1. Depp pages /Topical pages
Keyword: menu, depp pages, overview, topical pages
Last modified: 12-apr-2019


1.1. Main page: gate to tasks

"Depp pages" are cover topics of structure determination and
analysis. They 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.

1.1.2. DEPP_MAIN / Topical pages

The top layer menu block "DEPP_MAIN", enables you to choose specific
topics and to load appripriate menu pages.

Top page menu names ( in yellow):
- MAPS  
- TRACE
- BUILD
- N_MOLECU
- MINIMIZE
- VALIDATE
- REFINE
- SUPERIMP
- UTILS

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

The depp_pages are loaded by the macro "MAIN_CMDS_NEW:load_depp_page.com".

1.1.3. Molecular images

The items of the "MOL_IMAGE" menu block display the default image
("RE_IMAGE"), its symmetry mates ("SYMMETRY", "SYMM_CA"), generate
surface "GEN_SURF" and provide link to rendring of the displayed
objects ("PLOT").

1.1.4. SAVE_FILE

The items of the "SAVE_FILE" menu block save and restores the
molecular model ("SAVE_FILE", "REST_FILE") and view ("SAVE_VIEW" and
"REST_VIEW") and open the main configuration window ("MAIN_cfg")

1.2. Topical 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

Provides control over electron density map calculation, density modification, display, 

It contains menu blocks
- NICE_SEL "nice_sel.txt"
- MAP_DO "map_do.txt"
- DENS_MOD "dens_mod.txt"
- SET_WEIGHT "set_weight.txt"
- MAP_MASK "map_mask.txt"
- IMAGE_MAP "image_map.txt"
- MAP_ACTIVE "map_active.txt"
- MAKE_DEL "make_delete.txt"


See also "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".

This menu page is loaded with the macro "MAIN_CMDS_NEW:load_page_maps.com".

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 blocks appearing on the page are
- USE_ATOMS "use_atoms.txt"
- NICE_SEL "nice_sel.txt"
- MAKE_DEL "make_delete.txt"
- "depp_mini.txt"
- "auto_seq.txt"

1.2.4.  BUILD 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.


It contains menu blocks
- NICE_SEL "nice_sel.txt"
- BUILD_RESI_AUTO "build_resi_auto.txt"
- MODELER "modeler.txt"
- DEPP_MINI_SHORT "depp_mini_short.txt"
- CENTER "center.txt"
- DEPP_HISTORY "depp_history.txt"
- MAKE_DEL "make_delete.txt"
- BUILD_SECONDARY "secondary.txt"
- SET_WEIGHT "set_weight.txt"
- UN_DO "un_do.txt"
- BUILD "build.txt"
- AUTO_SEQ "auto_seq.txt"
- CHANGE_RESIDUE "change_residue.txt"

See "MAIN_DOC:build/new_struct_manual.txt".
See "MAIN_DOC:build/build.txt".

This menu page is loaded with the macro "MAIN_CMDS_NEW:load_page_build.com".

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.  The only unique thing left is the surface
generation.

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")

See "MAIN_DOC:mol_images/mol_images.txt" for syntax - 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