CELL C-AXIS -1.764 -32.374 -70.439 > CRYSTAL MOSAICITY (DEGREES) 0.211 > LAB COORDINATES OF ROTATION AXIS 0.999962 0.007232 -0.004834 > DIRECT BEAM COORDINATES (REC. ANGSTROEM) 0.003134 0.005401 1.020962 > DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM 1230.87 1260.93 > DETECTOR ORIGIN (PIXELS) AT 1226.25 1252.96 > CRYSTAL TO DETECTOR DISTANCE (mm) 259.04 > LAB COORDINATES OF DETECTOR X-AXIS 1.000000 0.000000 0.000000 > LAB COORDINATES OF DETECTOR Y-AXIS 0.000000 1.000000 0.000000 > ... > > (XDS defines spindle as X and beam as Z) > > Converted to reciprocal lattice orientation matrix in mosflm axis conventions: > (output from xds2mos; manual calculation is consistent with this output) > -0.00273114 -0.00809777 -0.01150308 > -0.00724876 -0.01754758 0.00521075 > -0.02353677 0.00634416 -0.00027012 > 0.000 0.000 0.000 > -0.11022162 -0.39811300 -0.91068616 > -0.29254071 -0.86269689 0.41252918 > -0.94988163 0.31189970 -0.02138535 > 39.5280 48.1530 77.5420 90.0000 90.0000 90.0000 > 0.000 0.000 0.000 > > > As you can see they are different. You can note that the component of each > vector along the mosflm-Z (spindle) axis is consistent, suggesting that it is > only the angle of rotation around the spindle axis that is inconsistent > between the two. I know that for mosflm and DENZO the orientation matrix > defines the orientation of the reciprocal lattice when the spindle is at 0 > deg. XDS seems to be using a different reference point. Why is this and what > is the proper way to obtain the absolute reciprocal orientation at 0 deg from > XDS? > > (If anyone wants to test this on their own, I can provide the frames I used > to obtain these files.) > > Thanks, > - Igor Petrik > University of Illinois >
