Insight II



5       Builder Module

The Builder command activates the Builder module. This module allows you to construct new molecules from molecular fragments or individual atoms. It also allows you to modify such properties as atom type, hybridization, potential function parameters, bond order, and geometry of existing molecules. You can use the newly created or modified molecules in all of the normal ways throughout the Insight II program.


Command Summary

In addition to the core pulldowns in the top menu bar, the Builder module adds pulldowns to the lower menu bar. The pulldowns are Atom, Fragment, Modify, Forcefield, Pseudo_Atom, and Optimize. (The Sketch pulldown and the Toolbox comprise the Sketcher product, licensed separately and documented in the next chapter.)

Atom Pulldown

The Atom pulldown is used to modify molecules at the atomic level.

Charge Atom

The Charge Atom command is used to set or alter partial or formal atomic charges. This command sets discrete user supplied charge values in specified atoms. It does not perform any type of overall charge assignment. The charges for an entire molecule can be computed using the Charges command, which is accessed from the Forcefield pulldown.

Hybridization Atom

The Hybridization Atom command is used to change the hybridization of a molecule by adding or deleting hydrogen atoms as needed, and modifying the molecular geometry accordingly. The level for hybridization may be specified, or calculated automatically by the Insight II program. The Hybridization Atom command can also be used to add hydrogens to fill unfilled values, as determined by existing bonds and geometry. In this mode of operation, the desired hybridization is ascertained by looking at explicit bond orders first, if the hybridization is still ambiguous after looking at bond order the geometry of the atom and its surrounding environment will be used. By default, the Insight II program fills valences to a neutral state. Using this command, this mode is equivalent to the Hydrogens command in the Modify pulldown. The program never changes the actual bond orders of any bonds. It is left to the user to make sure that the bond order and geometry are consistent.

The naming scheme for hydrogens is as follows:

· If one hydrogen is bonded to X, it is HX; if two, they are HX1 and HX2.

· If one hydrogen is bonded to XA, it is HA; if two, they are HA1 and HA2.

· If one hydrogen is bonded to XD1, it is HD1; if two, they are HD11 and HD12.

Any hydrogens bonded to X1 are named H1n, where n is the relative number of the hydrogen being bonded to the heavy atom. Any hydrogens bonded to X11 are named H11n, where n is the relative number of the hydrogen being added. Any hydrogens bonded to X111 are named Hseq., where seq is the relative number of the hydrogen in the residue containing the heavy atom.

The addition of any hydrogen to a residue causes a look-up to be done in the currently defined residue library. The residue library used for the look-up is the one pointed to by the environmental variable RESIDUE_LIBRARY, in the directory pointed to by the environmental variable BIOSYM_LIBRARY. A match occurs when a residue has the same number of atoms as an entry in the library with the identical atom names. The atoms do not have to be in the same order; bond orders are not used when the look-up is done. If a match occurs, the residue inherits the residue type, partial charges, and potential types of the template.

Optionally, lone pairs can be added along with the hydrogens.

Planar Atom

The Planar Atom command is used to set or unset the out-of-plane flag for an atom. Out-of-plane atoms are used by the Discover program to mark atoms that are to be constrained to lie in the plane of the three atoms it is bonded to. You rarely need to use this command because the Insight II program automatically keeps track of out-of-plane atoms.

Potential Atom

The Potential Atom command is used to set or change the potential function type for an atom, according to the assigned forcefield library. This command is used to manually change the potential function types of individual atoms. The Potentials command in the Forcefield pulldown can be used to automatically set the potential function atom types for an entire molecule. The available potential function atom types in this command are taken from the forcefield library, which is defined by the environment variable FORCEFIELD and is in the directory defined by the environment variable BIOSYM_LIBRARY.

Delete Atom

The Delete Atom command is used to delete an atom from a molecule. If a heavy atom is deleted, all bonded hydrogens are also deleted. No attempt is made to fill valences left open by the deletion. When the last atom of a molecule is deleted, the molecule itself is deleted.

Replace Atom

The Replace Atom command is used to change the element type of an atom. Connected hydrogens are removed appropriately. The Insight II program allows the replacement of atoms that result in valences being exceeded. For example, an sp3 carbon with three ligands can be replaced by an oxygen. The deletion of the extra bond is left for the user to do.

