Hello paul I am completley naive with coot.I am using the coot present with the ccp4-6.0.2, which is an older version of coot. I am facing very difficulty in optimising the geometry of the model in coot.I follow the tutorial for optimisation of the geometry. i go like this.
1) a) real space refinement of particular zone and then regularization the zone.....real space refinement puts the selected model parts in the density and regularization again optimizes the model part. but, its very hard to maintain the perfect geometry for the model this way...... b) Rotate-translate zone followed by real space refinement and then regularaization..... but, this i am facing very difficulty in regularization.. I always set the coot real matrix weight around 20. Is this is the correct protocol or there is another way to control the refinement and regularization in coot. thnaks in advance Regards jhon
