Spartan 5.1 User's Guide

Chapter 7: The Build Menu

This section reviews the features and functions available under the Build menu. These include dialogs for building organic, inorganic and organometallic molecules, polypeptides and polynucleotides, for conformer searching and for providing guesses at transition structures. The Build menu also provides for setting up entire sets of calculations which follow normal vibrational modes or, more generally, any user-defined motion, as well as series of calculations on substituted molecules. Finally, the Build menu allows changing atomic masses.

Selection of Build results in display of the following menu:

Edit Structure

Conformer Search
Transition Search
Vibration Sequence
Coordinate Driving
Combinatorial Study

Isotopes

(Keystroke equivalents are given by the underlined letter in the menu entry.)

This provides access to Spartan's molecule builders and molecular mechanics energy minimizers (the builders are entered for the first time by selecting New from the File menu), as well as dialogs for searching conformation space, for generating transition-state guesses based on reactant and product geometries, for specifying series of calculations along a normal mode (or any other user-defined coordinate), for generating molecules related by substitution, and for changing default atomic masses.


Section 7.1: Edit Structure

Spartan presently provides four different builders: an entry builder suitable for the construction of most organic molecules, an expert builder for building organic molecules not easily represented in terms of classical valence structures, as well as inorganic and organometallic systems, a peptide builder for construction of polypeptides, and a nucleotide builder for construction of polynucleotides.

All builders are fragment based. The first two are very similar in that they utilize "atomic", functional group and ring fragments (and ligand fragments in the expert builder), while the peptide builder uses the set of amino acids as "fragments", and the nucleotide builder uses a set of bases. All build molecules much in the same manner as a chemist would assemble a structure from a model kit. That is, pieces are taken from the "kit" one at a time and added sequentially to the structure under construction.


Section 7.1.1: Entry Builder

The entry builder is presented initially upon selection of Edit Structure from the Build menu (or upon selection of New from the File menu).

The entry builder is the default for a molecule which has not accessed the builder during this session. The expert, peptide and nucleotide builders may be reached by clicking on Expert, Peptide and Nucleotide, respectively, in the entry builder. Selection of Edit Structure for a molecule which has previously accessed the builder during this session automatically leads to the builder (entry, expert, peptide or nucleotide) used in the previous access.

The display is divided into two regions, a work area and a model kit.

The work area, which occupies the left two-thirds of the screen and is where molecule construction occurs, is blank upon entry into the builder for the first time (following selection of New from the File menu). Reentry into the builder with an existing structure, or initial entry following selection of Open or Import from the File menu) results in a structure being drawn (as a ball-and-wire model) in the work area.

Molecule building/editing tools reside in the model kit which (upon initial entry) occupies the right third of the screen. (It can be moved if desired.) At the top, are a variety of "atomic fragments" that are displayed as icons to show their hybridization state.

From left to right and then top to bottom, these correspond to:

C(sp3) C(sp2) C(sp) C(aromatic) Si(sp3)
N(sp3) N(sp2) N(sp) N(aromatic) N(planar)
H F Cl Br I

Selection is effected by clicking on the appropriate icon; this results in the selected icon being highlighted. Once selected, the atomic fragment can be used to initiate building or appended onto an existing molecular fragment. To initiate building, the cursor may be positioned anywhere in the work area prior to clicking. To bond to an existing fragment, the cursor needs to be positioned onto the tip of a free valence (yellow vector) before clicking. Misses will be signaled by a bell; reposition the cursor and try again. Selection of bond type, i.e., single, double, triple or aromatic, in the case of atomic fragments with multiple bond types, e.g., sp2 carbon, occurs automatically depending on the nature of the free valence selected. Mismatches of bond type will result in a bell.

Two pull-down menus are located inside the model kit. These provide access to a number of pre-built fragments corresponding to common functional groups and hydrocarbon rings.

  1. Groups

    Clicking on Groups results in an icon of one group from a menu of groups being displayed to the left. Clicking inside the box immediately below this icon results in display of the following menu:

    Groups:

    Alkynyl
    Allenyl
    Amide
    Carbonyl
    Cyano
    Ester
    Nitro
    Nitroso
    Phosphinyl
    Sulfonyl
    Sulfoxide
    Vinyl

    Selection of a group other than the one shown is accomplished by clicking on the name of the group, or alternatively by holding down the left mouse button while sliding the cursor on top of the group name, and then releasing the button. The menu disappears and an icon of the selected group appears to the left. The selected group may then be used to initiate building by positioning the cursor anywhere within the work area and clicking, or may be added to an existing structure by positioning the cursor on an appropriate free valence and clicking. In the latter case, misses and mismatches result in a bell.

