Installation

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This article has some little script snippets that should ease the installation of XDS and related programs (XDS-viewer, xdsstat, xdsgui). It is assumed that binaries (or links to binaries) should go to /usr/local/bin .


Linux

Log in as root - we need write permission for /usr/local/bin .

To get the XDS package if you are an academic user,

 cd /usr/local/bin
 wget -O- ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz | tar xzvf -
 ln -sf XDS-INTEL64_Linux_x86_64/* .

To get the script generate_XDS.INP from its XDSwiki article,

 cd /usr/local/bin
 wget http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP -O - | \
   sed -e s/\&nbsp\;/\ /g -e s/\&gt\;/\>/g -e s/\&lt\;/\</g -e s/amp\;//g -e s/\&quot\;/\"/g -e s/\&\#\1\6\0\;/\ /g | \
   sed '/# end of generate_XDS.INP/,$d' | awk '/^#/,/rm -f tmp1 tmp2/' > generate_XDS.INP
 chmod +x generate_XDS.INP

Please note that to get the strings command, which is used by generate_XDS.INP, on some Linux distributions (e.g. FC23) you need to install the binutils RPM package.

To get XDS-Viewer,

 cd /usr/local/bin
 wget ftp://turn5.biologie.uni-konstanz.de/pub/xds-viewer-0.6.64bit -O xds-viewer
 chmod a+x xds-viewer  
 ln -sf xds-viewer xdsviewer

To get XDSSTAT,

 cd /usr/local/bin
 wget ftp://turn5.biologie.uni-konstanz.de/pub/xdsstat-linux64.bz2 -O xdsstat.bz2
 bunzip2 -f xdsstat.bz2
 chmod a+x xdsstat

To get XDSCC12,

 cd /usr/local/bin
 wget ftp://turn5.biologie.uni-konstanz.de/pub/xdscc12.rhel6.64 -O xdscc12
 chmod a+x xdscc12

To get XDSGUI,

 cd /usr/local/bin
 wget ftp://turn5.biologie.uni-konstanz.de/pub/xdsgui.rhel6.64 -O xdsgui
 chmod a+x xdsgui

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 http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSGUI#Installation if you have a problem with missing libmng2.

It is useful to install xxdiff or one of its alternatives (see below). The package 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.

On Centos7 (RHEL7, SL7) I went to http://rpmfind.net/linux/rpm2html/search.php?query=xxdiff and found that the Fedora 20 RPM can be installed using

yum install ftp://rpmfind.net/linux/fedora/linux/releases/20/Everything/x86_64/os/Packages/x/xxdiff-3.2-20.fc20.x86_64.rpm

Perhaps xxdiff will be available on EPEL some day - maybe it is available on RPMforge; I didn't check.

Alternatively, tkdiff may be installed, or other graphical comparison programs, like meld or kdiff3. vimdiff is also nice, and probably already installed.

For Eiger data processing, H5ToXDS should be installed as explained, and h5dump should be installed by e.g. yum -y install hdf5.

Mac (Intel)

Attention: generate_XDS.INP requires Xcode to be installed. Xcode is not installed by default, but can be downloaded free of charge from the Mac App Store: after installing Xcode, open Preferences, select the Downloads tab, and click the Install next to Command Line Tools. Or: open a Terminal window and type xcode-select --install. This will bring up a prompt to install the necessary command line tools.

You also have to explicitly agree to the License terms when running a Command Line Tool for the first time.

I'm not sure if Xcode can be installed without administrator privileges; you may also wish to look at http://guide.macports.org/#installing.xcode .

personal installation (experimental writeup)

Preparation:

  • make sure your $PATH includes your $HOME/bin - the programs will be put into that directory. To achieve this, open a Terminal window, and then
 cd $HOME
 echo 'export PATH=$PATH:$HOME/bin' >> ~/.profile 
 

(I'm not sure if it should be .profile or .bashrc; I have seen it work with .profile but not with .bashrc on a Leopard system)

  • create the $HOME/bin and $HOME/Applications directories. Still in the Terminal window, type
 mkdir $HOME/bin
 mkdir $HOME/Applications
 

To install generate_XDS.INP:

 cd $HOME/bin
 curl -L -o - http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP | \
   sed -e s/\&nbsp\;/\ /g -e s/\&gt\;/\>/g -e s/\&lt\;/\</g -e s/amp\;//g -e s/\&quot\;/\"/g -e s/\&\#\1\6\0\;/\ /g | \
   sed '/# end of generate_XDS.INP/,$d' | awk '/^#/,/rm -f tmp1 tmp2/' > generate_XDS.INP
 chmod +x generate_XDS.INP
 

To install XDS:

 cd $HOME/bin
 curl -L -o - ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-OSX_64.tar.gz | tar xvf -
 ln -sf XDS-OSX_64/* .

