There is crude refinement for pathological cases, and fine refinement for not to bad cases.
If the gap is big that needs to be bridged is big, say around 2-3 Angstrom, you should determine which residues are allowed to move, and use FIXCA or FIXRNG on all others. Now use the CRUDE option. Give CRUDE a range that includes at least one of the FIXed residues at either end. After this CRUDE, the gap is small and you can proceed as if it was always small. If the gap is still big after the CRUDE option, you should either think to see if the gap actually can be closed, or run CRUDE again, but now with 10 times more steps.
If the gap is small, you should first determine how many residues at either side of the gap can move around a bit. FIX the rest of the molecule, either with FIXCA if you are not sure that everything is perfect, or with FIXRNG if you are sure about the rest. Now REFI the range that you selected as involved in closing the gap. However, it is wise to include one FIXed residue at either side of the range you selected. This makes the REFI procedure much faster, and it assures that the bond lengths and bond angles between the refined and the non-refined residues are also fine afterwards.
Such loop closure is a very crude thing. So you better save the soup or the whole status with SAVSOU or SAVSTA respectively before you perform the closure.
If loop closure seems to require that certain residues are turned around, you better do things by hand... CRUDE gap fixing only works well if the residues need to traverse rather straight paths to get near each other.
If the gap is too big, WHAT IF will not even attempt to close it and it will suggest you a solution.
Normally, REFI stops if the Z-scores on bond lengths and bond angles are below 1.0. There is a parameter to change this criterium. However, if you really want to refine much further, you get nonsense unless you use the FIXCA option, and even in that case, over-refinement will not make things better.
If you see the Z-scores get constant or nearly constant from run to run, you better stop the refinement (with Control-C), because it most likely means that your molecules are getting worse.
Ideally, you first refine with a FIXCA on all residues, and when that no longer improves the situation, stop the run, use NOFIX and complete the regularisation with a short REFI run in which all atoms are free.
It regularly happens that REFI makes things better at first, but if you keep refining after convergence was reached, things will get worse again. I do not yet have any idea why this is.
You will be prompted for an amino acid range. There are no restrictions to this range, except that all residues, nucleic acids, drugs, etc., in this range should be present in the topology file. Things that WHAT IF does not understand just will not be refined.
The refinement will proceed in NCYCS cycles of NITS iterations. The parameters relevant to this refinement can be set using the PARAMS command.
Many parameters can influence the behaviour of REFI. See the FIX... options, the ANCHOR option and the PARAMS menu.
If you were to use REFI again, the now new coordinates will become the guiding coordinates where towards all atoms will be pulled back.
If, however, you use REFCNT, the coordinates that WHAT IF stored during the last execution of the REFI option will be used.
Dont execute very different options between REFI and REFCNT. Many options alter the guide coordinates for their own purposes. It is best to execute REFI and N times REFCNT in a continuous chain of options with only some of the simple GRAFIC options (GRABB, SHOALL, etc.) inbetween.
This means that if you fix atoms, you should do more cycles if you want the atoms that are fixed to move less. That sounds paradoxal, but it isnt. Later during REFI most big problems are solved, and only small corrections are still needed. The full stepsize that moves atoms back to their original position will however still be used. The force that keeps atoms at their original positions will thus relatively get stronger later during the REFI or REFCNT run.
Be aware that this is a crude option. It might be better to simply use the interactive TORS option on the two cysteine side chains to put the S-gammas at the optimal positions.
There are also some good reasons why using protons is better. The most important usages for protons are NMR analyses and energy minimisation and molecular dynamics.
If you want to work with protons, you need a topology file with protons. You find that file in the dbdata directory and it is called TOPOLOGY.H. Copy that file to your local directory and call it TOPOLOGY.FIL. If you want WHAT IF to always work with protons by default, ask your WHAT IF manager to remove the old file TOPOLOGY.FIL in the dbdata directory and rename the file TOPOLOGY.H to TOPOLOGY.FIL in the dbdata directory.
With the exception of the GRAHYD option in the GRAFIC menu, non of the proton related options can work if you dont have the proper topology file available to WHAT IF (either in the local directory, or in dabdata).
You can give the magical command
SETWIF 339 1
to force WHAT IF to use the slow but much better proton position calculation method.
829 What forces to include in the refinement. 124 Number of cycles. 125 Number of iterations per cycle. 842 100* desired final Z-score. 76 Z-score above which individual errors are listed. 61 Level of detail in REFI output. 50 Refine bad atoms too or not. 113 Force to be used if FIX or ANCHOR options have been used. 112 Always anchor the ends of residue ranges in REFI.Use SETWIF <PARNMB> <VALUE>
to change parameters the fast way.
WHAT IF will loop over the two ranges, and it will give atoms in the second range that are less than the cutoff value away from the corresponding atom in the first range the same coordinates as that corresponding atom in the first range. In case you give CA, only C-alphas will be condired; in case you give BB the whole backbone will be considered, and if you give ALL, WHAT IF will look at all atoms. If you give ALL, and the two ranges are not covalently identical, WHAT IF will do its best to guess what you really want, but that is only a best guess.
This option is of course nonsense, scientifically speaking. However, if you want to superpose two structures, the plot often becomes a total chaos. If however, you can hide all dirrerences that are smaller than, for example, 0.5 or 1.0 Angstrom, you can often make the plot much clearer.
May I suggest you study the options SAVSTA and RESSTA in the SOUP menu before you use SNAPIT?