    The amide and ester groups have more than one type of atom with free valences. The amide group actually has three different free valences, one on carbon and two on nitrogen. The free valence which will be used to connect these groups to a molecule under construction is marked with an "o". The marked position circulates among the possible positions with repeated clicking on the group icon.

  2. Rings

    Operation is analogous to Groups, and available rings are provided in a menu:

    Rings:

    Cyclopropyl
    Cyclobutyl
    Cyclopentyl
    Cyclohexyl

    Phenyl
    Naphthyl
    Anthryl
    Phenanthryl

    Cyclohexyl, naphthyl, anthryl and phenathryl rings have more than one kind of free valence. Except for cyclohexyl, the free valence which is used to connect these rings to the molecule under construction is marked with an "o". As with groups (see above), the marked position circulates among the available positions with repeated clicking on the ring icon. Selection of an axial or equatorial free valence in the cyclohexyl ring is accomplished in the same way, but is indicated by a label "ax" or "eq" appearing alongside the icon.

    Note that all rings provided in this menu are hydrocarbons. Heteroatoms may be substituted using the atom replacement feature (see Section 7.1.6).

A series of buttons appear at the bottom of the model kit, or alternatively in a menu bar immediately above the work area (the location is controlled from Preferences under the Logo menu; see Section 3.3). These buttons access some of the commonly-used building features.

  1. Add

    Accesses libraries of atomic fragments, functional groups and rings (see above) to be added to an existing structure. Selection results in a message in the menu bar.

    Add: Select an unfilled valence to add fragment.

    Following selection of a fragment, group or ring, clicking on the appropriate free valence adds that fragment, group or ring to the on-screen structure.

    Except for initial entry into the builder (New from the File menu), Add will always be selected. Most other modes (New, Delete, Bond, Break and Minimize) revert to Add following their completion.

  2. New

    Accesses libraries of atomic fragments, functional groups and rings (see above) to initiate building, or to initiate building of another molecule on screen (as, for example, in building a hydrogen-bonded complex). Selection results in a message in the menu bar.

    New: Place new fragment by clicking in the work area below.

    Following selection of a fragment, group or ring, clicking anywhere in the work area positions that fragment, group or ring at that location.

    New is selected upon initial entry into the builder (New from the File menu) and upon completion of Clear (see below). The mode reverts to Add immediately following introduction of the fragment, group or ring on screen, unless the Shift key is held down. This allows more than one fragment (functional group or ring) to be placed on screen without again needing to select New.

  3. Bond

    Allows free valences on different atoms to be bonded. Selection results in a message in the menu bar.

    Bond: Select two unfilled valences to define bond.

    Subsequent clicking on two unfilled valences (on two different atoms) will cause these atoms to be linked by a single bond. (The individual free valences will each be marked by a small yellow ball as they are selected.) If unfilled valences are selected on atoms that are already bonded, this will result in the bond order being increased by one, i.e., single Æ double, double Æ triple. The mode reverts to Add immediately following bond formation, unless the Shift key is held down. This allows more than one bond to be formed without again needing to select Bond.

  4. Break

    Allows breaking an existing bond resulting in one or more sets of free valences (more than one in the case of breaking a multiple bond). Selection results in a message in the menu bar.

    Break Bond: Select bond to break.

    Subsequent clicking on a bond will result in its removal; the valences on the respective atoms will automatically be replaced. Note that bond deletion may result in detached fragments. The mode reverts to Add immediately following bond breakage, unless the Shift key is held
    down. This allows more than one bond to be broken without again needing to select Break.

  5. Delete

    Allows removal of an atom and/or a free valence, as well as a user-defined point or plane. Selection results in a message in the menu bar.

    Delete: Select atom/valence/point to delete.

    Subsequent clicking on an atom, free valence, point or plane results in its removal. In the case of an atom, all associated free valences are also removed. Free valences for any atom to which the deleted atom was connected are restored. The mode reverts to Add immediately following deletion, unless the Shift key is held down. This allows more than
    one atom, free valence, point or plane to be deleted without again needing to select Delete.

