"Depp pages" are organized in two layers. The top layer, also reffered as the main depp page, contains menu items, which enable you to:
enter MAIN command "PROMT", where you can use MAIN command syntax interface and at the end also "QUIT" the working session.
The top layer menu block "DEPP_MAIN", enables you to choose specific tasks and loads appripriate menu page.
Top page menu names ( in yellow):
Topic of each Depp Page is covered or will be by one of the "General chapters on major topics" (../users_guide.HTML).
The items of the "SAVE_FILE" menu block display the default image ("RE_IMAGE") and its symmetry mates ("SYMMETRY", "SYMM_CA") and saves and restores the molecular model ("SAVE_FILE", "REST_FILE") and view ("SAVE_VIEW" and "REST_VIEW").
Depp Pages of the DEPP_MAIN block
On the top of each "Depp Page" is the item "RETURN", which returns back to the "Top Depp Page".
MAPS page: electron density map calculation
See MAIN_DOC:calc_map/calc_map.html and MAIN_DOC:dens_mod/dens_mod.html.
TRACE page: model tracing from map
For overview see MAIN_DOC:build/new_struc.html.
The Depp page menu block trace.html carries the functionality. whereas the accompanying menu blocks allow you to gain control over the process and manually intrefere with automated density interpretation and model generation including model rebuilding.
Assisting menu block appearing on the page are
BLD_MAIN page: main chain model building and rebuilding
The page is there to assist yuo to build chain trace of molecules in traditional way - that is manually.
See MAIN_DOC:build/new_struct_manual.html.
BLD_RESI page: residue chain model building and rebuilding
See MAIN_DOC:build/build.html.
N_MOLECU page: cross molecule building, exchange and switching
MINIMIZE page: local minimization
VALIDATE page: structure validatation and analysis
See MAIN_DOC:analysis/analyze.html.
REFINE page: crystallographic refinement
See MAIN_DOC:refine/refine.html.
IMAGE page: displaying of molecular images
After you have successfully loaded and displayed a molecular model (as described in MAIN_DOC:load_pdb/load_pdb.html MAIN_DOC:1mol/1mol.html)
See MAIN_DOC:mol_images/mol_images.html -although quite obsolete now.
SUPERIMP page: molecule superimposition
REN/SHOW page: rename and show of lists and names
MAP_MASK page: mask generation from map