==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 ===
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)=
Q: I am sure this exists somewhere through scripting in COOT, but can I apply NCS edits to only a subset of NCS copies? In other words, can I tell coot which are NCS related chains, and which aren't. I am working on this nightmarish case of asymmetrical homodimers, where the sequences are very similar, but the structures are not, so I need to tell coot which chains are actually related to each other.
A: Nightmare. If you have a recent [1632 or later for the scheme version, 1646 for the python version] Coot, you can do this:
There is also a GUI to activate this feature under Extensions -> NCS.
Description of problematic situation: I am using [[SHELXL]] to refine my 1.2 Å data and I am refining the hydrogen atoms. Subsequent rebuilding in coot is difficult though since hydrogens often does not "follow" when you do side chain rebuilding. For the moment I have quit transfering hydrogens to coot and add the hydrogens every refinement cycle, though it would be good I think if I could see them in coot without bothering about wrong positions. So these are my specific questions:
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.
Q: improvement of image quality on machines with NVidia cards?
Q: How to set the default to display symmetry related molecules?
A: Add (set-show-symmetry-master 1) to the appropriate file.
Q: I still have a ".coot" file in my home folder for a few coot preferences that I couldn't find in the new ".coot-preferences/coot-preferences.scm". There is a warning that I should not add commands to this file. So is a "~/.coot" still the proper place to add default commands for coot?
So you have a variety of places. Personally I mostly use ~/.coot.
Q: How do I use "torsion general"?
A: Thanks for pointing out the lack of documentation on this. I'll make a note to add some.
You need to click on the torsion-general icon, then click 4 atoms that describe the torsion - the first atom will be the base (non moving) part of the atom tree, on clicking the 4th atom a dialog will pop up with a "Reverse" button . Move this dialog out of the way and then left mouse click and drag in the main
window will rotate the moving/"top" part of the residue round the clicked atoms
2 and 3. When you are happy, click "Accept".
the "Reverse" button should invert the moving and "base" part of the residue.
Q: I have some peaks in my map which take water or sodium/magnesium or chlorine atom with out giving out any positive or negative density upon further refinement. Is there any easy way of calculating the peak height / number of electrons at a given position, say a mouse click point in coot? Is there any formula to calculate the number of electrons based on sigma level and peak height, as given in difference map peaks in coot?
A: First, go to the
coot wiki and pick up the scheme key bindings.
If you want density information at a given cursor point: point at the blob, press the 'g' key (which recentres on the biggest density under the cursor).
There is no user access to the peak integration code of coot as yet.
It should be noted that the answers ("A") are from Paul Emsley himself ( and were maybe slightly edited).