11/30/2021

Coot Software Download Mac

Once run on the victimized machine, COOT ransomware uses a sturdy encryption algorithm (RSA-2048) to lock all files, then sends the private key out to the cybercriminals’ remote servers. It can’t be accessed from there. This is the key that can decrypt.coot file extension files, but unfortunately, it is in control of the ransomware developers. Coot is an open-source (GPL) model-building program written by Paul Emsley. If a recent version of Coot (0.5 or later) with Python enabled is installed on your system, PHENIX can use it as a viewer for map and model files. The path to the Coot executable will be detected automatically if it is already part of the PATH environment variable or is. Coot is a graphics program for building, refining and analysing macromolecular models obtained with crystallographic procedures. However, little are the sources for Mac OS. The Scott Lab Page helps out. They also provide a lot of other Crystallography related software suits for Mac OS. Get your Coot for Mac OS here.

Overview

A reader sent me a link to a posting on the brilliant Crystallography on OS X website highlighting the availability of a stand alone version of Coot for Mac OSX. With considerable help from Nat Echols, we can now build coot automatically every night a new revision is available. Coot is free software, distributed under the GNU GPL. It is available from the Coot web site originally at the University of York, and now at the MRC Laboratory of Molecular Biology. Pre-compiled binaries are also available for Linux and Windows from the web page and CCP4, and for Mac OS X through Fink and CCP4. Additional support is available.

Coot (Linux) is a free (for academics) model-building software used in x-ray crystallography. I found Coot to be easy to learn and more user-friendly than other model-building programs such as O or XtalView.

Coot is NOT a molecular graphics program (ie programs for making pretty pictures for publications). There are plenty of programs for that purpose eg. Pymol, SwissPDB Viewer, or Molscript/Raster3D.

Coot is NOT a crystallographic refinement program. For that check out CNS and CCP4.

Materials

You need to download either Coot (in Linux) or WinCoot (in Windows) and install these.

Follow the links below on how to download and install these programs.

Various Procedures in Model Building using Coot

Using Skeletons in Model Building

  1. Open pdb file of model using File-->Open Coordinates...
  2. Open an mtz file with File -->Open MTZ, CIF or phs... This will pop up a dialogue window for map calculation. To make a 2Fo-Fc map, use the FWT and PHWT. To make an Fo-Fc map, use DELFWT and DELPHWT
  3. Now you should see both model and map in the Canvas. The 2Fo-Fc map is usually colored blue and the Fo-Fc map is colored green (positive density) and red (negative density).
  4. Click on Calculate-->Map Skeleton. In the Skeleton Dialog window, turn skeleton mode On (this will display the skeleton). You can 'Color and Prune', to delete possible side chain points so your skeleton looks cleaner. This procedure creates a skeleton (points and connection) in the map. The skeleton will serve as a guide of where to build atoms.
  5. Put the crosshair in the Canvas to a skeleton point where a continous polypeptide chain could be observed in the map
  6. Open Model/Fit/Refine-->Ca Baton Mode. This builds a Ca atom at the crosshair and connects that to another point 3.8A (distance of Ca-Ca) away. You can change where the 2nd Ca is by choosing 'Try Another' in the Baton window. You can also lengthen/shorten the baton with the appropriate options. When you're satisfied with the baton, click 'Accept'. If you make a mistake, click 'Undo'.
  7. Keep building the Ca frame until there is no clear direction on where to add Ca atom.
  8. In Model/Fit/Refine, choose Ca Zone-->Mainchain. Click on the range of Ca frame e.g. residue#2 and #10 that you want to have converted in mainchain atoms. Coot will process this request (takes a while, ~3min) and spits out a mainchain configuration if it can. Sometimes, the connection you make violate the geometry of mainchain atoms, in this case, nothing will be built.

External Links

  1. Paul Emsley's FAQ on Coot (Download the Linux version here)

Contact

Retrieved from 'https://openwetware.org/mediawiki/index.php?title=Coot_and_WinCoot_for_X-ray_Crystallography_Model_Building&oldid=574042'

ROOT is available on Linux, Mac, and (as a beta release) on Windows.
The latest stable ROOT release is6.22/02 (about ROOT versioning scheme).

