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XDSGUI: Difference between revisions
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XDSGUI is a GUI (graphical user interface) for XDS that is supposed to help both novice and experienced users. | |||
It graphically displays the ASCII and [http://www.bernstein-plus-sons.com/software/CBF cbf] files that XDS writes, and can run useful shell commands with a simple mouse click. The design goal of the program is to enable XDS data processing without the commandline, and to supply additional graphical information, in a simple, user-modifiable and user-extensible way. | It graphically displays the ASCII and [http://www.bernstein-plus-sons.com/software/CBF cbf] files that XDS writes, and can run useful shell commands with a simple mouse click. The design goal of the program is to enable XDS data processing without the commandline, and to supply additional graphical information, in a simple, user-modifiable and user-extensible way. | ||
== How to use the GUI == | == How to use the GUI == | ||
The program may be used to analyze graphically any existing directory with files earlier written by XDS, or may be used to create these files. It should be started in a terminal window which will show the output of the programs that are run ( | The program may be used to analyze graphically any existing directory with files earlier written by XDS, or may be used to create these files. It should be started in a terminal window which will show the output of the programs that are run (XDS, pointless, XDSCONV, ...). | ||
The user is supposed to use the tabs on the top, from left to right. | The user is supposed to use the tabs on the top, from left to right. | ||
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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]]. | 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]]. | ||
The current version of the program can be downloaded, by academic users, for Linux [ftp://turn5.biologie.uni-konstanz.de/pub/ | The current version of the program can be downloaded, by academic users, for Linux [ftp://turn5.biologie.uni-konstanz.de/pub/xdsgui.rhel6.64 64bit] (compiled on RHEL6), [ftp://turn5.biologie.uni-konstanz.de/pub/xdsgui.rhel6.32 32bit] (compiled on RHEL6), [ftp://turn5.biologie.uni-konstanz.de/pub/xdsgui.rhel5.64 64bit] (compiled on RHEL5, statically linked with Qt), [ftp://turn5.biologie.uni-konstanz.de/pub/xdsgui.rhel5.32 32bit] (compiled on RHEL5, statically linked with Qt), or [ftp://turn5.biologie.uni-konstanz.de/pub/xdsgui.dmg Mac] (works on OSX 10.6 and up). Industrial users of XDS: pls contact me directly. | ||
=== Dependencies === | === Dependencies === | ||
XDSGUI depends on [[generate_XDS.INP]], [[XDS-viewer]], and of course [[XDS|xds_par]], [[XDS]], and [[XDSCONV]]. The XDSSTAT tab requires [[XDSSTAT]]. One of the items in the TOOLS tab calls a graphical file comparison program; if the default (xdiff) is not available, [http://furius.ca/xxdiff xxdiff] or [http://sourceforge.net/projects/tkdiff tkdiff] may be used - please adjust the commandline below the button accordingly. | |||
Technically, the word "dependency" means that these scripts/programs should be in your $PATH - an 'alias' is often not good enough because the TOOLS commands use bash as a shell, and that shell does not inherit the aliases from e.g. (t)csh. | Technically, the word "dependency" means that these scripts/programs should be in your $PATH - an 'alias' is often not good enough because the TOOLS commands use bash as a shell, and that shell does not inherit the aliases from e.g. (t)csh. | ||
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In case of a Mac, 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''' | In case of a Mac, 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''' | ||
ln -s /Applications/ | ln -s /Applications/xdsgui.app/Contents/MacOS/xdsgui /usr/local/bin/xdsgui | ||
'''and to start the GUI from a terminal window, by typing | '''and to start the GUI from a terminal window, by typing xdsgui'''. In a similar way, XDS-viewer should be put into the $PATH under the name xds-viewer, e.g. using | ||
ln -s /Applications/XDS-Viewer.app/Contents/MacOS/xds-viewer-bin /usr/local/bin/xds-viewer | ln -s /Applications/XDS-Viewer.app/Contents/MacOS/xds-viewer-bin /usr/local/bin/xds-viewer | ||
== Known bugs, problems and workarounds == | == Known bugs, problems and workarounds == | ||
# ''Question concerning TOOLS: "Show frame..." on Mac: it creates everything shown in the commandline but it seem to us that everything runs in the background. Therefore xds-viewer does not open anywhere as it is not seen. Also, it would be great if this image together with the predictions would be re-directed to the FRAME tab.'' <br> Answer: On Linux, the xds-viewer window is brought to the foreground automatically, whereas on the Mac this does not seem to happen. However, an icon for xds-viewer appears in the dock (on the right) and I can double-click it to see the xds-viewer window. I have no idea how to bring xds-viewer to the foreground automatically, and I need input from people who know Macs and tell me how to do it (on the commandline!). The reason why we do not open automatically in the FRAME tab is that one can have several xds-viewer windows open at the same time, and compare the patterns. As a '''workaround''', you can manually open the resulting temp/FRAME_$X.cbf in the FRAME tab. | # ''Question concerning TOOLS: "Show frame..." on Mac: it creates everything shown in the commandline but it seem to us that everything runs in the background. Therefore xds-viewer does not open anywhere as it is not seen. Also, it would be great if this image together with the predictions would be re-directed to the FRAME tab.'' <br> Answer: On Linux, the xds-viewer window is brought to the foreground automatically, whereas on the Mac this does not seem to happen. However, an icon for xds-viewer appears in the dock (on the right) and I can double-click it to see the xds-viewer window. I have no idea how to bring xds-viewer to the foreground automatically, and I need input from people who know Macs and tell me how to do it (on the commandline!). The reason why we do not open automatically in the FRAME tab is that one can have several xds-viewer windows open at the same time, and compare the patterns. As a '''workaround''', you can manually open the resulting temp/FRAME_$X.cbf in the FRAME tab. | ||
# ''Another question concerning TOOLS: "Further analyses" on Mac: again pointless runs nicely but there is no output for the user.'' <br> Answer: Could it be that you started | # ''Another question concerning TOOLS: "Further analyses" on Mac: again pointless runs nicely but there is no output for the user.'' <br> Answer: Could it be that you started xdsgui by double-clicking its icon in the Finder? In that case, there is no output visible, because there is no console. Unfortunately, for all the Tools, the output is in the console window where xdsgui was started. We will try to find out how to open a window where the output is then shown. Thus, currently the '''workaround''' for this problem is to start xdsgui in a console window. | ||
# generate_XDS.INP does not seem to like spaces in file/directory names. While frame names rarely have a space in them, directories might, e.g. if an external disk has the label "John's USB disk" then this would be mounted on Linux as /media/John's USB disk/ and that would result in a error message from generate_XDS.INP . The '''workaround''' is to use a symlink on a different harddisk. | # generate_XDS.INP does not seem to like spaces in file/directory names. While frame names rarely have a space in them, directories might, e.g. if an external disk has the label "John's USB disk" then this would be mounted on Linux as /media/John's USB disk/ and that would result in a error message from generate_XDS.INP . The '''workaround''' is to use a symlink on a different harddisk. | ||
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== News == | == News == | ||
program | program update June 19: Fixes for TRUSTED_REGION on Pilatus, and for XDSCONV tab (thanks Folmer!). | ||
program update July 5: INTEGRATE plot showing crystal rotation; several bugfixes. Commandline name is now xdsgui. | |||