Showing posts with label installation. Show all posts
Showing posts with label installation. Show all posts

24 June 2013

461. Briefly: setting up SHELX on linux (crystallography)

Nothing difficult, but putting up instructions won't hurt anyone.

SHELX is THE crystal structure refinement software. I'm not a crystallographer, but it never hurts familiarising yourself with the tools of  your collaborators.

Register using this page (if you're an academic user):
To find the answer to the xtal question, use google.

You'll then receive an email with a password. Now go to
where you'll find instructions.

Download all the files:

Several of my files became corrupted the first time I downloaded them for some reason: anode.bz2, shelx[cde].bz2, shredcif.bz2.

I'm presuming that you're downloading the files to ~/Downloads

Here are the 'good' md5sums:
219183542ada47a17e5528bf217f9261 anode.bz2 61335e6b9cf2e654242db80822f32681 ciftab.bz2 918fe0a04e59589938a81a93d8e3eaff shelxc.bz2 e65580af087989aa4958eb53dcd8a473 shelxd.bz2 bc5cad6e4129fa61bbde49207cd4d244 shelxe.bz2 5390146a4b516425fb7b326533443ba7 shelxl.bz2 95617863be917743df55bd94509504fb shelxs.bz2

While you're at it, download the testdata from,,,,

sudo apt-get install bunzip2 xargs
mkdir ~/tmp/shelx-2013 -p
cd ~/Downloads
cp shredcif.bz2 shelxe.bz2 shelxd.bz2 shelxc.bz2 ciftab.bz2 anode.bz2 shelxl.bz2 shelxs.bz2 ~/tmp/shelx-2013
cd ~/tmp/shelx-2013/
ls *.bz2|xargs -I {} bunzip2 {}
chmod +x *
sudo cp * /usr/local/bin

If you downloaded the test data:

mkdir ~/tmp/shelx_examples
cd ~/Downloads
cp ~/tmp/shelx_examples
cd ~/shelx_examples
ls *.zip |xargs -I {} unzip {}

And you're done. Now, learning how to use SHELX, and how to use it properly, is a different matter on which I am not qualified to write.

08 June 2012

182. Oracle Java JDK (java, javac and javaws) in debian testing/wheezy

With ECCE I was having problems with getting the same version of java and javac on a computer where I was using sun java 6.0

Since I'm using SGE I (think I) need the closed source SUN java version.
Download (and click on the license agreement) here:

(v7u4 is available here:

Then follow this:
sudo apt-get install java-package
make-jpkg jdk-6u32-linux-x64.bin

and follow the instructions. Once the package is built, install:
sudo dpkg -i oracle-j2sdk1.6_1.6.0+update32_amd64.deb

Unpacking oracle-j2sdk1.6 (from oracle-j2sdk1.6_1.6.0+update32_amd64.deb) ...
Setting up oracle-j2sdk1.6 (1.6.0+update32) ...
update-alternatives: using /usr/lib/jvm/j2sdk1.6-oracle/jre/bin/ControlPanel to provide /usr/bin/ControlPanel (ControlPanel) in auto mode.
update-alternatives: using /usr/lib/jvm/j2sdk1.6-oracle/jre/lib/amd64/ to provide /usr/lib/iceweasel/plugins/ ( in auto mode.
update-alternatives: using /usr/lib/jvm/j2sdk1.6-oracle/jre/lib/amd64/ to provide /usr/lib/chromium/plugins/ ( in auto mode.
sudo update-alternatives --config java
There are 6 choices for the alternative java (providing /usr/bin/java).
  Selection    Path                                            Priority   Status
  0            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      auto mode
  1            /usr/bin/gij-4.4                                 1044      manual mode
  2            /usr/bin/gij-4.6                                 1046      manual mode
* 3            /usr/lib/jvm/j2re1.6-oracle/bin/java             314       manual mode
  4            /usr/lib/jvm/j2sdk1.6-oracle/jre/bin/java        315       manual mode
  5            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      manual mode
  6            /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java   1051      manual mode
sudo update-alternatives --config javac
There are 2 choices for the alternative javac (providing /usr/bin/javac).
  Selection    Path                                         Priority   Status
* 0            /usr/lib/jvm/java-7-openjdk-amd64/bin/javac   1051      auto mode
  1            /usr/lib/jvm/j2sdk1.6-oracle/bin/javac        315       manual mode
  2            /usr/lib/jvm/java-7-openjdk-amd64/bin/javac   1051      manual mode
sudo update-alternatives --config javaws
There are 3 choices for the alternative javaws (providing /usr/bin/javaws).

  Selection    Path                                              Priority   Status
  0            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/javaws   1061      auto mode
* 1            /usr/lib/jvm/j2re1.6-oracle/bin/javaws             314       manual mode
  2            /usr/lib/jvm/j2sdk1.6-oracle/jre/bin/javaws        315       manual mode
  3            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/javaws   1061      manual mode

While I was making the package this little guy popped up. Don't fret. I think it was meant to take me to the website or something similar. I don't like the sight of that /root/ thingy though -- what's oracle thinking of us punters?