1. Depp pages 
Keyword: menu, depp pages, overview
Last modified: 24-feb-2007


1.1. Main page: gate to tasks

"Depp pages" are organized in two layers. The top layer, also reffered
as the main depp page, contains menu items, which enable you to:

1.1.1. PROMPT

enter MAIN command "PROMT", where you can use MAIN command syntax
interface and at the end also "QUIT" the working session.

1.1.1. DEPP_MAIN

The top layer menu block "DEPP_MAIN", enables you to choose specific
tasks and loads appripriate menu page.

Top page menu names ( in yellow):
- MAPS  
- TRACE
- BLD_MAIN
- BLD_RESI
- N_MOLECU
- MINIMIZE
- VALIDATE
- REFINE
- IMAGE
- SUPERIMP
- REN/SHOW
- UTILS
- MAP_MASK

Topic of each Depp Page is covered or will be by one of the "General
chapters on major topics" ("../users_guide.HTML").

1.1.3. SAVE_FILE

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").

1.2. 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".

1.2.2. MAPS page: electron density map calculation
Keyword: map calculation, denisty modification, averaging

See "MAIN_DOC:calc_map/calc_map.txt", "MAIN_DOC:dens_mod/dens_mod.txt", 

For confuguring denisty modification tasks see "MAIN_MENU:dens_mod.txt".

1.2.3.  TRACE page: model tracing from map

For overview see "MAIN_DOC:build/new_struc.txt".

The Depp page menu block "trace.txt" 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
- "use_atoms.txt"
- "nice_sel.txt"
- "make_delete.txt"
- "depp_mini.txt"
- "auto_seq.txt"

1.2.4.  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.txt".

1.2.5.  BLD_RESI page: residue chain model building and rebuilding

See "MAIN_DOC:build/build.txt".

1.2.6.  N_MOLECU page: cross molecule building, exchange and switching

1.2.7.  MINIMIZE page: local minimization

1.2.8.  VALIDATE page: structure validatation and analysis

See "MAIN_DOC:analysis/analyze.txt".

1.2.9.  REFINE page: crystallographic refinement

See "MAIN_DOC:refine/refine.txt".

1.2.10.  IMAGE page: displaying of molecular images
Keyword: molecular image, 3-D images

Most of the functionality of this page replaced by the "RE_IMAGE" tk_gui
configuration tool.

After you have successfully loaded and displayed a molecular model
(as described in "MAIN_DOC:load_pdb/load_pdb.txt" "MAIN_DOC:1mol/1mol.txt")
- select ("nice_sel.txt") parts of the model, 
- define the color to be applied ("image_col.txt"), 
- or define the color to a chosen set of atoms ("image_col2.txt"), 
- specify atomic radii or generate a Connolly surface ("image_data.txt") and 
- display a molecular image ("image_do.txt"), 
- display a map image ("image_map.txt"),

See "MAIN_DOC:mol_images/mol_images.txt" -although quite obsolete now.

1.2.11.  SUPERIMP page: molecule superimposition

1.2.12.  REN/SHOW page: rename and show of lists and names

1.2.13.  UTILS page: utilities 

1.2.14.  MAP_MASK page: mask generation from map