  6. Minimize

    Minimizes the molecular geometry resulting from building using molecular mechanics. Either the Merck or SYBYL force fields may
    be employed. (Selection is made from Preferences under the Logo menu; see
    Section 3.3).

    Minimization is effected by clicking on Minimize. When minimization is completed, a refined structure will appear in the work area, along with a dialog.

    This displays the final strain energy (in kcal/mol) along with the symmetry point group. Continue allows structure minimization to continue in the event that it has not completed normally (the button is normally unavailable). The dialog is removed by clicking on OK, following which the mode reverts to Add.

    Structure minimization for large molecules may be interrupted if desired by clicking on Stop (this button replaces OK during minimization) and restarted by clicking on Continue.

  7. Move

    Allows independent movement (translation and rotation) of two or more fragments or molecules. It is particularly useful for building intermolecular complexes, or (following bond breakage) for moving a "substituent" from one part of a molecule to another. Selection of Move results in a message in the menu bar.

    Move: Select fragment to manipulate.

    To move a single fragment, click on it to select, and then translate/rotate in the usual way. To move a different fragment, click on it, and to move the entire set of fragments as a whole, click on the background. Move is available only if there are separated fragments on screen.

  8. Clear

    Clears the existing structure from the screen. A warning message is provided.

    Clicking on OK clears the molecule from the screen. Clicking on Cancel cancels the request. Both OK and Cancel lead back to Add mode.


Section 7.1.2: Expert Builder

At the top of the entry model kit are a series of buttons.

These provide access to Spartan's other builders (expert, peptide and nucleotide) as well as to a "library" accessible to all builders (see Section 7.1.5). Access to the builders and to the library follows by clicking on the appropriate button.

Clicking on Expert leads to the expert builder.

This allows construction of a much wider class of molecules (including inorganic and organometallic species) than permitted using the entry builder. Structures which violate conventional bonding rules may also be constructed, as this builder purposefully provides no valence checking.

The expert builder is similar to the entry builder previously discussed (Section 7.1.1), insofar as the screen is divided into two regions, a work area on the left and a model kit on the right. At the top of the model kit is a Periodic Table covering the first four rows of main-group elements, and the three rows of transition metals. Main-group elements appear at the top and transition metals at the bottom.

Immediately below is a listing of "atomic hybridizations".

A selection of metal centers with higher coordination are available in a library supplied with Spartan (see Section 7.1.5). For these systems, the central element may be replaced as desired (see discussion of "atom replacement" in Section 7.1.6).

Further down the model kit below the buttons marked Rings, Groups and Ligands (the first two of which are the same as found in the entry builder), is a listing of bond types.

Selection of element is effected by clicking on its atomic symbol inside the Periodic Table. The entry will be highlighted, and in addition the atomic symbol for the selected element will appear in a box near the center of the Periodic Table. Elements beyond those included in the Periodic Table may be specified by entering the appropriate atomic symbol inside the box. Invalid symbols will be signaled by a bell.

Selection of atomic hybridization follows by clicking on the appropriate icon which will then also be highlighted. Once fully specified, the "atom" (element + atomic hybridization) can be used to initiate building or append onto an existing molecular fragment. To initiate building, the cursor needs to be positioned anywhere in the work area prior to clicking. To bond to an existing fragment, the cursor needs to be positioned onto a free valence before clicking.

Two of the hybrids (pentacoordinate trigonal bipyramid and pentacoordinate square-based pyramid) may bond either axially or equatorially.

Selection of the appropriate bonding point, indicated by an open circle, is effected by repeatedly clicking on the icon; the bonding point alternates between the two sites.

All atoms are initially connected with single linkages.* Bond type (single, aromatic, double, triple or quadruple) may be changed by clicking on the appropriate bond icon, which is then highlighted, followed by double clicking on the bond for which the change is intended.

Notice that clicking (and double clicking) on a bond changes it from a solid line to a dashed line. This indicates that the bond is now "selected", enabling bond rotation or stretching (see Section 7.1.6).

Unlike the entry builder, no valence checking is performed in the expert builder. The user is free to construct any arrangement of atoms, although appropriate force field parameters may not be available. When not available, default parameters will automatically be supplied.

Three pull-down menus are located inside the model kit.

  1. Groups

    This contains the same functional groups as available in the entry builder. Operation is as described in Section 7.1.1.

