Many commands however, are logically grouped in menus. This part of the writeup deals with the menus that are mainly of interest to crystallographers.
Some of the commands that could be of interest to crystallographers, like for example the ab-initio model building module, are also of interest to normal users, and are therefore described in other parts of this writeup. The following chapters are described here:
WORKING WITH MAPS MANIPULATING MAP VALUES MANIPULATING REFLECTION FILES EDITING ENVELOPS AMINO ACID REGULARIZATION SYMMETRY XRAY MENUThe crystallographic datastructures that WHAT IF uses (maps, reflection files) are the Groningen style M*F's. A description of these file formats can be found in the apropriate chapters.
The menu called XRAY at present holds some options for real space refinement, and for detection of residues that are not in good density. This menu is likely to extend over the next couple of months.
One of the options presently being worked on is a general `check-my-structure` option. Since a true witch hunt for crystallographic errors is taking place, it might be nice for crystallographers to get some warning in case something is rotten...
The very X-ray specific menus for refelection file evaluation and evelop editing are actually stand-alone programs. These are only made part of WHAT IF in order to have quick access to existing datastructures and ready to go subroutines. It is however not possible to use the refelction file evaluation module or the envelop editting menu in the middle of a WHAT IF session. To use these modules, one should start WHAT IF, read in the data needed, run the option, and leave WHAT IF.