XDSGUI: Difference between revisions

* 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 conserves the inode. This bug will be fixed in the code. 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") 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

grep -s allow-duplicate-sequence-numbers ~/.coot || echo "(allow-duplicate-sequence-numbers)" >>~/.coot ; spot2pdb -r 1; coot SPOT-*.pdb

since that runs [[spot2pdb]] to show you the reflections of SPOT.XDS in reciprocal space, with coot. You see the indexed reflections (indexed in IDXREF) in yellow, the not-indexed ones in pink, the rotation axis in blue and the origin as a blue cross.

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; these may have to be renamed.

Alternatively, 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 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 '''Fedora''' or Redhat Enterprise Linux ('''RHEL'''; same as CentOS) distributions, you may have to

if you get the error message

or similar for libQtCore.so.4 or libQtOpenGL.so.4 .

 

RedHat Enterprise Linux 8 (CentOS 8) does not provide the needed libraries for the Qt4-based xdsgui binary. For such new distributions, you should install the new Qt5 xdsgui binary linked above.

'''Ubuntu''' needs the libglu1-mesa package if you get the error message

xdsgui: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory

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.” After installation of Xcode, run the <code>strings</code> command (once) and accept the license agreement!