Model rebuilding follows the initial chain trace steps, which are described in the MAIN_DOC:build/new_struc.html.
Also for model rebuilding one should first try to exploit the automated features before reaching for the manual tools.
Instead of using mouse and dials to drive your atoms into electron density or to fix their geometry there are a few tools which do these automatically.
For the complete list of functions see MAIN_MENU:auto_stuff.html. The "AUTO_STUFF" tools can be applied on single residue, a region or on all working set segments, depending on the mode of the key "active". See MAIN_MENU:nice_sel.html.
Item "FIX_PEPT" rebuilds geometry of peptide bonds to trans. "FLIP_PEP" flips the orientation of the last clicked or selecetd peptide bonds for 180 degrees.
"EXT_SIDE" builds an extended geometry for a side chain, "FIX_SIDE" looks for the closest side chain rotamer. "FLIP_SID" flipps the atoms of the last branch of a side chain
"FIT_PEPT" and "FIT_SIDE" fit peptide bonds and side chains to an electron density map by rotations only.
Note that "FIT_PEPT" relies on interactions with "CB". Glycines with no "CB" atoms are therefore not modeled well when density is ambiguous.
"RIG_SIDE" optimizes residue fragments.
"FIT_SIDE" fit side chains by rotatioan about all possible bonds and considers density as well as packing energy of a conformation. The most convinient way of setting the map density contour level is by using the mouse scroll.
All these commands should be followed by a "MINIMIZE".
Automated setting of atomic weights (occupancy)
"AUTO_WEI" define weights of atoms taking into consideration their position within the active map.
It is ment to define weights to be consistent with a map, so that after the weights are defined the electron density map is recalculated. For map model consitency the whole process is to be repeated twice.
Manual model rebuilding: Changing model geometry
A common rule is first to pick atom(s) and afterwords activate a function. The advantage of this logic is double: it enables you to correct the picked atoms list without a need to start all over again and the function does need no approval. You only hit a function once.
If the action has been activated by mistake you can cancel it by "OB_REJEC" or even later by "UN_DO"-ing the geometrical changes.
In order to pass atoms as arguments to the model building tools atoms must be clicked. When clicked they enter the history list from where they are passed to the geometry changing tools.
Shortcut is "u", which actually toggles between saved and modified cooridnate sets.
Also the "HISTORY" list is editable. You can either drop atoms consecutively "HIS_DROP" or clear the entire list with a single click of them "HIS_ERAS".
Menu blocks for geometry changes
There are two menu blocks dealing with manual model rebuilding: on depp pages "BLD_MAIN" and "BLD_RESI"
Only the "MODELER" menu block (MAIN_MENU:modeler.html) in dark green color, contains all full functions. You have to include it if you are in need of one of its functions.
"RT_ANGLE", "RT_CHAIN", "RT_BETWEE", "MOV_ATOM", "MOV_DIST", "ROTATE", "TRANSLATE", "INV_CHIR" and "CONNECT" define OBJECTS, while "OB_START", "OB_ACCEP" and "OB_REJEC" either return atoms to initial positions, by keeping active OBJECTS definitions ("OB_START"), or by rejecting definitions and returning to the previous stage ("OB_REJEC"), or accept changes ("OB_ACCEP").
"INV_CHIR" converts a chirality of an atom by swapping positions of its two selected side-chains. "CONNECT" brings together two molecules into a reasonable geometry and joins them with a covalent bond.
Each activation of a geometry change defines its own dial set. You can browse through them with repetitive clicking on "DIAL_RST" or go back to the viewing dial set with "DIAL_INI".
Further hints: main chain reposition - side chain rotate
Quite often one should improve the position, orientation as well as the side chain conformation of a residue. So click on CA atom, activate "MOV_RESI", click on the last atom of the side chain and click on "RT_CHAIN". Two dials sets are defined now and you can by switching between them optimally fit a residue into density.
Similarly one can also fit an inhibitor into the density first clicking "MOV_RESI" or "MOV_SELE" and then activate also all desired bond rotations ("RT_CHAIN")in the molecule from the center outwards, each time clicking the central atom and one from a branch.
Clicking "UN_DO" (depp page 9) retrieves the previous coordinate set in a case of an undesired change. Geometry of models can be changed also when no topology or parameter libraries have been read into the program or they do not include data to describe your current model.
ENERGY calculations and MINIMIZATIONS
Chemistry terms keep the geometry reasonable , whereas anchor and pair lists help you to enforce building the models the way you want.
