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XDSGUI: Difference between revisions
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→Libraries and software that the program depends on: small fixes
(→tools: explain a bit more the spot2pdb result) |
(→Libraries and software that the program depends on: small fixes) |
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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 | ||
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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 | |||
yum install qt qt-x11 | |||
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 | |||
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 | 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 https://extras.getpagespeed.com/redhat/8/noarch/RPMS/getpagespeed-extras-release-8-6.el8.gps.noarch.rpm | ||
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In addition, the qt-settings RPM may have to be installed. It is available from EPEL, or also from Fedora 29. | 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 | '''Ubuntu''' needs the libglu1-mesa package if you get the error message | ||