  2. Rings

    This contains the same hydrocarbon rings as available in the entry builder screen. Operation is as described in Section 7.1.1.

  3. Ligands

    This provides access to a number of pre-built ligands, useful in the construction of inorganic and especially organometallic molecules. Its operation is analogous to that for the Groups and Rings menus. Available ligands are provided in a menu:

    Ligands:











    Acetylene
    Ethylene
    Allyl
    Butadiene
    Cyclopentadienyl
    Benzene

    Carbon Monoxide
    Nitrogen Oxide
    Ammonia
    Water
    Phosphine

The buttons which appear at the bottom of the model kit in this dialog are identical to those described previously for the entry builder.

Other ligands as well as a selection of chelates are available in a library supplied with Spartan (see Section 7.1.5).


Section 7.1.3: Peptide Builder

Spartan provides a separate builder for construction of polypeptides. It is reached by clicking on Peptide which is located at the top of the model kit.

Like the other builders, the peptide builder is made up of two areas, a model kit on the right and a work area on the left.

Near the top of the model kit is a listing of the "natural" amino acids (specified by three-letter codes).

The icon of the selected amino acid is displayed above, along with the name of the amino acid and its letter code. Amino acids replace "atoms", functional groups, rings and ligands as the basic building blocks in the peptide builder. Because these other building blocks are missing, most modifications of peptides, aside from modifications in amino acid sequence and in overall conformation, need to be carried out either in the entry or expert builders.

There are two different modes of operation of the peptide builder, single amino acid mode and polypeptide mode. The former is used to initiate building with a single amino acid, or to add single amino acids to an existing structure, (brought into the builder or constructed using the entry or expert builders), while the latter is used to construct amino acid sequences (polypeptides). Switching between the two modes is accomplished with Build Sequence. "Off" corresponds to single amino acid mode and "on" corresponds to polypeptide mode.

With Build Sequence "off", choice of amino acid is made by clicking on the appropriate three-letter code from the selection given near the top of the model kit. By default, the stereochemistry is set to l, but may be changed if desired by clicking on the button to the left of d at the top of the model kit. To initiate building, position the cursor anywhere on screen and click; to add to an existing structure, position the cursor on top of an appropriate free valence and then click. Attachment will occur from the "N" end.

With Build Sequence "on", peptide construction is accomplished in three steps:

  1. Specification of amino acid sequence. This is accomplished by clicking in order on the amino acid codes. Building occurs from the "N end" to the "C end" of the peptide. In response to each selection, the name and structure of the amino acid appears in the box above the codes, and the letter code appears as part of a string separated by "-" in a box below Build Sequence. The stereochemical configuration of the amino acid is by default the l configuration; this can be changed (to the d configuration) prior to selection of the amino acid, by clicking on d (at the top of the model kit). It can be changed back to l by clicking on l. d amino acids are indicated by ".d" following the code in the box.

    At any time, the sequence can be altered by editing the box below Build Sequence. Existing amino acid codes can be deleted or changed or new codes added. The entire sequence can be specified in this way if desired. The sequence can be cleared, by clicking on Clear.

  2. Specification of macroscopic structure. Once sequencing is complete, macroscopic structure (y and f angles, and the angle w involving the amide group) may be specified by clicking on one of Alpha Helix, Beta Sheet or Other. For the first two, preset dihedral angles are displayed to the right; for Other, the desired dihedral angles need to be entered in the boxes which appear.

    At this point, the peptide needs to be used either to initiate building (clicking anywhere in the work area), or to be joined onto an existing structure (clicking on a free valance). In the latter case, attachment is made from the "N end", unless the free valence corresponds to an "unterminated" peptide fragment, in which case the appropriate end require to make an amide bond is used.

  3. Termination. The peptide is not yet terminated, and the two ends are still set up for addition of further amino acids.

    "*" indicates a free valence. Hydrogens occupy all free valences (except the *'ed positions at the two ends of the chain). If desired, these may be removed (replaced by free valences) by clicking on Delete at the bottom of the model kit (see discussion in Section 7.1.1).

    Termination follows by first selecting (clicking on) either CO2- or CO2H to the right of C:, and either NH3+ or NH2 to the right of N: (in the model kit) and then clicking on Terminate. Note that the choice of terminators is limited to simple neutral and ionic forms. If needed, these can be elaborated using either the entry or expert builders.

