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XDSGUI: Difference between revisions
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Several such scripts are pre-defined; the user may create her own scripts. If scripts are modified, they are saved to ~/.xds-gui . The names of the buttons (e.g. "User defined command 1") can be changed by editing ~/.xds-gui . | Several such scripts are pre-defined; the user may create her own scripts. If scripts are modified, they are saved to ~/.xds-gui . The names of the buttons (e.g. "User defined command 1") can be changed by editing ~/.xds-gui . | ||
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_$X.cbf (where X is the user-specified frame number) and remains in the temp subdirectory. It may of course be opened in the FRAME tab, but starting XDS-viewer automatically has the advantage that several frames with predictions may be inspected on the screen, at the same time. Please note: if the XDS directory resides in a FAT32 filesystem (which is often the case on a USB stick or disk), then "ln -s" should be replaced by "cp -p" since FAT32 does not support symlinks. | * The first item of the left panel ("Show frame with predicted spots") generates the predicted pattern of reflections for a user-specified frame, overlaid on the frame, for display with [[XDS-viewer]]. The file FRAME.cbf (produced by INTEGRATE) is renamed to FRAME_$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" should be replaced by "cp -p" since FAT32 does not support symlinks. | ||
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 XDS-gui (which is always the case) . Thus, one should simply press the "Reload" button. | * 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 XDS-gui (which is always the case) . Thus, one should simply press the "Reload" button. The user-definable commandline may be used e.g. for | ||
grep -v "JOB=" XDS.INP > x; echo "JOB= DEFPIX INTEGRATE CORRECT" > XDS.INP; cat x >> XDS.INP | |||
The third item ("Saving and comparing good results") offers commands to save/restore the current data processing files to/from a "save" directory. | * The third item ("Saving and comparing good results") offers commands to save/restore the current data processing files to/from a "save" directory. | ||
The last item ("Further analyses") may be used for commands that e.g. run [[pointless]] against the XDS_ASCII.HKL file. The user-definable commandline may be used e.g. for | * The last item ("Further analyses") may be used for commands that e.g. run [[pointless]] against the XDS_ASCII.HKL file. The user-definable commandline may be used e.g. for | ||
phenix.xtriage XDS_ASCII.HKL | phenix.xtriage XDS_ASCII.HKL | ||