The basic graphical item and molecular entity is called an entry, which has three possible functional states: invisible, visible (v), and active (a). An active entry is always also visible. Activity is a status that relates to energy calculations and some matching functions. In most situations only visible or active entries can be manipulated and modified. All active entries and only active ones are included in energy evaluation or minimizations. Other operation may use the active status as an entry selection criterion. In these cases there is a corresponding description in the relevant help text.
Entries can be subdivided into subunits (monomers). At present this is used for amino acid residues in proteins, and nucleic acids in DNA.
In addition to structural entries further display items are provided which we may call associated or auxiliary entries. They include surfaces, loci, or additions to elucidate features of Calf structures. Some of the manipulations of structural entries can also be performed with these entries. In some cases, their visibility is coupled with their parent structural entry, and they have no status "active".
Further display objects are maps which are, however, not pickable.
We separate modelling activities into two major classes, basic ones, which may be grouped together into what we call "TOOL units", and more specific ones, which we call "MODELLING units". Tools are of very general functionality and appear in many menus as items, whereas modelling units are more dedicated to special modelling activities and contain the appropriate tools as sub-choices. Modelling units are often located in the main menu or grouped together in a family of related units. Tools are designed to offer a maximum of flexibility for use in various different contexts. Modelling units, in contrast attempt to make particular activities as handy and convenient as possible.
The following sections list and explain the menus of the present units. Some of the menu items are by themselves tools or other new menus. This implies that choosing such an item, will lead to a menu change and a digression in level in the menu hierarchy. Only after exiting this tool the previous menu will reappear. Apart from the above mentioned help item "?", each menu carries in second place the "x: exit" (or seldom "c: continue") item which is omitted in our list for conciseness. Similarly, the display unit "." occurs in most menus and is also not explicitly mentioned. In brackets [] the symbol of the menu (one- and possibly three-letter version) is given.
There is a parameter called "savetime" in Moloc which determines after how many minutes recovery is made. If this parameter is non-zero, Moloc writes every "savetime" minutes a file in the current directory with name Moloc.rcv. This file is written in .cif format and contains all molecular entries that are in memory at the time the file is written. If the program happens to crash the user can start the program again and read in this file specifying it as a .cif file. By this token he will not have lost more than the las "savetime" minutes of work. Clearly, the time to write the file depends on the number of molecules kept in memory. If this is a lot, Moloc will need its time for file writing every "savetime" minutes. During that time other activities must wait!
The user should be aware of the fact that, if he happens to start Moloc several times from the same directory, recovery will not be guarantied for any of those starts, because they will overwrite each others recovery files. This is not a problem when starting from different directories.
The default value savetime = 0 omits crash recovery.