(Crystallographic Object-Oriented Toolkit) an application that supports model building and real space refinement. This application interfaces with refmac, Phenix, and several other applications. Coot was recognized as the best structural biology application in 2008 by SBGrid.
Usage
To list all executables provided by Coot, run:
$ sbgrid-list coot
Usage Notes
Version 0.9 contains a bug in hardware stereo display mode. To re-enable hardware stereo, run
echo "(set-display-lists-for-maps 0)" >> ~/.coot
A CryoEM workflow tutorial can be found here : https://pemsley.github.io/coot/blog/2020/10/20/Coot-Cryo-EM-basics.html
Installation
Use the following command to install this title with the CLI client:$ sbgrid-cli install coot Available operating systems: Linux 64, OS X INTEL
Primary Citation*
P. Emsley, B. Lohkamp, W. G. Scott, and K. Cowtan. 2010. Features and Development of Coot. Acta Crystallogr D Biol Crystallogr. 66: 486-501.
A little over a decade ago, Paul Emsley, biochemistry professor at the University of Oxford, was looking to ditch his white coat. What he really wanted was to spend more time programming in the computer lab. “I was happy using existing software tools,” said Emsley, who had used O and other tools in his research. “But you go down the pub and think, if only the tool did this, and if only it did that. That festered for years.”
In the late 1990s, Emsley had the opportunity to join the lab of Kevin Cowtan at University of York with the task of implementing software to perform crystallographic “ridge line tracing” in three dimensions, a concept first imagined in the 1970s by Johnathan Greer, now Director of Structural …
