After working on atomic positions when building residues in density, or
after making mutations that need manual intervention, you might end up
in a situation where atomic bond lengths and bond angles are no longer
reasonable. The refine options can help in this case.
There is crude refinement for pathological cases, and fine refinement for
not to bad cases.
The command CRUDE will prompt you for a residue range. It will then very quickly
but very crudely bring all bond lengths in this range between 1.3 and 1.75
Angstrom. No matter how bad they were initially. Bond lenghts of up to 1000 Angstrom can
be fixed with this option. Its crudeness is proportional to
the crudeness of the input structure. If there are gaps that are greater then
5 Angstrom, you might ocasionally end up R amino acids.
The command REFI activates the rather carefull regularisation. This option
was rewritten in jan-96, and rather than doing a full matrix optimisation,
it now works a bit more like an energy minimiser.
You will be prompted for an amino acid range there are no restrictions to
this range, except that all residues, drugs, etc., in thsi range should be present
in the topology file.
The refinement will proceed in NCYCS cycles of NITS iterations. The parameters
relevant to this refinement can be set using the PARAMS command.
The command REFPAR allows you to see or change the parameters needed by the
REFI option. The following parameters can be changed:
NCYCS Number of cycles.
NITS Number of iterations per cycle.
SFT1 Cycle 1 will be stopped once the maximal atomic shift is
smaller than this parameter.
SFT2 As SFT1 but for all other cycles.
ESDB Desired RMS error in bond lengths.
ESDA Desired RMS error in bond angles.
The command FIX allows you to pick atoms that thereafter will not move at
all when CRUDE is being executed, or will only move little in REFI.
The command NOFIX will remove all previously set FIX marks.
The command FIXCA will fix all alpha carbons in the range to be refined.
For CRUDE this fix is absolute. For REFI it means that the movements of
alpha carbons will be damped strongly. Be aware that the GROMOS menu also
offers the possibility to do refinement with fixed alpha carbons.
The command ANCHOR will fix the alpha carbons of the two extreme residues of
the range you want to refine. This option is very much advised if you
are refining small parts of molecules; both in CRUDE and in REFI.
The command NOANCH switches the ANCHOR mode off.
The command PARAMS allows you to see or change the parameters needed by the
REFI option. This option is identical to the REFPAR option. The latter is
only maintained for compatibility purposes.
NCYCS Number of cycles.
NITS Number of iterations per cycle.
SFT1 Cycle 1 will be stopped once the maximal atomic shift is
smaller than this parameter.
SFT2 As SFT1 but for all other cycles.
ESDB Desired RMS error in bond lengths.
ESDA Desired RMS error in bond angles.