Installing Coot on OS X
From OS X Scientific Computing
Installing a Coot stand-alone pre-compiled intel binary
New:
10.5 Intel
Works on 10.5 intel only: coot-0.5-pre-1-968 for Intel 10.5 only (April 20, 2008)
md5sum: f1604801d9fb6dead28465c041789ed8 coot-10.5-pre-1-968-intel-April20_2008.tgz
10.5 PPC
Works on 10.5 ppc only: coot-0.5-pre-1-968 for PPC 10.5 only (April 20, 2008)
md5sum: 661b23bc57accee0e3f40b88bdb1634d coot-10.5-pre-1-968-ppc-April20_2008.tgz
Older:
Most Current: Installing a Coot pre-compiled binary using Fink
Automatic Install
If you want to simply install coot automatically from my server, read Getting your fink installation to use packages that I have pre-compiled. Then all you will ever have to do is to type the commands
sudo apt-get update; sudo apt-get install coot
This will install coot and its dependencies and the dependencies for its dependencies and so on. Starting from scratch, apt-get installed these packages.
Once you have it set up, it works the same way for coot, cns, ccp4, and all the other fink packages I pre-compiled. To update everything at once, just issue
sudo apt-get update; sudo apt-get install coot
This is by far the easiest way to do things, but if you insist on doing it manually, this too can be done with fink's debian tools:
Manual Install
If you want to install my pre-compiled coot binary, and have installed all of the required dependencies with fink, then you should be able to grab the packages from my web server (using curl or wget, see below) and install them with dpkg -i. Here are some instructions that I hope will work to get you up and running with coot pretty quickly:
To install coot itself, just do this
1. Issue the commands
Download the latest coot debian files (get both coot and coot-shlibs please) from my webserver:
- For PPC
http://xanana.ucsc.edu/fink_10.4/dists/unstable/main/binary-darwin-powerpc/sci/
- For Intel
http://sage.ucsc.edu/fink_intel/dists/unstable/main/binary-darwin-i386/sci/
Double-check that this is the latest version on my server. If you find the above to be out of date, please edit the wiki and fix it. Thanks.
2. Issue the command
sudo dpkg -i coot*.deb
If dpkg warns of missing dependencies, use fink to install those (most are in the "unstable" branch of fink), and then return to step 1.
If you want to compile coot, first do this
1. Dowload my ccp4-onlylibs-dev debian file:
curl -O http://xanana.ucsc.edu/fink/dists/local/main/binary-darwin-powerpc/ccp4-onlylibs-dev_5.99.5-1_darwin-powerpc.deb
2. Install it by issuing the following command from the directory from which you just downloaded the file:
sudo dpkg -i ccp4-onlylibs-dev_5.99.5-1_darwin-powerpc.deb
(You actually only really need to do this if you want now or in the future to compile coot. If you are content to simply install coot binaries, you don't need the ccp4-onlylibs-dev pacakge (it contains only static libraries)).
Compiling Coot from source code on OS X
Use Fink. Please.
I've invested a lot of time, and Paul Emsley has invested a lot of time and effort, to get coot and all of its dependencies to compile seemlessly on OS X using Fink. I do my best to keep the package as up to date as possible (at least for 10.4 users. If you have 10.3.x and are willing, you can help me test backward compatibility).
The fink package is described here.
To compile and install the most recently available coot from fink, please do the following:
1. Activate the unstable unstable branch of fink
2. To update fink's database, issue the command
fink selfupdate
3. To compile coot as well as install all of its dependencies, issue the command
fink install coot
This will install a whole bunch of dependency packages, including the following:
Packages required to build coot:
ccp4-onlylibs-dev, glib, gtk+2, freeglut, gtkglarea, guile16, guile16-dev, gsl, libglade2, gtk-canvas (>= 0.1.1-20), libart2 (>= 2.3.16-2), libart2-shlibs (>= 2.3.16-2), guile16-net-http, gtk+2-dev, libgettext3-dev, imlib, libjpeg, giflib, libpng3, gnome-libs-dev, fftw, libiconv-dev, python24
Packages required to build and run coot:
guile16-shlibs, gtk-canvas (>= 0.1.1-20), gsl-shlibs, libglade2-shlibs, guile16-gtk, guile16-www, guile16-gui, guile16-goosh (>= 1.3-2), guile16, guile16-net-http, freeglut-shlibs, libart2-shlibs (>= 2.3.16-2), coot-shlibs (= %v-%r), python24
This is a classic example of why using fink makes your life easier. (Yes, it really did take me 20 attempts to get gtk-canvas right.)
All of the dependencies:
The dependencies in turn each have their own dependencies, so that if we were to start with a fresh install of Coot, you will find that there are about 145 Coot dependencies in fink in addition to those installed with the base fink package.
This is a compelling reason not to install Coot manually. (On the other hand, you might be able to figure out how to install 5 or 6 fewer packages if you spend the next six months experimenting with this yourself.)
As of 0.4, coot works with gtk+2
This permits use of themes for a more OSX-like experience, among other things.
Click on the thumbnail image below to see a full-size screenshot of Coot with a gtk+2 Aqua-like theme.
I've added this theme as a dependency in the coot fink package, but it is off by default. To activate it, issue the following command:
echo "include \"/sw/share/themes/Glossy_P/gtk-2.0/gtkrc\"" >~/.gtkrc-2.0 echo "gtk-font-name = \"LucidaGrande 15\" " >>~/.gtkrc-2.0
The second line makes the font match OS X menus in size and type. (Depending on your resolution and/or X11 setup, you might want to change the number 15 after LucidaGrande to 12, making the font size smaller)
(That syntax is specific to bash and other sh-like shells. If you have tcsh, just edit a file called ~/.gtkrc-2.0 and put into it the following lines:
include "/sw/share/themes/Glossy_P/gtk-2.0/gtkrc" gtk-font-name = "LucidaGrande 15"
If you insist on doing this manually
You are on your own. Feel free to look at my fink installation scripts (and those others have made for many of the dependency packages).
My first attempt left out two dependencies from the list. You may need to issue
fink install librsvg2 guile18-net-http
I'll correct this for revision 2.
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 wrote a coot wrapper shell script that lets you convert xplor/cns maps on the fly (you need to install mapman first) and has a few other 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
Hardware Stereo
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:
(set-display-lists-for-maps 0)
My old and obsolete Coot on OS X page
My Coot on OS X page is linked from here.
