Program (on Mac) to show 3D protein structures?
Jmol: how to install

Here are instructions for getting Jmol to run on a Mac (or with a slight variation in the runtime file you need to download and the security warnings, on a PC). 


Download Jmol from
https://sourceforge.net/projects/jmol/files/latest/download?source=files  
The name of the file will be something like Jmol-14.29.16-binary.zip. Double-click to unzip.  
The unzipped folder has a confusing variety of files. This is because most are used for setting up web pages with Jmol embedded. However there is a double-clickable desktop application without any icon and the unpromising name of: Jmol.jar. When you double-click to launch it you will most likely get a message as shown below (1):




To get round this you must either control-click or right-click and select `Open With > Jar Launcher as shown above (2).

Click ‘Open’. (Next time it will just launch without right-clicking.)


Now, in my case the program launches because I have the Java runtime installed on my machines, but you will probably have to download and install this.  
Go to the Oracle Java website at http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html
Download and install the appropriate Java SE Runtime Environment, e.g jre-8u172-macosx-x64.dmg
Try launching jmol.jar again. It should work this time.  


Jmol: how to use

Because of their emphasis on Jmol in relation to the web, the developers of Jmol do not provide an easy entry to the desktop program. However you can find a clearly illustrated series of web tutorials at the MSOI Centre for Biomoleclar Modelling. I’d highly recommend this as a starting guide.

Although I am not going to describe how you can visualize particular amino acids as that is part of the poster’s project and can be found in the instructions. there are a couple of pointers I would make about things that are not entirely obvious.


After you have loaded a protein from the file menu, you will probably want to change its representation, not least because it may be surrounded by red balls (oxygens from water). To do this you need to right click (or click on the Jmol text on the bottom right) and go through two levels of submenus to select an appropriate representation, as shown.





In order to make the selections you require you will need to issue commands in the ‘Console’. This can be selected from the File menu: