Hi,
xdsme has xds2mos.py script.
https://code.google.com/p/xdsme/
https://code.google.com/p/xdsme/source/browse/XOconv/xds2mos.py
Best regards,
Takanori Nakane
On 2014/12/29 6:37, Igor Petrik 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
>
|