Coot is a graphics program for building, refining and analysing macromolecular models obtained with crystallographic procedures.
There is a [http://
www. biop. ox.ac.uk/coot/ homepage] with extensive [http:// www. biop. ox.ac.uk/coot/docs .html documentation]. The program may be downloaded for Linux , Mac and Windows computers from the [http:// www. ysbl. york.ac.uk/ ~emsley/software/binaries/ 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 [ftp:/ /turn5.biologie.uni- konstanz.de/ coot external mirror]. The license of Coot is GNU GPL.
==Installing Coot on OS X==
Please refer to the [http://sage.ucsc.edu/xtal/wiki/index.php/Installing_Coot_on_OS_X Installing Coot on OS X] page
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) [http://www.ysbl.york.ac.uk/%7Eemsley/coot/coot-faq.html 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/.
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) [ http:/ /diablo. ucsc. edu/~wgscott/debian/coot_hardy/ 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 [http:// diablo.ucsc.edu/ ~wgscott/ debian/ rpm/coot/ resulting packages] available.
=== Installation from source code via autobuild scripts ===
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 Powermate dial can be used with coot. One could just assign the rotations to +/-y keys and be done with it, but this script gives you a way of having positive and negative rotations in all three cartesian directions. The F1 key is mapped to positive rotation, the F2 key to negative rotation, and the F3 key permits you to toggle through x, y, and z, on successive key presses. I then map F1 and F2 into the ordinary rotations on the powermate (using send key equivalents) and then I map F3 into the single click on the dial, making it easy to toggle through x, y and z. The press-and-rotate options remain available; I map these into scroll up and down, and put them on the slowest response setting, which makes contouring density easier to control than it is from my mouse scroll wheel.
===Example Scheme Script 7: Applying arbitrary value to "B" factor column ===
For (re-)colouring maps blue:
# bluefy last map def blue_map_func1(): ls = map_molecule_list() ls. reverse() for map_mol in ls: if (not map_is_difference_map(map_mol)): set_map_colour(map_mol, 0.1, 0.5, 0. 68) graphics_draw() break add_key_binding( "Blueify the Latest 2FoFc Map", "b", lambda: blue_map_func1())
# bluefy all 2FoFc maps def blue_map_func2(): for map_mol in map_molecule_list(): if (not map_is_difference_map(map_mol)): set_map_colour(map_mol, 0. 1, 0.5, 0.68) graphics_draw() add_key_binding("Blueify all 2FoFc Maps", "B", lambda: blue_map_func2())
To (re-)colour coordinate molecules yellow:
# yellowify last coordinate molecule # Note: this may overwrite the 'usual' short-cut of 'y' to add a terminal residue def yellow_coords_func1(): ls = model_molecule_list() if (len(ls) > 0): set_molecule_bonds_colour_map_rotation(ls[-1], 20) graphics_draw() add_key_binding("Yellowify last coordinates", "y", lambda: yellow_coords_func1())
# yellowify all coordinate molecules add_key_binding("Yellowify all coordinates", "Y", lambda: (map(lambda imol: set_molecule_bonds_colour_map_rotation(imol, 20), model_molecule_list()), graphics_draw()))
==Python to Scheme and return==
Here some simple rules how to translate from Scheme to Python. To translate the other way around, i.e. Python to Scheme, just turn the rules around:
replace all '-' with '_' (except in equation when you need arithmetic '-' minus signs)# move the brackets around the argument(s)# separate multiple arguments by commas rather than spaces# replace 'define' for functions with 'def' and for assignments with an '='
# Make sure to use indentation for the function content [Python is indentation sensitive] and a ':' after the function definition.
Alternatively, if you use gnome or xfce4, you can open the theme manager and just make it open the downloaded Glossy_P tarball, and it should add this as a theme.
How can I get involved with Coot development?=
Join the [[Coot Janitors]] project. This is a project to get new people involved in improving Coot, by acting as a clearing house for simple tasks which need doing, and providing documentation for doing them.
Assorted questions and answers ( from the mailinglist) =
It should be noted that the answers ("A") are from Paul Emsley himself (and were maybe slightly edited).
A: Yes this fails. Hydrogens are named differently to SHELX hydrogens. In principal this could be made to work if the dictionary was reworked to use SHELX hydrogen names. This would also fix the chi angles problem too of course.
==Image quality on NVidia cards==
(apply density-at-point (imol-refinement-map) (rotation-centre))
There is no user access to the peak integration code of coot as yet.