Installing XCRYSDEN on UBUNTU(Linux) – Tutorial

XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. It runs on GNU/Linux.
XCrySDen has been also ported to MAC OSX (requires X11) and Windows (requires CYGWIN).
The name of the program stands for Crystalline Structures and Densities and X because it runs under the X-Window environment.

In this tutorial I will show you how to run it on Linux and more specifically on UBUNTU.

Downloading

Download the source file from this page: http://www.xcrysden.org/Download.html

Make sure you download the semi-shared package, as it will contain the required libraries. Also make sure you download the correct version(32 bit or 64 bit) depending on your operating system. 32 bit versions are not available for newer versions, the latest version that supports 32 bit is 1.24 I guess.

The file would probably be compressed an in the .tar.gz format.

Installing

You can extract the contents by right clicking on the file and choosing ‘Extract here’, or you can execute the following in the terminal:

tar zxvf xc-version.tar.gz

Once you have extracted the file, open your terminal, and change the directory to the XCRYSDEN directory.
In my case I exctracted the tar.gz file in the Home, so I used the command:

cd XCrysDen-1.5.24-bin-semishared

Now execute the command ./xcConfigure

and follow the on-screen instructions. (say no if it asks you if you have a crystal package)

Run

Once the configuration is complete, you will be shown the following message on the terminal screen.

Now you can run ./xcrysden or just xcrysden in the terminal to launch xcrysden.

IMPORTANT NOTE:

The most recen versions of XCRYSDEN for Linux, only support 64-bit and don’t have a xcConfigure file in the source package. To be honest I am not sure how to install such versions. The above tutorial works for 32-bit versions like 1.25,18 etc that have an xcConfigure file.
If you know how to install the newer 64 bit versions, please do let me know in the comments section below, so that the community can benefit from that information.

Another thing I noticed was, that if you had an unsuccessful or corrupt install of one of the versions of XCRYSDEN, then it could be difficult to make a newer version work.

That’s it!
Hope this post helps you!

 

 

 

PhD researcher at Friedrich-Schiller University Jena, Germany. I'm a physicist specializing in theoretical, computational and experimental condensed matter physics. I like to develop Physics related apps and softwares from time to time. Can code in most of the popular languages. Like to share my knowledge in Physics and applications using this Blog and a YouTube channel.
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One thought on “Installing XCRYSDEN on UBUNTU(Linux) – Tutorial

  1. cd

    rm index.html

    rm -rf xcrysden*

    sudo rm /usr/bin/xcrysden

    sudo apt-get update

    sudo apt-get purge xcrysden

    sudo apt-get build-dep xcrysden

    sudo apt-get install tcl tcl-dev tk tk-dev itcl3 itk3 itk3-dev tk8.4-dev tk8.4

    sudo apt-get install iwidgets4 tcl8.5 tcl8.5-dev tk8.5 tk8.5-dev libtogl-dev

    sudo apt-get install libxmu-headers libxmu-dev libxmuu-dev unp build-essential

    wget http://www.xcrysden.org/download/

    FILENAME=`grep xcrysden index.html| grep tar\.gz index.html| tail -n 1|cut -d”\”” -f8`

    wget http://www.xcrysden.org/download/`echo $FILENAME`

    unp $FILENAME

    cd xcrysden*

    sudo ln -s ~/xcrysden*/xcrysden /usr/bin/xcrysden

    cp system/Make.sys-semishared Make.sys

    make all

    xcrysden -v

    xcrysden –help

    XCRYSDEN uses a few external utility programs. These are the following:

    1.) the “Open Babel” program is needed to display molecular structure from
    Gaussian Z-matrix file.

    2.) the ImageMagick’s suit of programs is used to print-to-file (PNG/JPG/GIF/…),
    to create animated-GIFs, and to screen dump windows.

    3.) the “Mplayer’s mencoder” program is used to create AVI/MPEG movies
    from the animation snapshots.

    4.) xcrysden may also use other programs such as gifsicle, xwd, ppmtompeg, …

    Links

    Open BABEL: http://openbabel.org/
    IMAGEMAGICK: http://www.imagemagick.org/
    MENCODER: http://www.mplayerhq.hu/

    sudo snap install openbabel

    Install ImageMagick 7.0.2-1 on Ubuntu
    Run the following commands in Terminal to install ImageMagick 7.0.2-1 on Ubuntu 16.04, Ubuntu 15.01, Ubuntu 15.04, Ubuntu 14.04 and other Ubuntu Derivatives:

    wget http://www.imagemagick.org/download/ImageMagick.tar.gz
    tar -xvf ImageMagick.tar.gz
    cd ImageMagick-7.*
    ./configure
    make
    sudo make install
    sudo ldconfig /usr/local/lib

    Once installed, start ImageMagick by running “display” (without quotes) in Terminal

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