Rename Atom

The Rename Atom command is used to change the name of an atom. Insight II requires that all atom names in a molecule be unique. This command allows you to explicitly change the name of individual atoms.

List Atom

The List Atom command lists information about a specified atom, including the atom name, element type, coordinates, sequence number, and connected atom sequence numbers. Additional information can be displayed, including the group name, potential function type, fractional space coordinates, charge, switch and out-of-plane flag values. The listed information may be displayed or output to a file.

Fragment Pulldown

The Fragment pulldown is used to maintain the fragment library, create or modify a fragment, or repeat the fragment to create a polypeptide or polymer.

Get Fragment

The Get Fragment command is used to create a molecule by copying a fragment from the fragment library. This command also displays the contents of the fragment library in a separate window. You can configure which fragment libraries to display via the Fragment Libraries... button. Once a molecule has been created with this command, it can be modified and manipulated just as a molecule from any other source. The available categories for storing and retrieving a fragment are Aminos, Atoms, Groups, Hydrocarbons, Rings, Metal templates, Metal ligands, Cage Clusters, Metal Complexes, and User.

Put Fragment

The Put Fragment command is used to add a newly-defined fragment to the fragment library, or replace an existing fragment in the fragment library. Once a fragment is added, it appears in the fragment display of the Builder module. New fragments are added at the end of the list of the fragments of that type.

The available categories for storing and retrieving a fragment are aminos, atoms, groups, hydrocarbons, rings, metals, ligands, and user. Before storing a fragment, you might want to minimize its geometry, or adjust its potentials and charges.

You may need your own copy of the fragment library to be able to use the Remove Fragment command. (See the section Setting Up Your Own or a Shareable Repeat Unit/Fragment Library, and the section Repeat Unit Tutorial.)

Remove Fragment

The Remove Fragment command is used to remove a fragment from the fragment library.

You may need your own copy of the fragment library to be able to use the Remove Fragment command. (See the section Setting Up Your Own or a Shareable Repeat Unit/Fragment Library, and the section Repeat Unit Tutorial.)

Define Fragment

The Define Fragment command is used to make a molecule, which may itself contain multiple fragments or monomer/residues, into a fragment suitable for
addition to the fragment library or for polymerization via the Repeat command. During the process, the molecule is collapsed into a single monomer/residue. If the fragment is to be repeated, and head and tail atom must be identified.

Repeat Fragment

The Repeat Fragment command is used to create polypeptides or polymers by repeating an amino acid, monomer, or existing polypeptide or polymer that has forward and backward bonding hydrogens defined. An optional dihedral angle for the bond created may be given.

Delete Fragment

The Delete Fragment command is used to delete a single fragment, residue, or monomer from a molecule. No change is made to the geometry of the portion of the molecule which remains. In the case that the molecule is a single monomer or residue as in the case of a fragment or repeat unit, the whole molecule is deleted. An energy minimization may be used to readjust the geometry of the molecule in the cases where a nonphysical situation occurs.

List Fragment

The List Fragment command lists the coordinate and topology details for a specific repeat unit, fragment, or residue. Using this command, you can also list molecular mechanics information such as partial charges and potentials.

Modify Pulldown

The Modify pulldown contains various commands for modifying molecular structures.

Bond

The Bond command is used to create, delete, or modify intermolecular and intramolecular bonds.

Intermolecular bonding requires choosing two atoms, usually hydrogens, that are lost when the bond is created. When intermolecular bonding is done, the smaller of the molecules is repositioned so as to make the length and geometry of the bond reasonable. If a peptide bond is created via intermolecular bonding, its bond order automatically is set to partial double. The bond lengths used by the Insight II program are specified in the file elements.dat, which is located in the Insight II program's help directory. This file is read each time the Insight II program is run, and can be modified by the user.

For intramolecular bonding, the bond is created directly between the specified atoms. When possible, the Insight II program deletes hydrogens that would cause valences to be exceeded when the bond is formed. The program allows heavy atom valences to be exceeded temporarily while bonding. These inconsistencies must be corrected by the user before potential function atom types can be assigned.

