Regularization Overview (980216)
Model regularisation is used to force standard bond lengths, angles and fixed dihedral angles on a model (or part of one). At the end of the regularisation, the user is prompted to accept or refuse the new coordinates. In proteins, start and end main chain atoms remain fixed.
refi_setup <dictionary_file>
Define the dictionary of standard bond lengths and angles. This is the same dictionary used by Hermans & McQueen, and in FRODO. It can be found in $ODAT/dict.pdb as default. When modifying a dictionary, it is necessary to make a refi_setup to force the reading of the latest dictionary file.
refi_zone <id two atoms> or <mol res1 res2>
Regularize a zone of residues. Residue types must be described in the dictionary for each kind of residue in the zone. They can be picked at the screen or typed at the console. YES or NO to accept new or restore old coordinates.
refi_continuous <define a zone>
This command allows the user to regularize a zone of residues. The command stays active so that if an atom is grabbed and moved around, the other atoms will be forced to move to maintain stereochemistry.
The command must be deactivated with Clear_flags
Use this at your own risk, it needs some practice.
refi_fix_atom <id>
This command allows the user to fix an atom so that it does not move during a model regularization. The command stays active and must be cleared with the Refi_Clear_flag command. After a round of Refi_zone or Refi_On_the_fly, the fixed atom(s) remains fixed until reset with the Refi_Clear_atom or Refi_Clear_group commands.
refi_clear_atom <id>
This command allows the user to clear an atom that has been previously fixed so that it can move during a model regularization. The command stays active and must be cleared with the Refi_Clear_flag command.
refi_clear_group <id>
This command allows the user to clear a group of connected atoms that may have been previously fixed so that they can all move during model regularization. The command stays active and must be cleared with the Refi_Clear_flag command.
Datablocks for the Refi Option
file_refi_dict is a text datablock containing the name of the dictionary file.
.refi_dict is a text datablock of the contents of the dictionary file.
.refi_real is a datablock containing real variable.
.refi_c6 is a datablock of character variables.
None of these datablocks should be tampered with.