The buttons which appear at the bottom of the model kit are identical to those described previously for the entry and expert builders.


Section 7.1.4: Nucleotide Builder

Finally, Spartan also provides a separate builder for polynucleotides. It is reached from any of the other builders by clicking on Nucleotide at the top of the appropriate model kit.

Like the other builders, the nucleotide builder comprises a model kit on the right and a work area on the left.

At the top of the model kit are a series of switches for selecting what is to be built from among the following:

Selection of DNA, DNA (single strand) or DNA-RNA leads to one selection of bases designated by their icons.

Selection of RNA, RNA (double strand) or RNA-DNA leads to a second selection, the only difference is that uracil (U) has been substituted for thymine (T).

These bases replace "atoms", functional groups, rings and ligands as the basic building blocks in the nucleotide builder. Because these other building blocks are missing, most modifications of nucleotides, aside from modifications in base sequence and in overall conformation, need to be carried out either in the entry or expert builders.

There are two different modes of operation of the nucleotide builder, single base mode and polynucleotide mode. The former is used to initiate building with a single base or base pair, or to add a single base or base pair to an existing structure (brought into the builder or constructed using the entry or expert builders), while the latter is used to construct strands of DNA or RNA (or mixed strands). Switching between the two modes is accomplished with Build Sequence. "Off" corresponds to single base (base pair) mode and "on" corresponds to polynucleotide mode.

With Build Sequence "off", choice of base or base pair follows by clicking on the appropriate icon. To initiate building, position the cursor anywhere on screen and click; to add to an existing structure, position the cursor on top of an appropriate free valence and click.

With Build Sequence "on", polynucleotide construction is accomplished in three steps:

  1. Specification of base sequence. This is accomplished by clicking in
    order on the base codes. In response to each selection, the letter code appears as part of a string separated by "-" in a box below Build Sequence. At any time, the sequence can be altered by editing the box. Existing base codes can be deleted or changed or new codes added. The entire sequence can be specified in this way if desired. The sequence can be cleared, by clicking on Clear.

  2. Specification of helical structure. Once sequencing is complete, helical structure may be specified by clicking on A or B. These lead to "standard" A and B helices, respectively. Selecting Customize allows user modification of the rise (in Å) per base (Rise/Base) and twist (in degrees) per base (Twist/Base) for either A or B helices.

    At this point, the polynucleotide needs to be used either to initiate building (clicking anywhere in the work area), or to be joined onto an existing structure (clicking on a free valance). In the latter case, attachment is made from the " phosphate end".

  3. Termination. The polynucleotide is not yet terminated, and the two ends are still set up for addition of further bases or base pairs.

    "*" indicates a free valence. Hydrogens occupy all free valences (except the *'ed positions at the two ends of the chain). If desired, these may be removed (replaced by free valences) by selecting Delete at the bottom of the model kit (see discussion in Section 7.1.1). Termination follows by clicking on Terminate in the model kit.

The buttons which appear at the bottom of the model kit are identical to those described previously for the entry, expert and peptide builders.


Section 7.1.5: Library

All of Spartan's builders share a central "library". This accesses previously built Spartan molecules, allowing them to be used to initiate building (of new molecules) or to be added to molecules presently under construction. In addition, a number of "collections" are available:

    reaction_archive
    interesting_molecules
    ligands
    chelates
    high_coordination

These collections may serve either as building blocks (high_coordination, ligands and chelates), or templates (reaction_archive) or simply provide an opportunity for browsing (interesting_molecules and reaction_archive). The collections comprise only structures. No data (other than structures) from quantum chemical calculations or graphics are supplied.

Access to the library is via Library at the top of each model kit. Selection replaces the present model kit with a new display.

This comprises a file browser and a viewport for display and manipulation of the selected molecule, as well as for selection of a free valence (to act as an attachment point).

Entries from the "library" may be used either to initiate building, or to add to a molecule already under construction. In the former case, all that is required following selection of a molecule from the file browser is to click inside an empty work area (or to select New if a molecule is already on screen). In the latter case, selection of an attachment point (in addition to molecule selection) is required. This is easily accomplished using the viewport. Here the selected attachment point (indicated by a yellow circle) may be changed by clicking on a different free valence.


Section 7.1.6: Molecule Building Functionality

The user has access to a variety of functionality that is not associated with a button or an icon, but rather with menus inside the builder dialogs and with the mouse. Menu functions are discussed later (Section 7.1.7).

In addition to molecule manipulation (rotation, translation, scaling) the mouse is used to rotate about bonds, as well as to alter bond lengths. Bond rotation is accomplished via the following sequence of operations:

  1. Clicking on the desired bond (double bonds can be rotated about, but terminal bonds or bonds incorporated into cyclic structures may not be rotated about). The selected bond is indicated by a dashed line. (Note that the bond connecting the last "atom", functional group, ring or ligand added to the molecule is automatically selected and drawn as a dashed line rather than a solid line).

  2. Simultaneously pressing the space bar and the middle mouse button and dragging the mouse.

Altering bond length is accomplished by way of a similar sequence of operations:

  1. Clicking on the desired bond (bonds incorporated into rings may not be altered).

  2. Simultaneously pressing the space bar and the right mouse button and dragging the mouse.

Another function of the mouse is atom replacement, e.g., carbon by silicon; this is accomplished by double clicking on an existing atom (not a free valence) while the desired replacement atom icon is highlighted. Free valences will be adjusted to accommodate the replacement, e.g., replacement of sp3 carbon by sp3 oxygen would result in two free valences being removed. Atom replacements, which violate rules of atomic valence, are not permitted in the entry builder, and result in a bell. No checking is done in the expert builder; atom replacement merely changes the atomic number. Atom replacement is not available in the peptide and nucleotide builders.


Section 7.1.7: Menus in the Builders

Other molecule building/editing functions are accessed by way of menus. The same menu bar is at the top of all of Spartan's builders.


Section 7.1.7.1: Logo

Shortcut Key for Logo: (alt W)

About Spartan
Colors
Preferences

These are the same functions already described in Sections 3.1 and 3.3, although some functions do not apply to operations in the builder.


Section 7.1.7.2: File

Selection results in display of the following menu:

Save
Save As

Quit

Save

Saves a previously named file. It is useful for protecting an intermediate structure in the building of a complex molecule. If Save is selected for an unnamed (not previously saved) molecule, it behaves as Save As (see Section 4.5). The screen is not cleared, and the builder dialog is not exited.

Save As

This is the same function already described in Section 4.5. The screen is not cleared, and the builder dialog is not exited.

Quit

Exits the builder. Selection first results in display of a dialog.

Clicking on Cancel returns to the builder with no action taken. Clicking on
No exits the builder without saving the molecule; clicking on Yes results in the usual file browser. The user must supply a name for the molecule which is to be saved. If the name supplied already appears in the current working directory,
the user will be provided a message warning that the pre-existing information is to be overwritten.

Clicking on Overwrite overwrites the information and exits the browser; clicking on Cancel returns to the file browser allowing the user to select another name. Once an appropriate file name has been supplied, clicking on Save, saves the information and exits the browser. Clicking on Cancel exits the browser (and the builder) without saving the structure which has been built.


Section 7.1.7.3: Edit

Selection results in display of the following menu:

Undo/Redo

Add
New
Bond
Break
Delete

Minimize

Move

Grow Hydrogens

Clear
  1. Undo/Redo

    "Undoes" the previous action taken in the builder from among the following possibilities: Add and New (fragments, groups, rings and ligands), Bond, Break, Delete, Minimize, Move, Clear, structure termination (peptide and nucleotide builders only), edits or constraints on geometrical parameters and introduction of points or planes. Undo is unavailable (dehighlighted) upon initial entry into the builder (before any action has been taken) and is replaced by Redo immediately following an Undo. Redo "undoes" Undo, i.e., returns to the original state, and is available until the next builder action is taken.

  2. Add, New, Bond, Break, Delete, Minimize, Move.

    These have already been discussed in Section 7.1.1.

  3. Grow Hydrogens

    The primary use of this is to add hydrogens which might be missing from X-Ray crystal structure data.

  4. Clear

    This has already been discussed in Section 7.1.1.


Section 7.1.7.4: Model

Selection results in display of the following menu:

Wire
Ball and Wire

Labels

Wire

Ball and Wire

Labels

These have already been described in Section 5.1, 5.2 and 5.8, respectively.


