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→Libraries and software that the program depends on: small fixes
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After finally moving to the [[XDSGUI#XDS.INP|XDS.INP]] tab, other parameters can be adjusted by the user, and finally XDS may be run by clicking a button. The resulting output files from XDS will then be displayed in the next tabs. | After finally moving to the [[XDSGUI#XDS.INP|XDS.INP]] tab, other parameters can be adjusted by the user, and finally XDS may be run by clicking a button. The resulting output files from XDS will then be displayed in the next tabs. | ||
After finishing this first round of processing, the [[XDSGUI#TOOLS|TOOLS]] tab may be used, which - among other things - offers those three options that I found most useful to optimize the data processing. After choosing (by mouse click) one of these three options, the user should go back to the [[XDSGUI#XDS.INP|XDS.INP]] tab, specify | After finishing this first round of processing, the [[XDSGUI#TOOLS|TOOLS]] tab may be used, which - among other things - offers those three options that I found most useful to optimize the data processing. After choosing (by mouse click) one of these three options, the user should go back to the [[XDSGUI#XDS.INP|XDS.INP]] tab, specify JOB=DEFPIX INTEGRATE CORRECT, and run XDS again. Ideally, each of the three options should be tried separately, and its effect should be compared with the previous processing to verify that it ''really'' improved the processed data. A significant increase in [[ISa]] (> 1%) indicates that the processing has improved; a slight decrease in ISa (<1%) often is accompanied by an increase of CC1/2 at high resolution, and thus should be tolerated. | ||
Those options that improve ISa can then be used in combination. | Those options that improve ISa can then be used in combination. | ||
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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. 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 | * 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 | * 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 | 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. | 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. | ||
=== statistics === | === statistics === | ||
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=== Installation === | === Installation === | ||
The current version of the program can be downloaded, by academic users, for Linux [ | The current version of the program can be downloaded, by academic users, for Linux [https://{{SERVERNAME}}/pub/xdsgui.rhel6.64 64bit] (compiled on RHEL6) or [https://{{SERVERNAME}}/pub/xdsgui.dmg Mac] (works on OSX 10.6 and up). | ||
Industrial users: pls contact me directly. | Industrial users: pls contact me directly. | ||
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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 ('''RHEL'''; same as CentOS) distributions, you may have to | |||
In case of | |||
yum install qt qt-x11 | yum install qt qt-x11 | ||
if you get the error message | if you get the error message | ||
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 similar for libQtCore.so.4. | ||
Similarly, the error message | |||
xds-viewer: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory | |||
means that you need to | |||
yum install libpng12 | |||
Generally, if in case of RHEL or related distributions you don't know the name of the package, e.g. | |||
yum provides "*/libQtCore.so.4" | |||
would tell you about it. | |||
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). Alternatively, the Fedora 29 packages can be installed: | |||
if you get the error message | wget https://archives.fedoraproject.org/pub/archive/fedora/linux/releases/29/Everything/x86_64/os/Packages/q/qt-4.8.7-41.fc29.x86_64.rpm | ||
xdsgui: error while loading shared libraries: | wget https://archives.fedoraproject.org/pub/archive/fedora/linux/releases/29/Everything/x86_64/os/Packages/q/qt-common-4.8.7-41.fc29.noarch.rpm | ||
wget https://archives.fedoraproject.org/pub/archive/fedora/linux/releases/29/Everything/x86_64/os/Packages/q/qt-x11-4.8.7-41.fc29.x86_64.rpm | |||
dnf install qt-4.8.7-41.fc29.x86_64.rpm qt-common-4.8.7-41.fc29.noarch.rpm qt-x11-4.8.7-41.fc29.x86_64.rpm | |||
In addition, the qt-settings RPM may have to be installed. It is available from EPEL, or also from Fedora 29. | |||
'''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 | |||
If in the case of Ubuntu you don't know the name of the package that provides a certain library, the | |||
sudo apt-file search libGLU.so.1 | |||
command would find it for you. This needs a one-time installation by | |||
sudo apt install apt-file | |||
sudo apt-file update | |||
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! | 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! | ||