By using SELECT menu items a user is enabled to utilize flexibility of many menu item blocks. By picking the SELECT menu items four KEYs can be accessed ('active', 'pasive', 'image' and 'anchor') and modified by logical operations of the SELECT ... END command sentence. ITEMS including boxes are setup flags, that are at the moment, when a SELECT command item is picked, transformed into a SELECT ... END command sentence specifying a new key definition.
KEY 'active' is the selection used in most of menu driven actions. KEY 'passive' is used for ENERGY calculations serving as interaction to 'active'. Positions of atoms that are included in KEY 'passive' only and not in KEY 'active' as well, are not modified during an ENERGY MINIMIZATION run.
KEY 'image' defines pickable atoms from images.
KEY 'anchor' is the selection used for anchoring atoms by distance constraints, where atoms and their anchors can be moved and minimized separetely. For example picking MIN_ANCH minimizes the anchors in the specified electron density map.
Tags:
Tags are organized in three groups each consisting of three items: (SEL_LAST, SEL_RANG, SEL_HIST), (SELE_NAM, SELE_nn, SELE_SEQ) and (SEL_ATOM, SEL_RESI, SEL_MOLE). In each group only a single item flag can be set at a time. A tag is composed by putting together an item of each Tag group in a meaningful entity. The first group flag specifies how many atoms from the history list will enter a tag. The second group specifies wheter atoms will be selected according to names, numbers or sequence names. The third group specifies whether tag refers to atom, residue or a molecule (segment) level of molecular structure organization.
Setting flags does not affect any key as long an item in the Select group (SELE_ALL, SEL_COPY, SEL_ARO?, SEL.not., SEL .or., SEL_.and.) has been pressed.
Sets current SELECTION to the 'active' key.
Sets current SELECTION to the 'passive' key.
Sets current SELECTION to the 'image' key.
Sets current SELECTION to the 'anchor' key.
> key ... select .not. all end
Clears the currently ('...') chosen SELECTION. After this command the chosen selection includes NO atoms.
> key ... select all end
Includes ALL atoms into the currently ('...') chosen selection.
> key ... select active end
Copies the contents of 'active' to the currently ('...') chosen selection ('anchor' or 'image').
> key passive select active .or. by resid by bond active end
The 'passive' selection is thereby also enlarged for the residues, that form a covalent bond with an 'active' atom.
> key active select passive end
In the case when the currently chosen SELECTION is 'active' then the contents of KEY 'passive' is copied to key 'active'.
> key ... select ... .or. - > by resid around key active dist real from image end
Modifies the currently chosen SELECTION. All residues that have at least one atom closer than the specified distance from the active KEY and are included in the KEY image are merged (.OR.) into the current selection. The distance should be typed in to the prompt appearing in the standard input window.
> key ... select ... .and. .not. tag end
Modifies the currently ('...') chosen SELECTION so that the logical '.and. .not.' operation is performed.
> key .. select ... .or. tag end
Modifies the currently ('...') chosen SELECTION so that the logical '.or.' operation is performed.
> key ... select ... .and. tag end
Modifies the currently ('...') chosen SELECTION so that the logical '.and.' operation is performed.
The chosen tag refers to the last picked atom only.
The chosen tag refers to the last two picked atoms.
The chosen tag refers to all picked atoms available in the history list.
Selects atoms according to (ATOM, RESIDUE or SEGMENT) NAMES.
Selects atoms according to (ATOM, RESIDUE or SEGMENT) NUMBERS. In the case when SEL_MOLE is chosen, there is a slight modification of the common rule (see SEL_MOLE).
Selects atoms according to their SEQUENCE names.
Selects atoms according to their ATOMic names or numbers.
Selects atoms according to their RESIDUE names or numbers.
Selects atoms according to their SEGMENT names or numbers. In the case of SELE_NAM selection always relates to SEGMENT NAMES, while in the case of SELE_nn, the select sentence depends on the current range mode (SEL_LAST, SEL_RANG, SEL_HIST). When SEL_LAST mode is chosen, a molecule is selected. Molecule is defined as a group of atoms attached to the last picked atom through a network of covalent bonds. In both the other cases (SEL_RANG or SEL_HIST) tag refers to already existing SEGMENT numbers.
> IMAGE MARK ON
OFF
Controls displaying of the currently choosen key atom marks on the image screen.
ANCHOR is an extremly flexible tool that in combination with the energy minimization enables you to model the desired geometry of a molecular model. Anchors are target positions for your atoms. They are pooling their origin atoms towards the desired position without destoring the geometry (bond length, angles, impropers) of a molecular model. Anchors positions can be easyly moved. Each atom can have its anchor.
When created anchors are displayed as green crosses connected with a line to their origin atoms so that you can always keep track of your atom - anchor pairs. Hiting ANCHOR creates an anchor for each atom included in the key 'anchor'. New anchors are created at positions of their origin atoms. Already existing anchors remain on their positions. Anchors that lose their partner atom (orig atom is not any more included in the key 'anchor') are deleted.
Anchor positions can be optimized regarding to their correlation within an electron density map (MIN_ANCH). This way a better (real space) fit of your model to an electron density can be derived.