Manual model building
The first session "Editing topology a model" explains you how to build a new chain, change a residue, attach some residues to an already existing segment and how to build N- and C-termini of a polypeptide.
The session "Changing geometry of your model" lists the menu functions and briefly explains how they can modify positions of displayed atoms.
The session "Defining keys 'active' and 'passive'" brings the elementaries about the two keys, via which you are enabled to apply secondary structure definitions (see the section "SECONDARY structures") and perform energy calculations (see the section "ENERGY calculations and MINIMIZATIONS"). The session "Use of anchors" explains you how to create and use anchors in order to pull your model atoms to desired positions with help of distance constraints.
The last session explains briefly how to perform some model building without the use of interactive display.
A brief survey through manual model building steps
If you see helices or beta sheets build one helix or strand of appropriate length.
Similarly you can proceed with building of beta strands as the second most frequent secondary structure element.
Editing topology of a model
Use the molecular BUILDER menu (MAIN_MENU:build.html. It works in 3 modes (START, ATTACH, INSERT or CHANGE residue). The current mode is indicated by the filled area. Only the "RESID ??" item really acts, all the others set flags or variable names only.
When picking SEGMENT you are required to type in a new SEGMENT name that will be applied when you will start creating new segments. Similar yields for CHAIN, where a new SEQUENCE root is applied when new residues are being created. "RESID ??" requires a string of RESIDUE names as
10 ALA CYS TRP 2 ASP
When the builder is in the CHANGE mode only a single RESIDUE name is accepted, where in other two modes any combination of RESIDUE names and their repetitions is valid. However, it is not possible to place 10 solvent MOLECULES at the same positions with "10 H2O". Only RESIDUE type topology library entries can be APPEND. Topology object named MOLECULES can also not be attached to RESIDUES.
STARTING a new chain
For example we want to build alanine chain 10 residues long followed by a tryptophan and 3 cysteines. The chain starts to grow from the current position of the image center, so it should be set properly by dials or mouse. The BUILD menu should be in START mode, a SEGMENT name and SEQUENCE root are supposed to be defined. Afterwards picking item "RESID ??" activates a chain generation.
The "RESID ??" prompt should be answered with desired residue sequence "10 ALA". The desired sequence appears as an extended chain growing from the middle of the image screen.
CHANGING a residue
You can change a residue by setting the CHANGE mode and picking an atom of the residue you want to change. This should be followed by a click on item "RESIDUE ??" which prompts for a new residue. A<return> is followed by a residue change and an IMAGE update.
Modification of amino acid residues usually results in appropriate geometry, however, nucleic acids have atoms with equal names but positioned at different rings, so that a two step procedure is recommended: CHANGE first a THY to NONU (no nucleic) and then to ADE.
We may APPEND a new chain of peptides to the C-terminal of a residue by picking an atom of the selected residue, setting the ATTACH mode and responding to the "RESID ??" prompt with appropriate residue names.
N- and C- termini
For attaching the N-terminal atoms set the builder mode to APPEND click an atom of the N-terminal residue, and APPEND to it the NTR residue. 3 new (HT) hydrogen atoms will appear. Click the old H atom and delete it (by clicking the DELE_ATO in the RENAME menu block). Now click an HT atom and then some other atom from the N-terminal residue and merge the two residues into a single one (click the MERG_RES from the RENAME menu block). Appending NTR (or NTRP for prolines) deletes the bond between the C atom of the terminal residue and N atom of the next one. So restore it (click the two atoms and then MAKE_BON item from the MAKE_DELE menu block).
Similarly the C- terminal carboxylic group is created. First rename the C-terminal carbonyl oxygen into OT1 (click the atom, clock "REN_ATOM" in the "RENAME" menu block and then type OT1). Switch on the "APPEND" model building mode and append "CTR" residue to the C-terminal residue. Now click the "OT2" atom and merge the "CTR" residue into the C-terminal residue (click the MERG_RES from the "RENAME" menu block).
Defining keys "active" and "passive"
The keys "active" and 'passive"have to be defined if you want to perform energy calculations including minimization or modify secondary structure of your model"structure of your model.
The simplest way to define the selections is to hit the depp page 9 items "ACT_NEIGH", "ACT_SEGM" or "ACT_2RES". The active atoms will be for a short time highlighted with white marks.
"ACT_NEIGH" selects atoms that are within a certain range of covalent bonds away from the last picked atom. "ACT_SEGM" selects all atoms included in the covalent bond network of the last picked atom. "ACT_2RES" selects all residues that are between the last two picked atoms. This function can be applied. when you want to select only a single residue: hit two different atoms in the same residue.
For more see MAIN_MENU:nice_sel.html.
Select part of the structure into key "active" and change its secondary structure to one of the following:
Secondary structure elements can be applied in block ("HEL_ALPH", "HEL_3-10", "COLLAGEN", "POLI_PRO", "BET_ANTI", "BET_PARA", "EXTENDED") by acting on the ACTIV selection or as turns ("TURN_I", "TURN_II", "TURN_III" and their 'primes', "GAMMA" and "GAMM_IN"-verse turns) acting on the next four or three residues. The model can fold "FORWARDS" or "BACKWARDS".
See also MAIN_MENU:secondary.html.