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Log in as root - we need write permission for /usr/local/bin. Package If you are an academic user, cd /usr/local/bin wget -O- ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64Linuxx8664.tar.gz tar xzvf - ln -sf XDS-INTEL64Linuxx8664/. Other programs:,. Can be downloaded from.
A simple way to obtain them is to create an empty folder, 'cd' to that folder and then wget chmod +x getfolder.sh./getfolder.sh Please note that to get the strings command, which is used by, on some Linux distributions (e.g. FC23) you need to install the binutils RPM package. Since XDSGUI depends on graphics packages that may need to be installed, you can check the xdsgui binary with ldd `which xdsgui` and that should show you the libraries it found, and more importantly, those that it didn't find. Your friendly system administrator will then work out the specific commands to install those libraries; on RedHat-type distributions that would typically be e.g. Yum provides libXfixes.so.3 the output of which will tell you that this is in the libXfixes RPM. Ubuntu 14 users: please read if you have a problem with missing libmng2.
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Ubuntu 16.04 and 18.04: if libQtOpenGL.so.4 is missing, use sudo apt install libqt4-opengl. Of course, this still requires installation of xxdiff (or alternative), and for.h5 data: HDF5 package, and H5ToXds and/or library. Xxdiff is likely available for your distribution - google for it, or try e.g. Yum -y install xxdiff on RHEL6/CentOS6/SL6 systems, or apt-get install xxdiff on Ubuntu. An xxdiff binary that runs on CentOS7 (RHEL7, SL7) is provided by the getfolder.sh script.
Alternatively, tkdiff may be installed, or other graphical comparison programs, like meld or kdiff3. Vimdiff is also nice, and probably already installed. For data processing, H5ToXDS should be installed as, and h5dump should be installed by e.g. Yum -y install hdf5. Attention: requires the to be installed (free of charge). In my experience, you have to explicitly agree to the License terms when running a Command Line Tool (e.g.
Strings) for the first time. Become familiar with the concept and ways to run commands as 'root' - google 'mac osx become root'. All the tasks that are run in a Terminal window require root privileges, since some of the programs and their links are written to /usr/local/bin. (As an alternative that does not require root, one may create a directory $HOME/bin and use that for the programs and links. That would also require modification of the $PATH, by a one-time echo 'export PATH=$PATH:$HOME/bin' /.profile) So, prepare the following steps by opening the Terminal window, and then sudo su # this will make you root, and ask for your password mkdir /usr/local/bin # only if /usr/local/bin was not created before package If you are an academic user, echo you may have to 'sudo su' first, to obtain administrator permissions! Cd /usr/local/bin curl -L -o - tar xvf - ln -sf XDS-OSX64/.
Other programs:,. Can be downloaded from.
A simple way to obtain them is is to open a Terminal, and type: sudo su which asks for the password and gives you administrator permissions. Then, # any folder would do; here we use /usr/local/bin/macbin mkdir -p /usr/local/bin/macbin cd /usr/local/bin/macbin curl -O -R chmod +x getfolder.sh./getfolder.sh If you want to update the programs some time later, just run these commands again. In order to enable data processing, the getfolder.sh script. copies Dectris' Neggia library into /usr/local/lib64. copies into /usr/local/bin, but under the name H5ToXds. copies of h5dump into /usr/local/bin Lastly, it is useful (for e.g. XDSGUI) to install xxdiff from Troubleshooting If any of the commands ls -l /usr/local/bin/generateXDS.INP ls -l /usr/local/bin/xdsgui ls -l /usr/local/bin/xds-viewer # in the same way, check the other programs that should be used returns a message like file or directory not found then this means that you do not have the symlink.
But even if these commands do not return errors, you should also check the targets of the symlink: ls -l /Applications/xdsgui.app/Contents/MacOS/xdsgui ls -l /Applications/XDS-Viewer.app/Contents/MacOS/xds-viewer-bin Again, these commands should not return an error message. If they do, the programs are not installed in the location where the symlink points to. You'll have to either install the programs properly (in /Applications) or make the symlink point to the correct location. A quick way is also which generateXDS.INP xdsgui xds xds-viewer xdsstat xdscc12 and this should return a line for each of the programs asked for. The programs of the package as well as, and so on may be run on 64bit Windows 10 within the (WSL).
This (easily!) installs a Ubuntu 14.04.5 LTS environment, which supports the apt package manager, so in principle any software available for Ubuntu may be installed. (CU) allows to install (or update to) Ubuntu 16.04 (or other distros, see ), and fixes many bugs.
Graphical Linux programs require installation of a X server like or on the Windows host. There are helpful writeups (e.g.,). To use the X server, one has to say in the shell window export DISPLAY=:0 before running the program. Running XDSGUI under WSL's Ubuntu 14.04 requires installation of a few packages with sudo apt-get install libgomp1 libqtgui4 and requires a number of packages (some of which are only for specific detectors!); I'd start with sudo apt-get install coreutils binutils gawk sed bc grep and if required, also install python and hdf5-tools. The CU fixes many aspects of the interoperability between Windows and Linux, so is recommended.
Without it, only single-processor xds runs smoothly, whereas the parallel xdspar stops with an error message. XDSSTAT and the conversion to MTZ files by XDSCONV require a CCP4 installation accessible by WSL. In principle, CCP4 may be installed within WSL (have not tested this), or on the Windows host. (Screenshot provided by Gustavo Lima).
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K-PACS offers a Free to download DiCOM Server and a DiCOM viewer. The author notes that this can not be used for diagnostic purposes, however it’s a nice free tool to use. K-PACS Server. Store SCP (Service Class Provider) K-PACS Viewer Server connection and file import/export:. Query/Retrieve SCU (Service Class User) on patient, study and series level. Move SCU. Store SCU from local K-PACS database or external DICOM data (e.g.
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CDs) to target archives. Supported DICOM data compression: uncompressed, JPEG-Lossless (J1), JPEG-lossy (J4).
Export of native DICOM data (with option for anonymization) e.g.