# Difference between revisions of "Coot"

Coot is a graphics program for building, refining and analysing macromolecular models obtained with crystallographic procedures.

There is a homepage with extensive documentation. The program may be downloaded for Linux, Mac and Windows computers from the primary server (as of July 10, 2009 there's a new site at http://www.biop.ox.ac.uk/coot/devel/build-info.html) or, if that is not available, from an external mirror. The license of Coot is GNU GPL.

# Installing Coot

## Installing Coot on OS X

Please refer to the Installing Coot on OS X page

## Installing Coot on Linux

Installing coot on linux is rather more straightforward than on OS X, because most linux systems are based on gnome and/or kde, and tend to have many of the required components already installed. Most of the other dependencies are also readily available.

### Installation from a distributed binary tarball package

This is the recommended way for those who do not want to delve into the mysteries of compiling and linking a great but complex piece of software. Read the (somewhat outdated, it seems) Coot FAQ to find "Additional Notes" for your operating system.

In short, just go to http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/ and pick a suitable binary, e.g. coot-0.5-pre-1-revision-1003-binary-Linux-i386-fedora-5.tar.gz for a Red Hat Enterprise Linux 5 or CentOS-5 system (Fedora 6 corresponds to RHEL5, thus Fedora 5 binaries are OK). If you prefer a "stable" binary, these are at http://www.ysbl.york.ac.uk/~emsley/software/binaries/stable/.

Then un-tar it under /usr/local/src (or in your $HOME), and establish a symlink (ln -s) between /usr/local/bin/coot and the bin/coot of the freshly unpacked distribution. If you then run coot, and the loader complains that a certain library is missing, just ask yum whatprovides <thatlibrary>  and install the library, again using yum (assuming yum is available in your distribution, otherwise use apt or whatever is there for this purpose). ### Installation on Debian/Ubuntu from debian archive files As an alternative, you might wish to exploit the debain dpkg/apt/synaptic package management system on Ubuntu and other Debian linux distributions using (unofficial) pre-compiled debian packages for coot and its dependencies. (These will be discontinued when official packages become available.) To do so, simply download the deb files and install with the command sudo dpkg -i *.deb  dpkg will complain if a dependency is missing rather than install a broken program. ### Converting to rpm packages You can convert any debian package file into an rpm file using the program alien. I have done this and have made the resulting packages available. ### Installation from source code via autobuild scripts Installation of coot and all of its dependencies are handled automatically through the autobuild scripts. There are two versions: • GTK1 - the old user interface. This script builds coot and all its dependencies. • GTK2 - the new user interface. This script builds coot and most of the dependencies, excluding GTK2. To build Coot, all you should need to do is edit a few settings in the top of the build script, or alternatively specify those settings as environment variables. For example, the following sequence of instructions will build the latest pre-release of the GTK 2 version with python support: wget http://www.ysbl.york.ac.uk/~emsley/build-logs/build-it-gtk2-simple export AUTOBUILD_INSTALLED=${HOME}/autobuild/coot
export AUTOBUILD_BUILD=${HOME}/autobuild/ export LOGS=$AUTOBUILD_BUILD/logs
export NIGHTLY_DEST_DIR=$AUTOBUILD_BUILD export STABLE_DEST_DIR=$AUTOBUILD_BUILD
export build_coot_prerelease=1

bash build-it-gtk2-simple python > build.log


(This script works in bash. For tcsh, replace 'export' with 'setenv' and '=' with ' '.

In some cases you may need to download additional development packages in order to build all the components.

### Installation from source code manually

There are also instructions for Custom building Coot from source code.

# Running Coot

## General Topics

### Stereographic Display

Coot has several options for stereographic display, ranging from cross-eyed and wall-eyed split-screen stereo, to hardware-stereo modes that work with CRT systems and most recently the new Zalman 3-D LCD monitor.

#### Side-by-Side

Either cross-eyed or wall-eyed split-screen stereo mode can be invoked using the "Stereo" menu item under "Draw", as is shown in the image below:

#### Hardware Stereo

Similarly, hardware stereo can be invoked (assuming you have the CRT, correct graphics card, emitter, etc) using the same menu item, by selecting "Hardware Stereo".

#### Zalman Stereo

The first viable LCD monitor for stereographics display is made by Zalman and costs about \$300: Zalman ZM-M220W

The attributes for this monitor have been tested and described rather extensively by Warren DeLano on the PyMOL site. Please read it for important details and suggested purchasing sources.

3d lcd

The coot zalman page describes specifically how to get this to work with coot on Mac OS X, but the instructions should be generalizable to linux and Windoze.