Tag Archives: Jmol

shrink_traj v0.4: xyz with unit cell info

One of the limitations of xyz coordinate format is generally the lack of extra information, such as the unit cell dimensions or lattice vectors. This can become annoying when we are working with solids, or we want to check whether our molecule has enough space around, in order avoid interaction with its own periodic replicas.
The new shrink_traj v0.4, includes the possibility to include the Jmol readable unit cell info the second line of the xyz file. This way, we can shrink a trajectory (or keep it as it is), and generate a new one which allows us to visualize the unit cell.

It also contains an option to insert Jmol commands directly into the xyz file, such as “background white”, which enables the possibility to customize the view of the structure/trajectory. Continue reading

Automate molecular figures

One of the things I like most from being a computational chemist, is the possibility to automate tasks by using scripts.
There is usually no problem for automating almost anything, but unfortunately, there are a few tricky to automate tasks, for example, when it comes to generate atomic/molecular figures.
Let’s think that we have to calculate the energies of a lot of different molecules, and after doing that, we certainly need to check the results. We can easily “grep” the total energy (or any other numerical/ASCII value) from the output files but usually, the only way to take a look to the geometry of the structures is by going trough all the outputs and opening them with a graphic molecular viewing program (such as molden, vmd, xmakemol, jmol, …). This task can be quite painful, specially for the geek people who does not like wasting their energy using the mouse if it is not completely necessary. Continue reading