Bonds can be specified with atoms in fragments or repeat units. A copy of the fragment is made automatically and the bond created to it. The copied fragment is positioned as to the make the bond length and geometry reasonable.

When the Bond command is used to break an existing bond between two atoms, the program does not attempt to fill open valences created when a bond is broken. Open valences can be filled by adding alternative bonds or adding hydrogens.

The Bond command can also be used to modify the bond order of a single bond or determine appropriate bond orders for an entire molecule. The Insight II program uses a very simple scheme for determining bond orders; it recognizes planar rings and carbonyl groups. The program does not try to determine conjugation. Hydrogens can be added or deleted to maintain the correct valence for the bonded atoms.

Fuse_1

The Fuse_1 command is used to create fused ring systems by performing intramolecular fusion of a pair of heavy atoms. The fusion is performed by connecting all the bonds of the second heavy atom to the first heavy atom, then deleting the second atom. After all the bonds from the second atom have been added to the first atom, hydrogens that violate the heavy atoms valence are deleted. The Fuse_1 command is also useful for cleaning up any unfused pairs remaining after a 2- or 3-pair fusion.

Figure 18 . Example of the Fuse_1 command

Heavy atoms labeled 1 and 2 are picked to create the structure shown at the bottom.  

Fuse_2

The Fuse_2 command is used to create fused ring systems by fusing component rings together intermolecularly. Two atoms (usually heavy), are used in each of the two molecules to identify the atom used for superposition. A third atom in each molecule is picked that defines a plane using the first two atoms picked. The fusion is accomplished by superimposing the second molecule or fragment on the first, such that the first two pairs of atoms picked are coincident. The molecules or fragments are then merged. The atoms that comprised the second molecule or fragment are then rotated to bring the alignment atom into the same plane as the alignment atom of the first molecule or fragment. The two pairs of atoms used for superposition are fused, then, any atom pairs brought within .5 Å of one another by the superposition are fused. Hydrogens that violate the valence of an atom are deleted from all heavy atoms that were fused.

Figure 19 . Example of 2-pair Intermolecular Fusion

Figure 19 illustrates the creation of cap-decalin by fusing two cyclohexanes. The resulting molecule is created by first picking atoms 1, 2, 3, and 4 successively. This identifies the atoms used for the superposition of the second molecule onto the first (Figure 19a). Next, atoms 5 and 6 are picked which identify the atoms which will be used for alignment rotation. The second molecule is then rotated through (Figure 19b is the angle between the planes formed by atoms 5, 1, and 3, and 2, 4, and 6. Finally, coincident heavy atoms are fused (Figure 19c).

Fuse_3

The Fuse_3 command is used to create fused ring systems by fusing component rings together intermolecularly. Three heavy atoms in each molecule are usually used to identify three pairs of atoms used for superposition. The fusion is accomplished by superimposing the second molecule or fragment on the first such that the pairs of fusion atoms are coincident. The molecules or fragments are merged, then the specified pairs are fused. Any other atom pairs brought within .5 Å of another by the superimposition are also fused. Hydrogens that violate the valence of an atom are deleted from all heavy atoms that were fused.

Figure 20 . Example of 3-pair Fusion

Figure 20 illustrates the creation of a triphenyl unit using the Fuse_3 command to fuse napthalene and benzene together. The triphenylene was created by picking atom pairs 1, 2, and 3.

Fuse_Close

The Fuse_Close command is used to fuse all the close atoms (atoms within 0.5 Å of each other) either in one molecule, or between two molecules. Close atom fusion between two molecules results in the second being merged into the first, and then all close atoms being fused. No superimposition is done. Hydrogens that violate the valence of an atom are deleted from all heavy atoms that were fused.

Figure 21 . Example of Close Atom Fusion

Figure 21 above illustrates the creation of a corenene molecule by fusing two anthracene molecules. The corenene molecule is created by first manually superimposing one of the anthrazenes. The final molecule is then created using the Fuse_Close command.

