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.


Download
Register using this page (if you're an academic user): http://shelx.uni-ac.gwdg.de/SHELX/register.php
To find the answer to the xtal question, use google.

You'll then receive an email with a password. Now go to
http://shelx.uni-ac.gwdg.de/SHELX/download.php
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 http://shelx.uni-ac.gwdg.de/~gsheldr/bin/test_data/: cdetutorial_andrea.zip, ciftab_templates.zip, difficult_sad.zip, ltests.zip, pn1a.zip


Installation
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 cdetutorial_andrea.zip ciftab_templates.zip difficult_sad.zip ltests.zip pn1a.zip ~/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.

1 comment:

  1. Thanks so much. It has been of great help.

    ReplyDelete