O-on-a-stick - a standalone, drag-and-drop implementation of O

O-on-a-stick - a standalone, drag-and-drop O for Mac OS X

Introduction :
O-on-a-stick is a standalone, drag-and-drop implementation of Alwyn Jones' molecular-modelling program O. It is a droplet that allows Mac OS X users to use O without having to install the program and its dictionaries, and without having to know about Unix command-line instructions. It is particularly useful for occasional users and for those who would just like to look at the results from servers that output results as O tarballs (for examples of some of these servers in Uppsala, see the bottom of this page).

System requirements :
Mac OS X v10.4 or later. Universal binary - Intel or PowerPC.

Usage :
Drag and drop an O file on to the application, and O will open in the parent folder of the file, then execute the O file.
Drag a folder, and O will open in that folder, awaiting your instructions.
Subsequent file saving will be done to the appropriate folder.

If a folder contains an on_startup file, instructions in that file will be executed before anything else, as usual.
Folders that are extracted from the tarballs from our servers contain on_startup files that do everything that is needed to display the results, so these folders can simply be dropped on to the application.

Double clicking on the application opens a window showing the O version that it contains, along with minimal instructions for its use.

Environment variables :
If you want to use the batch system in O, or if you have stereoscopic hardware, then you will need to set some environment variables for O-on-a-stick. This you do by dropping a file called "o.env" on to the application, and that file should contain environment variable statements with the usual C-shell syntax, eg :
setenv OBAT /mydisk/mydir
setenv OTMP /mydisk/myotherdir
setenv STEREO ON

The application will remember these envs until you download a new version, or drop another o.env file.

Known issues :

It's possible that funny characters in file names or folders may cause problems. Neither O nor O-on-a-stick tolerate spaces in folder paths where they live or work.
The current version doesn't work if your default shell is bash. Until I find a more elegant solution, you can use this bash download, but note that the O batch system doesn't work with bash either.
If you have bash and stereo, you can make use of the stereo by renaming the application from O.app to O_stereo.app.
But the question is whether you really want bash as your default shell. Unless you are a purist programmer, you probably don't, and most likely you got moved to bash against your will when you upgraded your system. If you yearn back to tcsh, you can change back through SystemPreferences/Accounts/right-click-on-YourName. You may need to unlock the option.

Licencing :
Alwyn Jones provides Macintosh versions of O free of charge, and blesses the free distribution of this version.

Download :
The droplet is a single Mac OS X application bundle, which you can download as a compressed tar archive. Simply download to your mac and double-click on the tar file to get your droplet, which you can then move anywhere you want. You can even carry a copy on a memory stick take it on holiday with you (hence its name).

Download latest O-on-a-stick (O version 13.0.0, Build 090421)

Links :

Alwyn Jones O pages

Mark Harris email

Mark Harris Home Page

Thanks to Sveinbjorn Thordarson for Platypus, which was used to create the droplet.

Uppsala servers that output O-tarballs :

EDS, the Uppsala Electron Density Server

AuStrAliS - The Automated Structural Alignment Server

CavitySearch - Find cavities and tunnels in proteins

Morphtician - Morph between protein chain conformations

Visits :