To install XDS-Viewer, click https://sourceforge.net/project/platformdownload.php?group_id=239755 , open up the downloaded XDS-Viewer.app by clicking, and then (once you see it in the Finder), go to the Terminal and

cp -pr /Volumes/XDS-Viewer/XDS-Viewer.app/ $HOME/Applications
ln -s $HOME/Applications/XDS-Viewer.app/Contents/MacOS/xds-viewer-bin $HOME/bin/xds-viewer

To install XDSSTAT,

 cd $HOME/bin
 curl -L -o xdsstat.bz2 ftp://turn5.biologie.uni-konstanz.de/pub/xdsstat-i386-mac.bz2
 bunzip2 -f xdsstat.bz2
 chmod a+x xdsstat

To install XDSCC12,

 cd $HOME/bin
 curl -L -o xdscc12 ftp://turn5.biologie.uni-konstanz.de/pub/xdscc12-mac
 chmod a+x xdscc12

To install XDSGUI, please download from ftp://turn5.biologie.uni-konstanz.de/pub/xdsgui.dmg, open up the downloaded xdsgui.app by clicking, and then (once you see it in the Finder), go to the Terminal and

cp -pr /Volumes/xdsgui/xdsgui.app/ $HOME/Applications
ln -s $HOME/Applications/xdsgui.app/Contents/MacOS/xdsgui $HOME/bin/xdsgui

Please also check XDSGUI#Installation.

It is useful to install xxdiff from http://furius.ca/downloads/xxdiff/releases/macosx/xxdiff-4.0b1.osx.dmg (or newer). After downloading, open up the downloaded xxdiff.app by clicking, and then (once you see it in the Finder), go to the Terminal and

cp -pr /Volumes/xxdiff/xxdiff.app/ $HOME/Applications
ln -s $HOME/Applications/xxdiff.app/Contents/MacOS/xxdiff $HOME/bin/xxdiff

(the names of the files may not be entirely correct in these two lines)

system-wide installation (requires root permission)

To get generate_XDS.INP:

 cd /usr/local/bin
 sudo sh -c 'curl -L -o - http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP | \
   sed -e s/\&nbsp\;/\ /g -e s/\&gt\;/\>/g -e s/\&lt\;/\</g -e s/amp\;//g -e s/\&quot\;/\"/g -e s/\&\#\1\6\0\;/\ /g | \
   sed '/# end of generate_XDS.INP/,$d' | awk '/^#/,/rm -f tmp1 tmp2/' > generate_XDS.INP'
 sudo chmod +x generate_XDS.INP

To get XDS:

 cd /usr/local/bin
 sudo sh -c 'curl -L -o - ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-OSX_64.tar.gz | tar xvf -'
 sudo ln -sf XDS-OSX_64/* .

To get XDS-Viewer, click https://sourceforge.net/project/platformdownload.php?group_id=239755 , install in the usual graphical way to your /Applications and then

sudo ln -s /Applications/XDS-Viewer.app/Contents/MacOS/xds-viewer-bin /usr/local/bin/xds-viewer

To get XDSSTAT,

 cd /usr/local/bin
 sudo curl -L -o xdsstat.bz2 ftp://turn5.biologie.uni-konstanz.de/pub/xdsstat-i386-mac.bz2
 sudo bunzip2 -f xdsstat.bz2
 sudo chmod a+x xdsstat
 

To get XDSCC12,

 cd /usr/local/bin
 sudo curl -L -o xdscc12 ftp://turn5.biologie.uni-konstanz.de/pub/xdscc12-mac
 sudo chmod a+x xdscc12

To get XDSGUI, please download from ftp://turn5.biologie.uni-konstanz.de/pub/xdsgui.dmg and then

sudo ln -s /Applications/xdsgui.app/Contents/MacOS/xdsgui /usr/local/bin/xdsgui

Please also check XDSGUI#Installation.

It is useful to install xxdiff from http://furius.ca/downloads/xxdiff/releases/macosx/

For Eiger data processing, eiger2cbf-osx should be sym-linked into a directory in your $PATH, but under the name H5ToXds, and h5dump should be installed from a .dmg file.

Troubleshooting

If any of the commands

ls -l /usr/local/bin/generate_XDS.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 generate_XDS.INP xdsgui xds xds-viewer xdsstat xdscc12

and this should return a line for each of the programs asked for.

Windows

The programs of the XDS package as well as XDSGUI, XDSSTAT, XDSCC12 and so on may be run on 64bit Windows 10 within the Linux Subsystem for Windows (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. Windows 10 Creators Update (CU) allows to install (or update to) Ubuntu 16.04 (or other distros, see [1]), and fixes many bugs.

Graphical Linux programs require installation of a X server like Xming or VcXsvr on the Windows host. There are helpful writeups (e.g. [2],[3]). 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 generate_XDS.INP 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 xds_par 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.

Xds win.PNG

(Screenshot provided by Gustavo Lima)