Download Coot For Linux
Imogene Gilley
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.
In short, just go to -lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/ and pick a suitable binary, e.g.coot-0.9.4.1-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz for a Red Hat Enterprise Linux 7 (or CentOS-7) or newer system.
First of all, SL (Scientific Linux) is a derivative of RHEL, as is CentOS. So all three OSs behave exactly the same.The binaries with "x86_64" binaries are for 64bit systems; the "i386" binaries are for 32bit systems. Since my notebook is 64bits ("uname -a" reports "x86_64" more than once), I download coot-0.7-pre-1-revision-3999-binary-Linux-x86_64-centos-5-python-gtk2.tar.gz. As root, I "cd /usr/local/src" and un-tar. Next, have to find out which libraries are missing. This can be achieved by (note the use of LD_LIBRARY_PATH in the second command - do not permanently modify LD_LIBRARY_PATH !):
Control stereo separation / depth in coot 0.9: the transformation between the eyes is no longer a rotation and is now a shear. Which means that now we don't get part of the map showing up in the left eye but not the right (or vice versa).
This example can be found in the coot scheme sources (the function name is molecule-centres-gui and is in the xxx/share/coot/scheme/coot-gui.scm file). It is a simple function that creates a button box - a button for each coordinates molecule in Coot. It is annotated. Reproduced as coot-scheme1.
This CNS data reading script is a Cootenization of the CN2COOT script written by Joel Bard (it is based on his csh script) and can be used to compare and contrast scheme programming and shell script programming (the coot version is longer to some extent because it does extra error checking).
Here we create a small function to save part of a molecule and add a gui interface, it can be used in the usual way (i.e. with --script on the command line, Calculate->Run Script... or add the script to your /.coot file.
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.
Note also that you will need a recent version of Coot to use this, as it stands. This will not work on stock Coot version 0.4.x. You can enable this for use with 0.4.x if you update/replace your xxx/share/coot/scheme/coot-gui.scm file from here.
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.
Q: I want to prepare scripts to run coot functions like water picking or rotamer fitting in command line. Therefore I am looking for some examples of simple coot scripts, e.g. load ref.pdb, load ref.mtz, fft create map.
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.
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:
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?
A: Coot does not create a /.coot file for you, but will read it if it exists. Likewise, /.coot.py in which you can write python commands./.coot-preferences is a directory in which all .scm files and .py files are executed. coot-preferences.scm and coot_preferences.py there are generated by using the Edit -> Preferences dialog (and thus it overwrites older versions - hence the warning).
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: The other language is a form of Lisp, called Scheme. You can learn about programming python in many ways of course (not least the python tutorial, which is what I read first). The coot python extensions are described in the documentation. There is a standard trivial formatting change that has to be made to get the syntax right for python, see "Python Scripting" [[1]]. There is a growing collection of coot scripts in this Wiki article.
Q: We've noticed a new behavior in real space refinement in coot 0.8.1 whereby dragged atoms are more tightly restrained to their initial positions than in earlier versions. This seems to be described in the release notes by:
Q: This structure has been solved and refined using phenix in the hexagonal setting of space group R 3. There is one copy per asymmetric unit in R 3. As you can see from the attached image, coot is rendering some but not all of the symmetry mates.
For about 20 years I maintaned a coot package in fink. The standalone coot package was in fact based on fink as well. Homebrew is now miles ahead of fink, both in terms of ease of use, and in terms of running natively on "Apple Silicon/M1x" processors. In addition, fink had fallen far behind with respect to maintaining packages upon which coot relies for its GUI functionality. For that reason, I recommend installing Homebrew (which can peacefully coexist with other package management systems).
If you are using Coot 0.6.2, you must install RCrane separately. To do this, first unzip rcrane.zip. If you are installing RCrane for all users of the computers, it is recommended that you put the RCrane directory within the Coot installation directory (e.g. /opt/coot/rcrane or C:\WinCoot\rcrane). If you are installing RCrane for only yourself, you may put the rcrane directory anywhere within your home directory (i.e. /home/name/Documents/rcrane or C:\Users\name\Documents\rcrane).
If you are using Coot 0.7, edit the rcrane.py file within your .coot-preferences directory. In Linux and OS X, this file is located at /.coot-preferences/rcrane.py. In Windows, this file is located within the WinCoot directory at WinCoot/.coot-preferences/rcrane.py. If the file does not exist, create it. Add the line
rcane.createRCraneMenuWithCheck()
to the file.
There are a small number of options that control how RCrane operates. Note that you do not need to set any of these options to use RCrane with the default settings. To change the options, first install RCrane (see TO AUTOMATICALLY LAUNCH RCRANE EVERY TIME COOT IS STARTED above). Next, edit the rcrane.py file within your .coot-preferences directory. In Linux and OS X, this file is located at /.coot-preferences/rcrane.py. In Windows, this file is located within the WinCoot directory at WinCoot/.coot-preferences/rcrane.py. If rcrane.py contains a run_python_script line, all setting commands must be added *after* that line.
RCrane is included with Coot 0.7 and newer and cannot be uninstalled. If you are using Coot 0.6.2, you may prevent RCrane from running when Coot is started by deleting the rcrane.py file within your .coot-preferences directory. In Linux and OS X, this file is located at /.coot-preferences/rcrane.py. In Windows, this file is located within the WinCoot directory at WinCoot/.coot-preferences/rcrane.py. To completely uninstall RCrane from Coot 0.6.2, delete the RCrane directory as well.
Our intention is not to providein-depth model building support here at SSRL, but to offer an easy-to-use graphicsprogram so that users who have collected data here can quickly look at theirmaps. For example, if a MAD data set hasbeen collected and roughly phased using our solve script, the user may wish toquickly check the quality of the resultant maps to determine whether additionaldata should be collected to improve the solution. To this end, we have found the program COOTto be very easy to run and inspect electron density maps with no priorknowledge of the program.Coot is molecular graphics program developed in Yorkand is used for model building, model completion and validation. It has some features that resemble those ofTurbo-Frodo, O, Quanta and XtalView's XFit, such as pull-down menus (see the image below), however Coot does not do many aspects of structure representation. Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, and Ramachandran plots. It also has a very robust superposition algorithm.Screen capture from COOT showing a molecule and electron density.
Files, References and DocumentationCoot reads coordinate files in pdb format, and can also read pdb files which have been compressed with gzip. Coot reads maps in CCP4 format (such as those generated with FFT). Coot is also able toreads mtz files and can either calculate maps from data columns in the mtz file specified by the user, or it can automatically generate maps from mtz files containing map coefficients with column labels FWT, DELFWT, PHWT and PHDELWT (such as those produced by REFMAC).
ReferenceThe reference for the coot is:Emsley P, Cowtan K (2004). Coot: model-building tools for molecular graphics.Acta Crystallogr. D60, 2126-2132.
If using "SSM Superposition", please cite:Krissinel E, Henrick K (2004). Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions Acta Crystallogr. D60, 2256-2268.
DocumentationIf you have detailed questions about these programs, please refer to theCOOTdocumentation, available on-line.In order to get you quickly startedwith Coot so that you can look at your MAD maps, here are some of the maincommands you might need to know. This isnot meant to be a detailed description of how to build you model or fit yoursequence to the electron density. If youwish to continue using Coot once you leave SSRL we suggest that you downloadyour own copy, go through the manual and the tutorialand have fun!