Hydrogens

The Hydrogens command automatically adds hydrogens or lone pairs to entire molecules. This command can also be used to add hydrogens to fill unfilled valences, as determined by existing bonds and geometry. In this mode of operation, the desired hybridization is ascertained by looking at explicit bond orders first. If the hybridization is still ambiguous after looking at bond order the geometry of the atom and its surrounding environment is used. By default, Insight II fills valences to a neutral state. Insight II never changes the actual bond orders of any bonds. It is up to you to make sure that the bond order and geometry are consistent.

This command also allows you to add hydrogens based on target pH of the solution. During pH based hydrogenation, the number of hydrogens to be added for an atom is decided by doing a look-up of the residue in the currently defined residue library. The residue library used for the look-up is the one pointed to by the environmental variable RESIDUE_LIBRARY, in the directory pointed to by the environmental variable BIOSYM_LIBRARY. A match occurs when either of following two conditions are met:

If a match occurs, the atom inherits the number of hydrogens of the same atom in the template. Otherwise, valences are filled to a neutral state.

The naming scheme for hydrogens is as follows:

In addition, you can specify to rename the hydrogen atoms in sidechains of amino acid residues to conform to IUPAC nomenclature rules, by turning the Assign_IUPAC_Names parameter On.

To resolve any name conflicts, hydrogens are prefixed with the bonded heavy element name, e.g., hydrogens bonded to C3´ and O3´ are H3´ and HO3´.

Any hydrogens bonded to X1 are named H1n, where n is the relative number of the hydrogen being bonded to the heavy atom. Any hydrogens bonded to X11 get named H11n, where n is the relative number of the hydrogen being added. Any hydrogens bonded to X111 get named Hseq, where seq is the relative number of the hydrogen in the residue containing the heavy atom.

The addition of any hydrogen to a residue causes a look-up to be done in the currently defined residue library (described above). A match occurs when a residue has the same number of atoms as an entry in the library with the identical atom names. The atoms do not have to be in the same order; bond orders are not used when the look-up is done. If a match occurs, the residue inherits the residue type, partial charges, and potential types of the template.

For protein molecules, the Capping Mode parameter determines whether the termini are capped by the Modify/Hydrogens command. In addition, the termini can be capped with charged or un-charged capping groups.

Merge

The Merge command combines two molecules into a single molecule. The separate atom and monomer/residue lists are merged and henceforth treated as a single object. Note that Merge is different from the Associate command, in which the two molecules are maintained as two separate objects.

Replicates created by the Symmetry command can also be merged into other molecules. Since replicates are dependent on the given symmetry operation and state of the molecule that derived them (i.e., the asymmetric unit), special steps are necessary to not break the symmetry relationship of replicates with the asymmetric unit. Replicates cannot be merged into the asymmetric unit because this operation would break the symmetry relationship of the replicates; however, the replicates can be merged into a copy of the asymmetric unit. To merge replicates back into a molecule that created the replicates, perform the following steps:

1. Make a copy of the asymmetric unit molecule by using the Copy Object command.

2. Use the Merge command and reference the newly-created Copy molecule for the Molecule Name parameter.

3. Use a given replicate for the Molecule_to_Merge parameter.

By using a copy of the asymmetric unit, the symmetry is preserved as well as the integrity of the original asymmetric unit. Additional symmetry operations can then be performed on the original asymmetric unit without affecting the molecule copy containing merged replicates.

Unmerge

The UnMerge command allows you to create a new molecule by extracting a piece from an existing molecule. The piece to be unmerged must not be bonded to any atoms of the part(s) that are to remain in the original object. The UnMerge command can be used to make a separate molecule out of one subunit of a protein complex, for example.

Geometry

The Geometry command is used to modify distances, angles, and dihedrals in and between molecules. Distances can be modified between bonded or unbonded atoms not connected by rings. Angles can be set between any three atoms not connected by rings. Dihedrals can be set between four atoms not connected by rings; however, they must all be in the same molecule.

Ring_Conf

The Ring_Conf command is used to interactively modify the geometry of rings in molecules without breaking a bond. A fragment of a ring, which is specified by two anchor atoms, can be moved up and down relative to the ring plane.

There are two types of operations you can perform. The first one is called flipping. In this operation, the ring is flipped using the negative value of the current plane angle. A typical example is flipping a cyclohexane ring from chair to boat conformation, or vice versa.

The second operation is called flapping. In this operation, you specify the angle to apply either by typing in the value (in degrees) or by using the valuator. In the latter case, the molecule's structure is changed interactively. Once you select <Execute>, the molecule adopts the displayed conformation. If you select <Cancel> instead, the original structure is restored.

You specify the moving fragment by selecting two anchor atoms. These atoms must be in the same and in a unique ring, and there must be at least one atom separating them. The side of the ring containing less ring atoms is the moving fragment. If both sides contain the same number of atoms, the fragment connecting to fewer atoms is moved.

The plane angle is defined by two ring planes formed by the anchor atoms and the two fragments. Each ring plane is defined by three points:

1. The coordinate of anchor atom 1;

2. The coordinate of anchor atom 2;

3. Either:

a. If there is only one ring atom between atom 1 and atom 2, the coordinate of this atom.

b. If there is more than one atom separating the two anchor atoms, the coordinate which is the center of the two ring atoms connecting to atom 1 and atom 2.

The moving fragment is flapped by rotating two bonds connecting the anchor atoms on the fixed fragment.

Invert

The Invert command is used to invert the chiral sense of an atom in an existing molecule or one that is being built. Inverting the chirality about an atom is accomplished using a 180º rotation around the axis defined as the mid-vector of the two bonds to be inverted (see Figure 22). To invert chirality, choose the atom that is the chiral center and two bonded atoms that specify the atoms to be inverted. Chirality inversion can be done even if the two bonded atoms are connected to each other in a ring, but cannot be done if either is connected back to the chiral atom via another path. Atoms in templates cannot be changed with the Invert command.

The chirality of the central atom is inverted by picking atoms 1, 2, then 3, using the Invert command.

Figure 22 . Inversion of a Chiral Center

Reflect

The Reflect command generates the mirror image of a molecule. This is done by changing the sign of either the x, y, or z coordinates of all atoms of the molecule. The choice of which coordinate is reflected is controlled by the Reflection Axis parameter. For example, setting this parameter to X causes all the x coordinates in the molecule to change sign, thereby effectively reflecting the molecule along the x axis or, equivalently, in the yz plane. The Molecule Name parameter specifies the molecule for which the reflection operation is performed.

In addition, the molecule's transform is altered such that the molecule's center of mass screen location is unchanged, and so that its center of rotation undergoes the same reflection as the molecule itself.

Element

The Element command is used to define elements and their attributes. Explicit bond lengths between pairs of elements can be defined. If the element specified is already defined, the defaults for the parameters are the current values for that element.

The attributes of an element that can be modified include the van der Waals radius, covalent radius, maximum valence, minimum valence, and common valence. The common valence is defined as the valence that results in a neutral state. The van der Waals radius is used for van der Waals overlap checking, and surface and CPK generation. The covalent radius is used for determining bond lengths when explicit bond lengths are not known. The maximum and minimum valences are used when adding and deleting hydrogens. The original definition of an element is made in the file elements.dat, which is located in the help directory.

Atom_Position

The Atom_Position command allows you to move an atom to a new coordinate position manually. You can move the atom to a new position in either the world coordinate system or within the coordinate space of the object to which the atom belongs. Movement can be specified relative to the atom's current location or relative to the absolute coordinates in the chosen space. Any bonds to the atom are adjusted without affecting the accompanying atoms.

Forcefield Pulldown

The Forcefield pulldown contains commands to fix, check, or accept the potential atom types and partial charges of a molecule, to fix or accept formal charges of a molecule, and to select a new forcefield type. It also contains the commands to perform charge group validity checks and editing. These commands are used to assign partial charges and potential function atom types to molecules for energy calculations by either the Insight II or the Discover program.

The Forcefield pulldown appears in the Builder and Biopolymer model-building modules.

Select

The Select command allows you to determine the current forcefield type, select a new forcefield, or copy the forcefield file without exiting your current session.

The Copy option of the Select command allows you to make a private copy of the forcefield file and the associated rule file and residue library so that you can modify it using the forcefield editor.

The Select command automatically resets the FORCEFIELD, RESIDUE_LIBRARY, and INSIGHT_POTENTIAL_TEMPLATES environment variables each time you select a new forcefield. However, these variables revert to their original values defined prior to the current session using the Insight II program. Therefore, all changes to these variables apply to the current session only. The selected forcefield is displayed in the lower left corner of the screen, beneath the dial boxes.

Since the potential atom types and/or charges associated with the previously built molecules may not be compatible with the forcefield, the Select command allows you to erase all of the previous atom type and charge assignments.

Potentials

The Potentials command is used to check, fix, or accept the potential function types of the atoms in a molecule.

This command is automatically activated when you leave the model-building module (in which Forcefield appears) if there are any molecules with inconsistent potential function atom types. Most operations performed in a model-building module change the model and necessitate reassignment of the potential function atoms types. Potential function atom types must be assigned before charges can be assigned. Potential function atom types must be assigned prior to running a simulation with the Discover program.

The Insight II program assigns potential types by looking at an atom and its surrounding environment. The potential function atom type assignment rules reside in an external file to facilitate potential function atom type assignment to any forcefield. When assigning potential function atom types, Insight II first looks for matches in the currently assigned residue library. If a match is found, the residue library entry is used to assign the potential function atom types. If a match is not found, the program looks for an entry in the potential template rule file. The potential template rule file describes the chemical environment using a SMILES-like language. You may add new potential function atom types by making additions to the template rules file (refer to the Potential Template Rules appendix for a complete description on how to add rules to the template rules file). A rule file is provided for each forcefield. As potential atom types are changed, this information is reported to the information area and the textport. You should also note atoms that could not be assigned a potential type, which are flagged with a question mark (?). These atoms did not pass any potential template tests, and are not usable in Discover program simulations. The appropriate forcefield file must also have been defined before running the Insight II program.

The out-of-plane values are assigned for each atom based on the rules in Appendix H.

Groups

The Groups command is used to edit or perform validity checks on charge groups. Potentials and charges for the atoms must be fixed or accepted prior to Groups command execution. Also, objects that are animated or contain active torsions cannot have their charge groups edited.

The validity checks that are currently performed on the charge groups are:

Charge Group Formal (int +- tolerance) Charge,

Single Switching Atom, and

Charge Group Sum (for Monomer and Molecules) Formal Charge,

The Edit enumerated choice of the Charge Group Action parameter enables you to assign atoms to charge groups as well as to assign switching atoms.

Assign_CFF Forcefield

The Assign_CFF command is used to assign the CFF force field. The corresponding atom types and partial charges are assigned if "Fix" is set for Potential_Action and Partial_Chg_Action (this is the default). Therefore, unlike "Select" command in the Forcefield pulldown, after Assign_CFF, it is not necessary to use the "Potential" command to assign potential functions.

Tabulate Forcefield

The Tabulate Forcefield command creates the table of a Forcefield previously loaded using the Select Forcefield command. It allows browsing, editing, and analyzing of Forcefield parameters. In addition to the Search, Sort, and Summary commands in the Data pulldown of the spreadsheet, browsing of Forcefield parameters is controlled by the View Data command (or the View icon), and updating by the Update Data command (or the Update icon). Editing is performed using spreadsheet operations. The modified table can be saved as a new Forcefield file using Save_As File command (or the Save icon) in Forcefield table for use in Discover.

Forcefield Support

The Insight II program supports the CFF91 forcefield, the CVFF forcefield, the AMBER forcefield, CHARMm, and the ESFF forcefield, specified through the Forcefield/Select command. Insight II also supports the CFF forcefield, which is licensed separately. These environment variables are set:

BIOSYM_LIBRARY Points to the directory which contains the rule files, residue libraries, and forcefield files

RESIDUE_LIBRARY Points to the residue library currently being used for potential function atom type assignments. The default is cvffa.rlb.

INSIGHT_POTENTIAL_TEMPLATES
Points to the potential template rule file being used for potential function atom type assignment when a match cannot be found in the residue library. The default is cvff_templates.dat. If this environment variable is not defined, the Insight II program uses the hard-coded rules consistent with the CVFF forcefield.

FORCEFIELD Points to the forcefield file being used for element type look-up and bond-increment look-up. This file must be consistent with the currently assigned residue library and template rule files.

Pseudo_Atom Pulldown

The Pseudo_Atom pulldown contains commands to create and modify pseudoatoms. It contains the following commands: Define, Rename, Delete, and List.

Pseudoatoms are defined as the instantaneous average of the coordinates of a set of real atoms. For example, the centroid of a phenyl group could be displayed as a pseudoatom created from the six carbon atoms in the ring. Pseudoatoms are referenced in the same way as atoms: their names can be explicitly specified at the time of their creation or can be generated automatically.

In the DeCipher and Analysis modules, pseudoatoms can be defined and used to study geometric properties. In the DeCipher module, pseudoatoms can be used in conjunction with the commands in the Functions and Geometrics pulldowns to plot and visualize several user-definable properties. In the Discover module, pseudoatoms can be defined and used to define NOE constraints.

Pseudoatoms can also be used in the Color, Display, Label, and List commands in the Molecule pulldown; the Distance, Angle, Dihedral, and XYZ commands in the Measure pulldown; the Center, Move, Overlay, and Superimpose commands in the Transform pulldown; and the commands in the Subset pulldown.

Define

The Define command is used to create new pseudoatoms. Five computational criteria (charge, geometry or arithmetic mean, center of mass, temperature factor, and van der Waals radius) are provided to define the pseudoatom relative to other atoms. The Pseudo_Atom Name (maximum of four characters) can be user-specified. The default value of Auto indicates the automatic generation of the names. The Definition_Mode allows you to add or remove an atom set from the definition of a pseudoatom. The Molecule Spec can be applied to generate one specific pseudoatom. The Per_Monomer and Per_Molecule parameters can be used to apply the specification to each monomer or molecule. The ability to use wildcards and multiple residue:atom combinations in the Molecule Spec allows you to specify a virtually unlimited number of atoms in defining the pseudoatom.

Rename

The Rename command is used to rename pseudoatoms created by the Define command.

Delete

The Delete command is used to delete a pseudoatom or a group of pseudoatoms.

List

The List command is used to list information about any specified set of pseudoatoms. Coordinate information can be obtained by toggling the Extdetails parameter to on. All output can be directed to a file.

Optimize Pulldown

The Optimize pulldown contains the Optimize command, which provides convenient and rapid access to a minimization of a molecule or molecular system, using the Discover program.

Optimize

The Optimize command uses a Discover program minimization strategy which automatically cycles through three different minimization algorithms. Each minimizer may be accessed separately in the Discover module, but Optimize provides a quick and convenient route to minimizing a molecule within the Builder module without moving to Discover, and without defining a new minimization when the previous minimization is complete.

A minimization defined with Optimize commences with steepest descents, moves on to conjugate gradients, and finishes with the BFGS algorithm. Maximum derivative criteria are used to select the next algorithm in the cycle; conjugate gradients is selected when the maximum derivative in the molecule is less than 10., and BFGS is selected when the maximum derivative drops below 1.

The total number of iterations for the complete minimization cycle and the final convergence criterion¦ (i.e., the maximum derivative) can be specified. Note that the optimization terminates if the total number of iterations is exceeded, even if the convergence criterion is not satisfied. It is also possible to specify whether or not to include charges in the Discover energy calculation. The energy calculation uses a harmonic term for bond stretching and does not use cross terms.


Builder Tutorials

As of this release, most tutorials are now available online for use with the Pilot interface. To access the online tutorials, click the mortarboard icon in the Insight II interface.

Then, from the Open Tutorial window, select Insight II tutorials. Select the Builder module, and choose from the list of available lessons. For molecule-building functionality in particular, refer to the following Sketcher chapter.

Once you are running Pilot, you can access the Open Tutorial window at any time by clicking the Open File button in the lower left corner of the Pilot window.

For a more complete description of Pilot and its use, click the on-screen help button in the Pilot interface or refer to the Insight II User Guide.




Last updated December 17, 1998 at 04:26PM PST.
Copyright © 1998, Molecular Simulations Inc. All rights reserved.