Installing Coot on OS X
From OS X Scientific Computing
Installing a Coot stand-alone pre-compiled package
This is nothing more than a repackaged fink installation, combined with an automatic nightly build system. It should have the most current bleeding-edge pre-release. If you need something more current than what is in fink, or you just don't want to install fink, then use this.
Compiling Coot from source: Please use Fink
By far the most straightforward way to compile Coot from sourcecode is to use the Fink package management system. Paul Emsley and I have invested considerable time into getting this to work well, and it is the best pathway to obtain the most stable version. Once you have a working fink installation, all you have to do is issue the command
fink -y install coot
whenever you require the latest version.
A more detailed description on how to install coot with fink is linked here.
Installing a Pre-Compiled Coot using Fink
If you have set up fink to use my pre-compiled debian binaries, you can speed up the process considerably. Just issue the command
sudo apt-get update; sudo apt-get install coot
A more detailed description on how to install a pre-compiled coot with fink is linked here. Be sure to use the so-called "unstable" branch of fink to get the latest pre-releases of coot: How to Activate the Unstable Branch
The Official Coot Wiki
Making Ray-Traced Images with Coot
The fink package for coot recommends installing raster3d and/or povray. When this is set up, simply pressing on the "F8" key on your keyboard will result in a ray-traced image of the display popping up in Preview. Preview in turn will let you enhance the image, as it comes out a bit subdued by default. The following screenshot shows how this enhancement works. (You can see I tweaked exposure slightly, and gamma a bit, and saturation a fair amount).
Click here or on the image above to see a full-sized screenshot.
Optional Wrappers and Shell Script Enhancements
I also made a Coot OS X applet that allows you to drag and drop a cns/xplor or ccp4 mapfile or any other coot-compatable file (mtz or pdb file, for example). Using the File > Get Info dialog, you can program this applet to open all .map and all .mtz files, if you want to, making these files double-clickable.
Download the Applet (requires a separate working coot installation)
Stereo Display options
LCD Stereo: Zalman monitor
The least expensive and perhaps best option for stereographic display is the new Zalman LCD monitor.
Please refer to the COOT wiki page that describes how to set everything up.
Please note: Apple broke stereo support in earlier versions of 10.5, but with 10.5.6, it is now reported to be working correctly.
Apple now supports stereo in a window with Apple's implementation of X11, so coot should be able to work with this if you have the appropriate hardware (CRT and video card, as well as transmitter and glasses). I do not, so I will have to leave this for someone who does.
To get this to work, you need to have the latest version of Apple's X11.app installed, and then each user needs to issue the following command:
defaults write com.apple.x11 enable_stereo -bool true
Hardware stereo on coot requires you compile with gtkglext1. The fink version of coot forces you to do so, so it should just work.
Side-by-side crosseyed stereo
As of version 0.2, coot can also have a side-by-side cross-eyed stereo display. Then all you have to do is cross your eyes and you see stereo. Never mind that this will destroy your vision and eye muscles, it works really well. I only got the map displayed on one side until Paul suggested including the following in my .coot(rc) startup file: