Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data. 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, Ramachandran plots, skeletonization, non-crystallographic symmetry and more.
Steps to run the application
$ module add coot-0.8.9a module add gui gui start
And after then in the GUI
Despite the Coot is graphics program, it needs GUI (therefore there is needed gui module). More information about running GUI application in MetaCentrum you can find at the page Remote Desktop
Mostly GPLv3, some GLPv2+, some LGPLv3.