Section 7.1.7.5: Geometry

Selection results in display of the folowing menu:

Distance
Angle
Dihedral

Freeze Center

Constrain Distance
Constrain Angel
Constrain Dihedral

Define Ligand Point
Define Point
Define Plane

Report Symmetry

Distance

This is an elaboration of the function previously described in Section 6.1. Not only does it provide distance measurement, but in some cases it also allows a distance to be changed. Selection results in a message in the menu bar.

Distance: Select 2 atoms, a bond, or a distance constraint.

Clicking on two atoms or, if the atoms are bonded, the interconnecting bond, or, if a distance has previously been constrained, the constraint vector, leads to display of a dialog.

This provides the distance (in Ångstroms). For bonded atoms which are not incorporated into rings, this distance may be changed by changing the contents of the Distance box, and then pressing Enter.

Note that the altered distance will not be maintained during molecular mechanics minimization. If this is what is desired, Constrain Distance should be used (Section 6.5).

To obtain another distance, click on another pair of atoms or alternatively on a bond or constraint vector. To exit the dialog, click on Done or select any other menu or model kit entry.

Angle

This is an elaboration of the function previously described in Section 6.2. Not only does it provide angle measurement, but in some cases it also allows an angle to be changed. Selection results in a message in the menu bar.

Angle: Select 3 atoms, 2 adjacent bonds, or an angle constraint.

Clicking on the appropriate atoms or bonds in the proper order, or on the constraint vector, leads to display of a dialog.

This provides the angle (in degrees). In the case where all three atoms are not incorporated into a ring, the angle may be changed simply by changing the contents of the Angle box, and then pressing Enter.

Note that the altered angle will not be maintained during molecular mechanics minimization. If this is what is desired, Constrain Angle should be used (Section 6.6).

To obtain another angle, repeat the operations above To exit the dialog, click on Done or select any other menu or model kit entry.

Dihedral

This is an elaboration of the function previously described in Section 6.3. Not only does it provide dihedral angle measurement, but in some cases it also allows a dihedral angle to be changed. Selection results in a message in the menu bar.

Dihedral: Select 4 atoms, 3 adjacent bonds, or a dihedral constraint.

Clicking on the appropriate atoms or bonds in the proper order, or on the constraint vector, leads to display of a dialog.

This provides the dihedral angle (in degrees). In the case where no more than two atoms are incorporated into a ring, this dihedral angle may be changed by changing the contents of the Dihedral Angle box and then pressing Enter.

Note that the altered dihedral angle will not be maintained during molecular mechanics minimization. If this is what is desired, Constrain Dihedral should be used (Section 6.7).

To obtain another dihedral angle, repeat the above operations. To exit the dialog, click on Done or select any other menu or model kit entry.

Freeze Center

Constrain Distance

Constrain Angle

Constrain Dihedral

These have already been described in Sections 6.4 to 6.7, respectively.

Define Ligand Point

Defines a pair of attachment ("ligand") points extending from the centroid of two or more atoms and above and below of the plane formed by these atoms.* Selection results in a message in the menu bar.

Define Ligand Point: Select 2 or more atoms to define a centroid.
Repeat an atom to end.

Clicking on a series of atoms in any order, with the end of the series signaled by clicking on an atom which has already been selected, defines a pair of ligand points and exits the dialog. Note that points may not be used to define a ligand point.

Three atoms uniquely define a plane, and the plane resulting from selection of more than three atoms represents a best fit.

One or both ligand points may be used to attach fragments, groups, rings or ligands. Note that if both ligand points are not needed, it is necessary to delete one of them (Delete; see Section 7.1.1). Otherwise it will turn into a hydrogen atom upon exiting the builder.

Define Point

Define Plane

Report Symmetry

These are the same functions already described in Sections 6.8, 6.9 and 6.12, respectively.

* Three (non-colinear) points are required in order for the normals to be uniquely defined. Spartan allows ligand points to be constructed from a centroid based on only two atoms (or three or more colinear atoms). Here, the orientation of the ligand points is arbitrary and may need to be adjusted (Dihedral from the Geometry menu; see Section 6.3).


Section 7.1.7.6: Help

Selection results in display of the following menu:

Builder Overview

Builder Overview

Describes the operation of Spartan's entry, expert, peptide and nucleotide builders.


Notes for Section 7

* The expert builder accesses a table of single-bond lengths stored in the file bondlengths under the .spartanrc directory (see Appendix B). These may be changed by editing this directory. Selecting other bond types scales the tabulated values by preset factors.


Chapter 7, Continued


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