Coot will read the geometry restraints for refmac and use them in fragment (zone) idealization - this is called “Regularization”. The geometrical restraints are, by default, bonds, angles, planes and non-bonded contacts. You can additionally use torsion restraints by Calculate -> Model/Fit/Refine... -> Refine/Regularize Control -> Use Torsion Restraints. Truth to tell, this has not been successful in my hands (sadly).
“RS (Real Space) Refinement” (after Diamond, 1971 1) in Coot is the use of the map in addition to geometry terms to improve the positions of the atoms. Select “Regularize” from the “Model/Fit/Refine” dialog and click on 2 atoms to define the zone (you can of course click on the same atom twice if you only want to regularize one residue). Coot then regularizes the residue range. At the end Coot, displays the intermediate atoms in white and also displays a dialog, in which you can accept or reject this regularization. In the console are displayed the \chi^2 values of the various geometrical restraints for the zone before and after the regularization. Usually the \chi^2 values are considerably decreased - structure idealization such as this should drive the \chi^2 values toward zero.
The use of “Refinement” is similar - with the addition of using a map. The map used to refine the structure is set by using the “Refine/Regularize Control” dialog. If you have read/created only one map into Coot, then that map will be used (there is no need to set it explicitly).
Use, for example,
(set-matrix 20.0)
to change the weight of the map gradients to geometric gradients. The higher the number the more weight that is given to the map terms 2. The default is 60.0. This will be needed for maps generated from data not on (or close to) the absolute scale or maps that have been scaled (for example so that the sigma level has been scaled to 1.0).
For both “Regularize Zone” and “Refine Zone” one is able to use a
single click to
refine a residue range. Pressing <A> on the keyboard while
selecting an atom in a residue will automatically create a residue
range with that residue in the middle. By default the zone is
extended one residue either size of the central residue. This can be
changed to 2 either side using (set-refine-auto-range-step
2).
Intermediate (white) atoms can be moved around with the mouse (click and drag with left-mouse, by default). Refinement will proceed from the new atom positions when the mouse button is released. It is possible to create incorrect atom nomenclature and/or chiral volumes in this manner - so some care must be taken. Press the <A> key as you left-mouse click to move atoms more “locally” (rather than a linear shear) and <Ctrl> key as you left-mouse click to move just one atom.
In more up to date versions, Coot will display colour patches (something like a traffic light system) representing the chi squared values of each of types of geometric feature refined. Typically “5 greens” is the thing to aim for, the colour changes occurring at chi squared values 2, 5 and 8 (8 being the most red).
To prevent the unintentional refinement of a large number of residues,
there is a “heuristic fencepost” of 20 residues. A selection of
than 20 residues will not be regularized or refined. The limit can be
changed using the scripting function: e.g.
(set-refine-max-residues 30).