Depp page "MINIMIZE" deals with most of functions you need for local model energy minimization.
Energy can be calculated for each energy term turned on assuming that all necessary force filed PARAMETERS have been read and assigned to atoms. The bonding ("BOND", "ANGLE", "DIHEDRAL" and "IMPROPER") and non-bonding ("VDW" and "ELEC") terms are defined as in X-PLOR. In addition to these energy terms, there are also the "PAIR", negative "DENSITY" correlation and "DIHEDRAL" constraints terms.
"CHEMISTRY" terms can be turned on and off all together on the Depp page "MINIMIZE". The squares of energy terms turned on are filled, while the others appear in the ENERGY menu as empty. Clicking the items turns each individual term on or off.
When an ENERGY calculation is initiated from the DIALOG mode by picking the MENU item "SHOW_ENE" the "active" key atoms interact with the "passive" key atoms.
> energy select all end > energy select active end sele passive end
To calculate ELECTROSTATIC and VDW interactions partial atomic CHARGES and atom CLASSES have to be assigned to each atom individually. Atom CLASSES are further used to "DEFINE" lists for energy the bonding energy terms: "BOND", "ANGLE", "DIHEDRAL", "IMPROPER" and "HBONDS". See also MAIN_MENU:minimize.html.
Further hints: Minimization with energy terms manipulation
Go to page "MINIMIZE".
To drastically improve you model fit to density, switch off all energy terms and leave only the density term on. "MINIMIZE" the model. Since atoms will be overlapping apply a small "KICK_ACT" to get them appart, switch on "CHEMISTRY" all energy terms and keep clicking "MINIMIZE" until model is in the density. (Pressing "k" will do the kick and "m" minimize).
If this minimization procedure has not been sufficient swicth off non bonding terms ("ENE__VDW" and "ENE_ELEV"). If ven that is not enough go back one more step and swicth of "ENE_DIHE" and "ENE_IMPR").
If peptide bonds are totally screwed go to page "BLD_MAIN" or "BLD_RESI" and fix the peptides. (Pressing "p" will do the same.)
Hydrogen bond list manipulation
Hydrogen bonds list is utilized in MAIN as geometrical non-bonding restraints of the model during energy minimizations and when visualized as a way of structure analysis. Here hydrogen bond list generation and editing for purposes of model building are described only.
Hydrogen bonds are as important as covalent bonds. They guide you to build models as they should look like. On So first calculate a hydrogen bond list ("HBON_CAL"), display it ("RE_IMAGE") and then delete ("HBON_DEL") and add ("HBON_MAK") all hydrogen bonds that you think are appropriate for you current model. The meaningless hydrogen bonds generated by the program will immediately tell you that there is a place to work on it in the model.
Additional information: For the analysis purposes you are referred to the chapter "Structure analysis".
PAIR constraints require previously defined pair list. Two atoms in a pair are pooled together or apart to a specified distance with a force (stored in the variable "force_pair") acting as a harmonic oscillator (analytically identical to the BOND energy term). PAIRs defined with the menu items MAKE_PAR and ANCHOR are assumed to be pooled together to a zero distance, while clicking the PAIR_D_? inquires from you to type in the desired distance explicitly.
The last option is very useful when you try to model a complex of a small inhibitor with a protein as described in a paper. The structure of the complex is, not available to you, however in the paper some distances are often tabulated.
INI_PAIR initializes the pair list. All pairs are deleted.
Has become obsolete by other progress of other functions.
Anchor is a dummy atom connected by a PAIR with its original atom. A force acts between an atom and its anchor. It pools them together with a harmonic distance constraint, assuming that the PAIR energy term has been turned on. Anchors can be freely moved in space by the MOV_ATOM or TRANSLAT menu item. Their positions may be optimized in an electron density map (MINI_ANC). Properly set anchors can help you to get atoms to the exact positions you want to have them. They may also be used to mark initial chain tracing and can pull a chain to a desired position in an electron density map.
Anchors are supposed to be generated through menu options (see Dialog mode accessories) unless you have a strong reason to define them manually. (In such a case generate ANCHORS from the menu and see later the input.cop file for the syntax.)
The SELECT menu offers you more control over the key, however the simplest way to define anchors is to initialize the history list (HIS_ERAS) and then click the atoms for which you want to define anchors and then hit ANCHORS on the depp page 9, which will create anchors for each atom included in the history list.