There are several ways to install ROOT on your computer: they are all listed in the table of content on the right. Which one is best for you depends on your operating system and usage requirements.In all cases, make sure to always use the most recent ROOT release possible to get the latest bug fixes, features and quick user support.

We distribute pre-compiled ROOT for several major Linux distributions as well as MacOS and (as a beta) Windows.The steps to install a pre-compiled binary are simple:

  1. Install all required dependencies with the system package manager
  2. Download the release for the desired platform and ROOT version
  3. Unpack the archive
  4. Add the ROOT libraries and executables to your environment by sourcing the appropriate thisroot.* script. These setup scripts can be found in the ROOT binary release, in the bin directory.

For example, on Ubuntu 19, a user could execute the following bash commands to install ROOT v6.22/00, after installing all required dependencies:

To avoid having to source thisroot.sh every time one needs to use ROOT, it is typical to add the instruction to.bashrc, .profile or analogous configuration files.Note, however, that sourcing thisroot.sh might interfere with ROOT versions installed with different methods.

Supported by the community: these packages are not maintained by the ROOT team, but by helpful members of the community. Please go through each package manager’s standard channels to report any related issue. If you package ROOT and would like to be added to the list below, please contact us by clicking the letter icon at the bottom of the page.

Conda

For any Linux distribution and MacOS, ROOT is available as a conda package. To create a new conda environment containing ROOT and activate it, execute

More instructions about using the conda package are available in this blog post.

Please report any issues with the conda package here.

Linux package managers

ROOT can be directly installed from the operating system’s package manager in the following Linux distributions:

Fedora

Fedora’s ROOT package can be installed with

More typically, however, users will want more than just the base package. The full list of components can be seen athttps://src.fedoraproject.org/rpms/root/ by clicking in one of the offered versions.To install ROOT with support for python and notebooks, for example, run

CentOS

ROOT is available on CentOS via EPEL. To install ROOT on CentOS, just run

Arch Linux

Coot Software Download Mac

Arch’s ROOT package can be installed with

Gentoo

The Gentoo package for ROOT is sci-physics/root.It can be installed with

Ubuntu and Debian-based distributions

The ROOT team is working on the release of an official .deb package. More news on this topic very soon.
In the meanwhile, ROOT is available on Ubuntu via conda or our pre-compiled binaries.

MacOS package managers

Homebrew

On Mac, ROOT is also available as a homebrew formula.You can install it with

Macports

After installing macports, the ROOT port can be installed with

Pre-built ROOT without dependencies

If your platform mounts CVMFS (as, for example, CERN LXPLUS does),ROOT is directly available as an LCG release.

ROOT installations with minimal external dependencies are available for Fedora, Ubuntu, CentOS 7 and MacOS at:

For example, to set up ROOT 6.22/00 on a CentOS7 machine that already has all ROOT required dependencies installed, just run:

ROOT plus dependencies

On CentOS7, ROOT as well as its dependencies and many other packages are also available as an LCG view:

For example, to set up a full environment with ROOT 6.20/02 on CERN LXPLUS, you can run:

To check what ROOT version is contained in an LCG release, check lcginfo.cern.ch.

Gentoo Prefix on CVMFS

ROOT is also experimentally available in a Gentoo Prefix installationinside the contrib area of the SFT CVMFS repository. To use it from there, run

This will drop you into a new shell where all software from the prefix is available.

ROOT Docker containers for several linux flavours are available at ROOT’s official DockerHub.

For example, to try out the latest ROOT release just run docker run -it rootproject/root.

Users with a CERN computing account can simply connect to lxplus.cern.ch via SSH and start root: the latest stable version is installed as a normal system package.

Coot Download For Windows

Note that certain features (e.g. multi-threading capabilities) are not available on lxplus.cern.ch (or, equivalently, lxplus7.cern.ch) due to incompatible versions of certain ROOT dependencies on CentOS7. You can use lxplus8.cern.ch to get access to CentOS8, where this limitation is not present.

In case no other installation method is available, or if you want full control over the options ROOT is built with,it is possible to compile ROOT from source. See Building ROOT from source for detailed instructions.

Coot Software

As a quick summary, after installing all required dependencies, ROOT can be compiled with these commands on most UNIX-like systems: