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XDSGUI: Difference between revisions
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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. | ||
* The second item (" | * The second 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. If [http://www.globalphasing.com/autoproc autoPROC] is installed, I suggest to use the "User defined command 2" for <code>mkdir staraniso; cd staraniso; aP_scale -hkl ../XDS_ASCII.HKL; echo anisotropy-corrected files are in staraniso subdirectory</code>. | ||
* The third item (" | * The third 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. | ||
* The last item ("Further analyses") may be used for commands, e.g. running [[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, e.g. running [[pointless]] against the XDS_ASCII.HKL file. The user-definable commandline may be used e.g. for | ||
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== Availability == | == Availability == | ||
The [ | The [https://sourceforge.net/u/joseptrivino/xdsgui/ci/master/tree/ program's source code] is released under the terms of the [https://gnu.org/licenses/old-licenses/gpl-2.0.txt GPLv2]; it uses the [http://www.qt.io/ Qt library] which was released under the terms of the [https://gnu.org/licenses/lgpl.txt LGPL]. The program is under development and probably has bugs. If it crashes, it should simply be restarted. A crash of the program ''does not interfere'' with the operation of [[XDS]]; likewise, closing the program window does not influence any XDS run started from XDSGUI. | ||
=== Dependencies === | === Dependencies === | ||
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==== Libraries and software that the program depends on ==== | ==== Libraries and software that the program depends on ==== | ||
In case of Fedora or Redhat Enterprise Linux distributions, you may have to | RedHat Enterprise Linux 8 (CentOS 8) does not seem to provide by default the needed Qt libraries. They can be installed using | ||
dnf install https://extras.getpagespeed.com/redhat/8/noarch/RPMS/getpagespeed-extras-release-8-6.el8.gps.noarch.rpm | |||
dnf install qt-x11 mesa-libGLU | |||
and answering "y" to all questions (attention - this installs a non-default repository). | |||
In case of other Fedora or Redhat Enterprise Linux distributions, you may have to | |||
yum install qt qt-x11 | yum install qt qt-x11 | ||
if you get the error message | if you get the error message | ||
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update Oct 10, 2017: fix the bug that non-CBF files are not being displayed (see Bugs section above). | update Oct 10, 2017: fix the bug that non-CBF files are not being displayed (see Bugs section above). | ||
update Apr 27, 2018: fix the bug that the INTEGRATE tab is not updated when XDS runs. 32-bit Linux binaries are no longer made. | update Apr 27, 2018: fix the bug that the INTEGRATE tab is not updated when XDS runs. 32-bit Linux binaries are no longer made. Download source from https://sourceforge.net/u/joseptrivino/xdsgui/ci/master/tree/ . | ||
update June 15, 2018: SHELXC, SHELXD and SHELXE are available through the SHELX tab. | update June 15, 2018: SHELXC, SHELXD and SHELXE are available through the SHELX tab. | ||