Thursday, February 28, 2013

The Molecule Calculator v.1.1

+Jimmy Charnley Kromann has put a new version of the Molecule Calculator online.  The main new features are:

1. JSmol instead of Jmol.  This means that MolCalc now works on iPhones and iPads.  The only thing that doesn't seem to work there is measuring distances and angles.  This also means that the load button had disappeared.

2. New starting points for molecule building: the default starting structure is still methane, but this can now now be changed to benzene or the water dimer.  It is also possible to search for other structures using common names or SMILES.

3. One can now compute other thermodynamic properties in addition to the heat of formation.

The guts of the calculations are still the same as for version 1.0 except that the MMFF force field is used for pre-optimization instead of the UFF force field.

As always the source code is available on Github

The development of MolCalc is supported by the University of Copenhagen through the Education at its Best initiative (Den gode uddannelse).

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Sunday, February 3, 2013

Getting started with JSmol

Readers of this blog will know I am quite fond of Jmol. But Jmol uses Java, which has some securities issues and doesn't work on iOS.  Luckily, Jmol has been converted to JavaScript to create a program called JSmol.

JSmol accepts all the same commands as Jmol, but setting up a webpage with JSmol is a little bit different.  Here is a very simple page to help get you started and the HTML code and be found below.

The location of the jsmoltest.html is in my home directory while the jsmol code is in a folder called "jsmol" also sitting in my hope directory.  The jsmol folder is created when you unzip the JSmol zip file you can download here.

The JSmol distribution also includes a simple example of having two JSmol windows on one webpage.  You can find that file here.

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This work is licensed under a Creative Commons Attribution 3.0