Last modified: 2-nov-2012

Depp pages /Topical pages

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:

PROMPT

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

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):

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

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").

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")

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".

MAPS page: electron density map calculation

See MAIN_DOC:calc_map/calc_map.html, MAIN_DOC:dens_mod/dens_mod.html,

For confuguring denisty modification tasks see MAIN_MENU: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

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.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

UTILS page: utilities

MAP_MASK page: mask generation from map