BV_PubChem

Download molecules directly from Pub Chem

BALLView provides direct download of molecular structures deposited in the Pub Chem database. The dialog can be found in the main menu

{{{ File -> Open -> PubChem }}}

Enter coffein in the PubChem line edit and press the PubChem button.

The Results window will fill up with all entries matching your query. Double click onto a result and a structure sketch and a detailed description are provided.

Pressing the Add button will create the highlighted result and add it as a system to BALLView's Structure window.

In most cases the Pub Chem database offers molecules without any hydrogens, thus H-atoms have to be added.

For non proteins, this task is performed by the Saturate Hydrogens method {{{ Tools -> saturateHydrogens }}} This method assumes the bond orders to be are correct and adds hydrogens (if missing) according to free valences.

Finally, we have to optimize all atom positions. This task can be performed by BALLView's Quick Optimizer. Highlight the system who's atom positions you want to optimize and press the Quickly optimize button.