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305 bytes added ,  13:33, 10 July 2019
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* The first item of the left panel ("Show frame with predicted spots") generates the predicted pattern of reflections for a user-specified frame, overlaid on the frame, for display with [[XDS-viewer]]. The file FRAME.cbf (produced by INTEGRATE) is renamed to FRAME_$X.cbf (where X is the user-specified frame number) and remains in the temp subdirectory. It may of course be opened in the FRAME tab, but starting XDS-viewer automatically has the advantage that several frames with predictions may be inspected on the screen, at the same time. Please note: if the XDS directory resides in a FAT32 filesystem (which is often the case on a USB stick or disk), then "ln -s" (of the script line) should be replaced by "cp -p" since FAT32 does not support symlinks. Also note: for the script to work correctly, NAME_TEMPLATE_OF_DATA_FRAMES in XDS.INP has to specify an absolute, not a relative path.
 
* The first item of the left panel ("Show frame with predicted spots") generates the predicted pattern of reflections for a user-specified frame, overlaid on the frame, for display with [[XDS-viewer]]. The file FRAME.cbf (produced by INTEGRATE) is renamed to FRAME_$X.cbf (where X is the user-specified frame number) and remains in the temp subdirectory. It may of course be opened in the FRAME tab, but starting XDS-viewer automatically has the advantage that several frames with predictions may be inspected on the screen, at the same time. Please note: if the XDS directory resides in a FAT32 filesystem (which is often the case on a USB stick or disk), then "ln -s" (of the script line) should be replaced by "cp -p" since FAT32 does not support symlinks. Also note: for the script to work correctly, NAME_TEMPLATE_OF_DATA_FRAMES in XDS.INP has to specify an absolute, not a relative path.
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* The second item ("Optimizing data quality") offers commands that manipulate [[XDS.INP]] in several ways. Please note: the popup "XDS.INP has been changed externally" is emitted by the Qt system and cannot be switched off. It appears if one of the scripts changes XDS.INP while it is opened by XDSGUI (which is always the case) . Thus, one should simply press the "Reload" button. The user-definable command may be used e.g. for
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* The second item ("Optimizing data quality") offers commands that manipulate [[XDS.INP]] in several ways. Please note: the popup "XDS.INP has been changed externally" is emitted by the Qt system and cannot be switched off. It appears if one of the scripts changes XDS.INP while it is opened by XDSGUI (which is always the case) . Thus, one should simply press the "Reload" button. XDSGUI sometimes hangs (and must be killed with Ctrl-C) when running <pre>grep _E INTEGRATE.LP | tail -2 >x; sed -e 's/ BEAM_DIVERGENCE=/! BEAM_DIVERGENCE=/' -e 's/ REFLECTING_RANGE=/! REFLECTING_RANGE=/' XDS.INP >>x; mv x XDS.INP</pre> I suggest to replace the final part of the latter command <pre>mv x XDS.INP</pre> with <pre>cat x > XDS.INP; rm x</pre> because this workaround would conserve the inode. I would be glad to receive feedback if this helps - then the bug could be fixed in the code! The user-definable command may be used e.g. for <pre>echo RELRAD=7 ! default is 5 >> XDS.INP</pre> This provides more pixels to the background estimation (for another INTEGRATE), and is useful for weakly exposed data sets which have mostly pixels with zero counts.
awk '/BEAM_DIVERGENCE=/{print "",$1,2*$2,$3,$4}' INTEGRATE.LP>x; grep -v BEAM_DIVERGENCE XDS.INP>>x; mv x XDS.INP
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This multiplies the estimate of BEAM_DIVERGENCE in INTEGRATE.LP by 2 and thus provides more pixels to the background estimation (for another INTEGRATE). This is useful for weakly exposed data sets which have mostly pixels with zero counts. Of course, any other factor (other than 2) may be tried.
      
* The third item ("Saving and comparing good results") offers commands to save/restore the current data processing files to/from a "save" directory. Make sure to replace "xdiff" with "xxdiff" or "tkdiff", if one of the latter is available.
 
* The third item ("Saving and comparing good results") offers commands to save/restore the current data processing files to/from a "save" directory. Make sure to replace "xdiff" with "xxdiff" or "tkdiff", if one of the latter is available.
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