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* 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 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 ("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 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. The user-definable command may be used e.g. for <pre>echo RELRAD=7 ! default is 5 >x; grep -v BEAM_DIVERGENCE XDS.INP >>x; cat x > XDS.INP; rm x</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") | * The last item ("Further analyses") offers useful commands. "determine spacegroup with pointless" runs [[pointless]] against the XDS_ASCII.HKL file. The button "show spots in reciprocal space" runs [[spot2pdb]] to show you the reflections of SPOT.XDS in reciprocal space, with coot. You see the reflections that could be indexed in IDXREF in yellow, the not-indexed ones in pink, the rotation axis in blue and the origin as a blue cross. Ice rings and additional lattices can be easily identified - see [[spot2pdb]] for examples! | ||
=== statistics === | === statistics === | ||
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=== Installation === | === Installation === | ||
The program can be downloaded, by academic users, as Qt5 binary for Linux [https://{{SERVERNAME}}/pub/linux_bin/xdsgui 64bit] (compiled on RHEL6) and as Qt4 binary for [https://{{SERVERNAME}}/pub/xdsgui_qt4.dmg Mac] (works on OSX 10.6 and up). A Qt4 version is available for [https://{{SERVERNAME}}/pub/linux_bin/xdsgui.qt4 old Linux distributions] and a Qt5 version for [https://{{SERVERNAME}}/pub/mac_bin/xdsgui_qt5.dmg latest MacOS] is also available | The program can be downloaded, by academic users, as Qt5 binary for Linux [https://{{SERVERNAME}}/pub/linux_bin/xdsgui 64bit] (compiled on RHEL6) and as Qt4 binary for [https://{{SERVERNAME}}/pub/xdsgui_qt4.dmg Mac] (works on OSX 10.6 and up). A Qt4 version is available for [https://{{SERVERNAME}}/pub/linux_bin/xdsgui.qt4 old Linux distributions] and a Qt5 version for [https://{{SERVERNAME}}/pub/mac_bin/xdsgui_qt5.dmg latest MacOS] is also available. | ||
Industrial users: pls contact me directly. | Industrial users: pls contact me directly. | ||
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The easiest way to install XDSGUI, and all XDSGUI-related programs is documented in [[Installation]]. | The easiest way to install XDSGUI, and all XDSGUI-related programs is documented in [[Installation]]. | ||
If you want to install manually, in case of Linux, after downloading the binary file, its name should be changed to "xdsgui" and then be made executable ("chmod a+x xdsgui"). The binary may then be copied into e.g. the directory /usr/local/bin by the administrator, or to the $HOME/bin directory by the user. Any other directory should be suitable as long as it is in your $PATH. In case of MacOS, the DMG file may be installed in the usual way, by double-clicking it and dragging the icon into the Applications folder. It is advantageous to place a symbolic link, like | |||
sudo ln -s /Applications/xdsgui.app/Contents/MacOS/xdsgui /usr/local/bin/xdsgui | sudo ln -s /Applications/xdsgui.app/Contents/MacOS/xdsgui /usr/local/bin/xdsgui | ||
'''and to start the GUI from a terminal window, by typing xdsgui'''. In a similar way, XDS-viewer should be put into the $PATH under the name xds-viewer, e.g. using | '''and to start the GUI from a terminal window, by typing xdsgui'''. In a similar way, XDS-viewer should be put into the $PATH under the name xds-viewer, e.g. using | ||
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==== Libraries and software that the program depends on ==== | ==== Libraries and software that the program depends on ==== | ||
If on Linux you get an error message like | |||
xdsgui: error while loading shared libraries: libQtGui.so.4: cannot open shared object file: No such file or directory | xdsgui: error while loading shared libraries: libQtGui.so.4: cannot open shared object file: No such file or directory | ||
or similar for libQtCore.so.4 or libQtOpenGL.so.4 | or similar for libQtCore.so.4 or libQtOpenGL.so.4 , you may rather want to install the Qt5 version which is now the default. | ||
Procedures for identifying and installing missing libraries are shown in the [[Installation#tools_and_helper_programs_for_generate_XDS.INP_and_XDSGUI.2C_and_libraries|Installation]] article. | |||
On the '''Mac''' (e.g. Yosemite) one needs [https://itunes.apple.com/us/app/xcode/id497799835?ls=1&mt=12 Xcode] installed. Otherwise one may obtain a popup error “You can’t open the application because it is not supported on this type of Mac.” | On the '''Mac''' (e.g. Yosemite) one needs the (free) [https://itunes.apple.com/us/app/xcode/id497799835?ls=1&mt=12 Xcode] command line tools installed. Otherwise one may obtain a popup error like “You can’t open the application because it is not supported on this type of Mac.” | ||
== Known bugs, problems and workarounds == | == Known bugs, problems and workarounds == |