Jhon Thomas wrote:
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.
I doubt that that's what it says in the tutorial.
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..
What is wrong with the geometry?
b) Rotate-translate zone followed by real space refinement and then
regularaization.
You need RTZ? Urgh.
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
No.
or there is another way to control the refinement and regularization
in coot.
A rule of thumb: don't use regularization when you have electron density.
Go to a good area of the model. Triple refine. Are the traffic lights
all green? Good. If not change the weight until they are.
Now work on the problematic region...
HTH,
Paul.
