Category Archives: linux

Mounting a remote directory using ssh

In the checklist below, the "local" pc is the one you are working on, and the "remote" pc is the one that has the directory you want to access. Generate an ssh key for passwordless login, as follows: local: run … Continue reading

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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

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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 | 41 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 | 55 Comments

Splitting a pdf-file under Linux

The pdftk command (pdf toolkit) can perform many operations on pdf files. One that I found useful is extracting certain pages from a pdf file. For example, to extract page 115-142 from input.pdf and save it as chapter5.pdf, the command … Continue reading

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Installing avrdude on a Gentoo box

This post describes how to install avrdude on Gentoo Linux. Avrdude is software to "burn" a program on a microcontroller. I am using a MyAVR programmer board that is connected to the parallel port. I started out by following the … Continue reading

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Installing DSL on an old (16Mb RAM) laptop

A couple of days ago, I removed the dust from my old laptop, and installed Linux on it. I chose to install the damn small linux (dsl) distro and encountered some (small) problems during installation, which I describe below. Since … Continue reading

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Useful things in (gentoo) linux

This is just a collection of some commands and tricks that I keep forgetting Search and replace in multiple files, using perl perl -p -i -e 's/search/replace/g *.txtperl -p -i -e 's/search/replace/g *.txt Change the color of a (gentoo) bash … Continue reading

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Convert a LaTeX-created .pdf file to MS-Word .doc

Unfortunately, sometimes people want me to convert some beautiful LaTeX to MS-Word. I first tried to convert the .tex to .html and open the html file in MS-Word, but the result was usually a big mess. The best way I … Continue reading

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