Do you know this problem: A paper draft has seen changes by many different authors over an extended period of time and now has a bunch of old figure files that still lurk around in the file system but that are no longer relevant to the manuscript? Here’s a way […]
scientific writing
24 posts
Many journals require you to submit figures associated with a article manuscript in a way that does not allow for a separate graphics subdirectory. However, many people work with LaTeX such that they have a separate directory which is only for graphics generation and then include the resulting PDF files […]
In case you use your I, Librarian database together with BibTeX, you will most probably will be annoyed by the recurring task to export your current literature database to a bibfile. Here is a short script that dumps all entries from a I, Librarian instance to your command line. So […]
Using different programs for diagrams within one single document can be a never ending story of unmatching graphics. For example, matplotlib used a different interpolation method for colormaps than pgfplots. Disregarding alpha components, the following script produces a matching colormap. Just specify the matplotlib colormap name as command line argument […]
Sometimes chemical structures are not enough to present your data. Instead of adding tables, you can graphically annotate compounds. For example the results of a charge fitting procedure (hence the decimal values for electron charges) can be visualized as follows Here is how to do it: Download the indigo toolkit […]
As usual, a new day in the lab requires new function plots. But now that you have a different data source, you may observe some potential pitfalls with pgfplots.
Daily backups are always a good idea – but sometimes a convenient accessible history is more helpful than having to work with raw database dumps. For I, Librarian backups are rather easy. This document describes the workaround necessary in order to introduce shadowing and change history for the database used […]
Although mendeley is convenient, it lacks proper support for documents created using version control systems like subversion. Usually, it is a bad idea to put the BibTeX file of the project under version control. Using the API of mendeley, there is way to Avoid duplicate entries with the same doi […]
If you get errors similar to the following ones: Paragraph ended before \@@href was complete. or File ended while scanning use of \@@href or output related to problems with \href@split, you should check your .bib file for entries like this Pages = {{2879-2882}}, In general, they are perfectly valid (although […]
Unfortunately, there is a bug in the current debian package of the achemso package for LaTeX. Every time you use \ref{key}, you will only get “1” instead of “Figure 1” although the latter output is the expected one. On top, the current gentoo package is up-to-date, hence it does not […]
Under gentoo, the libertine font package may be installed using the sunrise overlay. If you prefer updating your local texmf by hand, you may obtain errors like these when executing the commands in missfont.log: $ mktexpk --mfmode / --bdpi 600 --mag 0+480/600 --dpi 480 LinLibertineT-tlf-sc-t1--base mktexpk: don't know how to […]