![]() Julen Larrucea on Troubleshooting OpenStack the cool way: ini_comparer.Aung Phone Maung on Checking the optimum cutoff for QE.Hamid AitMhid on Checking the optimum cutoff for QE.Omer on pw2cellvec: monitor vc-relax convergence in QE.Selim Romero on cube2xyz: convert cube data to xyz and slize segments/planes.Parsing OpenStack config files with susti.The easiest way to install OpenStack: BOMSI GUI.Troubleshooting OpenStack the cool way: ini_comparer.py.By the end of this tutorial, you will be familiar with the most commonly used Jmol commands and how to use. The best way to think about using Jmol is to imagine what you would actually like to do, then figure out which scripting commands fit your purpose. ll4D: the LXD(LXC)-LAMP environment For Development Jmol's seemingly endless list of commands can make it seem like a daunting tool to learn.I needed to add several hacks in order to for example, create proper balls and sticks, but finally I managed to get figures like this one: It is usually convenient to gather commands in script files. I found it to be quite good, but getting some acceptable (nice) figures is not so straight forward, and the defaults don’t include, for example, proper sticks for the bonds! You are now ready to enter Jmol commands into the Jmol Script Console. The first one was by using the Atomic Simulation Environment or ASE, which has endless possibilities for any kind of modeling calculations, and can also be used to automate molecular figures. If you are new to Jmol scripting, it is suggested that you spend time. I am one of these people, so I was researching how to avoid that tedious opening > clicking > clicking > typing name > clicking > more clicking. For a comprehensive list of Jmol commands, see the Jmol Interactive Scripting Doc. 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. Starting with Jmol 11.6, you can also use the script command with the APPLET option to send scripts to one or more applets. 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, …). 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. of the graphics machine, send data to the WebGL, and execute draw commands. 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. Test your JavaScript, CSS, HTML or CoffeeScript online with JSFiddle code. Copy and paste your script into the editor window. ![]() On the Editor Box that pops up, click 'script' then click 'clear' so you have an empty window. One of the things I like most from being a computational chemist, is the possibility to automate tasks by using scripts. Opening a Script in Jmol Once you have your script, run it as follows: Open Jmol.
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