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Subject:

Re: XDS orientation matrix inconsistent with Mosflm, DENZO

From:

Takanori Nakane <[log in to unmask]>

Reply-To:

Takanori Nakane <[log in to unmask]>

Date:

Mon, 29 Dec 2014 08:01:08 +0900

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (98 lines)

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
>

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