Category Archives: science

IPython notebook custom css

Here is the custom css I use for my ipython notebook. It is not finished but I think it is a great improvement from the default, the biggest change being that I removed the In/Out prompt. There are some changes … Continue reading

Posted in css, python, science | 3 Comments

Compiling Aria2, CNS, procheck and aqua for NMR structure calculation

A quick guide to compiling ARIA 2.2, CNS 1.21, AQUA 3.2 and PROCHECK, under Ubuntu Karmic 9.10 (32-bit) If you use Gentoo linux, you can find aria under sci-chemistry (masked by ~x86). Procheck is in the science overlay (see the … Continue reading

Posted in linux, nmr, science, ubuntu | Leave a comment

Using procheck_nmr on a large number of structures

After a structure calculation with the aria 2.2 software I used aqua and procheck_nmr to assess the result. Although procheck_nmr worked fine on my 20 refined structures (in aria's refine directory), it ran into trouble with the 100 structures after … Continue reading

Posted in nmr, science | Leave a comment

Compiling and installing MolMol under Linux

The molmol software that is available from the website of ETH Zurich does not compile on Ubuntu Linux without some changes. It seems that it is no longer supported by ETH Zurich, but can be downloaded from several other websites … Continue reading

Posted in linux, science, ubuntu | 35 Comments

Drawing structures of organic molecules in (Gentoo) Linux

In gentoo portage, there are several programs to draw structures of organic molecules. The best one is gchempaint. Not in portage, but also very interesting is bkchem. A Gentoo ebuild is available, but needs to be installed from a portage … Continue reading

Posted in gentoo, linux, science | 1 Comment

Some xmgrace tips

Xmgrace is a very nice piece of software to create publication quality figures. Even better is that it stores your data and graph layout options as plain text (which is especially nice in combination with subversion or scripts to edit … Continue reading

Posted in linux, science | 53 Comments

Draw a helical wheel plot from a pdb file

Many programs are available that draw helical wheels from a given peptide primary structure (sequence), assuming a perfect alpha helix. Sometimes it may be interesting to see what the helical-wheel plot of a non-ideal helix looks like. Because I could … Continue reading

Posted in science | 6 Comments