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Finding out ORGX ORGY: Difference between revisions
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There are different possibilities to find out where the direct beam would hit the detector: | There are different possibilities to find out where the direct beam would hit the detector: | ||
# visualize BKGINIT.pck (from INIT), or FRAME. | # visualize BKGINIT.pck (from INIT), or FRAME.cbf (from COLSPOT) with [[XDS-Viewer]], and click (left-mouse) into the middle of the beamstop shadow (or the attenuated direct beam itself, if it is recorded). Use the pixel coordinates displayed by XDS-Viewer as ORGX ORGY (in principle you should add 1 to both numbers, because for XDS-Viewer the pixels go from 0 to NX-1 whereas for XDS they go from 1 to NX).<br />Instead of these files written by XDS, one could directly use a measured frame. However this requires that one enters NX, NY, and the size of the header (which usually is <size of frame in bytes>, minus 2*NX*NY). | ||
# use adxv for visualization. Otherwise the same as with | # use adxv for visualization. Otherwise the same as with XDS-Viewer. (1.9.7beta version works for the PILATUS detector at SLS) | ||
# use MOSFLM for visualization. It prints out X BEAM and Y BEAM from the frame header, and you may click on the hypothetical direct beam position. However, ''x and y are swapped in MOSFLM when compared to XDS'', and the coordinates are in mm, not in pixels (so one has to divide by QX). Sometimes the X BEAM and Y BEAM from the header are not reliable. | # use MOSFLM for visualization. It prints out X BEAM and Y BEAM from the frame header, and you may click on the hypothetical direct beam position. However, ''x and y are swapped in MOSFLM when compared to XDS'', and the coordinates are in mm, not in pixels (so one has to divide by QX). Sometimes the X BEAM and Y BEAM from the header are not reliable. | ||
# use ice rings to find out (in | # use ice rings to find out (in XDS-Viewer, and with paper and pencil) where the direct beam would be. This should be rather accurate but may be tedious. | ||
# use the Unix command line tools to look at the header of the frame. E.g. "strings <frame-name>|more" would should you the (hopefully correct) information stored in the header, like wavelength, delta-phi, X and Y beamcentre and so on. | # use the Unix command line tools to look at the header of the frame. E.g. "strings <frame-name>|more" would should you the (hopefully correct) information stored in the header, like wavelength, delta-phi, X and Y beamcentre and so on. | ||
The error you make in the determination of ORGX ORGY should in principle be less than half of the distance between two spots. If you have a reasonable estimate (from one of the methods above), but the error is bigger than that, ''you can still find out the true ORGY ORGY by inspecting [[IDXREF.LP]] . This works best if [[COLSPOT]] has seen a significant fraction of all frames.'' | The error you make in the determination of ORGX ORGY should in principle be less than half of the distance between two spots. If you have a reasonable estimate (from one of the methods above), but the error is bigger than that, ''you can still find out the true ORGY ORGY by inspecting [[IDXREF.LP]] . This works best if [[COLSPOT]] has seen a significant fraction of all frames.'' | ||