The "DEFINE" menu block has two purposes:
The method ("MTH_") and energy term only ("ONL_") items are switches. They are organized as a radio button menu groups (choosing one turns the other two off). Only one shitch cabn be active at a time. They specify the way the "DEF_" items act.
The items "DEF_INIT", "DEF_DELE", "DEF_APPE", "DEFINE" do some job create and modify the energy lists.
For command syntax you see MAIN_COM:define.html.
When defining energy terms an automatic procedure ("active" atoms are used),
When defining energy terms topology library residue description ("active" atoms are used).
When defining energy terms the last atoms from the history lists are used editing the current "ONL_" energy term list. "BOND" take last two picked atoms, "ANGLE" three and "DIHEDRAL" and "IMPROPER" last four.
Before new terms are appended the particular list is initialized. It applies to "BOND", "ANGLE", "DIHEDRAL" and "IMPROPER" energy term lists.
All entries including the selected atoms are removed from the currently flagged energy term list. It applies to "BOND", "ANGLE", "DIHEDRAL" and "IMPROPER" energy term lists.
The most common use is in connection with "DEF_ATOM" and "DEF_IMPR", which allow you to choose an improper by clicking four atoms and remove all impropers that include these four atoms from the IMPROPER energy terms list.
New terms are appended to a flagged list. It applies to "BOND", "ANGLE", "DIHEDRAL" and "IMPROPER" energy term lists.
"DEFINE" actually invokes the macro to which "DEF_ALL" variable points to. Its only argument are the segment names included into the variable "WORG_SEGM". Applies to all energy terms and does not consider any of the provided DEFINE menu flags.
The "DEF_ALL" variable is "SET" in MAIN_UTILS:get_top_par_19_csd.com and points to the MAIN_UTILS:def_top_par_19.com macro.
> show vari DEF_ALL > show var WORK_SEGM
Only atomic CLASSES will be modified.
Only atomic "CHARGES" will be modified. It should be barred in mind that this option applies only when used in combination with a topology library as data source ("DEF_TOPO").
Only the list of covalent "BOND" terms will be effected.
Only the list of covalent bond "ANGLE" terms will be effected.
Only the list of covalent "DIHEDRAL" angle will be effected.
Only the list of covalent "IMPROPER" dihedral terms will be effected.
"CLASSES" of all clicked atoms are set to the string typed in. Be sure that your history list contains only the atoms you want. If you feel uncertain use "HIS_ERAS" and click the atoms again.
Creates (or recreates) the last entry in the topology library from the "active" key residues using the current energy lists.
For how to define the keys via menus see nice_sel.html and select.html , and MAIN_COM:select.html for mastering the "SELECT" command syntax.
For further reading see MAIN_DOC:top_par/top_par.html.