Build

Theme

Theme is a set of parameters recommended for particular activities. The parameters include the force field, temperature for molecular dynamics, Ad hoc mode, etc. Specifying a theme sets the parameters simultaneously in all models. Themes can be convenient in demonstrations for rapid transition between considered sections as well as in model construction to switch between quantum and classical calculations.

Boundary conditions

Allow periodic boundary conditions to be added to the model.

Crystal

This module creates molecular lattices.

Using this module is described in the Build crystal section.

Chain

This module creates and edits chain molecules. Chain molecules are molecules composed of residues. In this program, residues are fragments specified in the molecule layout rather than arbitrary chemical residues. Such layout is commonly present in model files or can be defined in this module when a molecule is created.

Using this module is described in the Chain editor section.

The Chain editor manipulates residues contained in mlm files, which are stored in the data/Repository folder. The appropriate residue files are grouped in specialized sets such as Amino Acids, Nucleic Acids, etc.

The user can also develop its own residues for model construction. Their main distinction from the common mlm files is the obligatory specification of the joints and an optional table specifying the Fine types with the types and charges accepted in molecular mechanics force fields. The mlm files in the data/Repository folder and its subfolders are considered as residues for the construction and are shown as buttons in the Chain panel.

The user can also define conformational prototypes of chain molecules, which are stored in files with conf extension. Nevertheless, their content is a part of the mlm format. It includes one or two tables. The first of them specifies the torsion angle types defining the residue conformation in the chain molecule. For instance:

This table specifies the φ and ψ angles for the polypeptide chain, which will be represented in the Chain panel as Phi and Psi. The Fine1–Fine4 columns specify identifiers of atoms that define the torsion angles. These identifiers can be atomic Fine types, names, or IDs. Note that atomic IDs are local for a given file and can be used within this file only, while the names and Fine types can be used to create conformational prototypes. Once specified, they are stored throughout the program session and can be applied to generate any model. Such conformational prototypes are used in the Chain editor. All identifiers should be either Fine types (if available for all four atoms), names (if Fine type is not available for at least one atom and names are available for all four atoms), or atomic IDs. The residue atoms of the types specified in the Fine2 and Fine3 columns define the bond about which torsional rotation is performed, while the Fine1 and Fine4 atoms associated with them define the Fine1–Fine2–Fine3–Fine4 torsion angle. Note that two central atoms always belong to the residue, while the lateral atoms can also belong to the neighboring residue. Essentially, they should have a corresponding Fine type (Name or ID) and the bond to the corresponding central atoms. The torsion angle of the bond between different residues should not be specified in this table. Special keyword Joint is reserved for this angle.

The second table specifies the torsion angle values:

This example defines the conformations consecutively applied to each odd and even residues of the polypeptide chain. Specific values are given for the φ and ψ angles for each step as well as the ω angle, which is denoted Joint since it applies to the bond between two different residues. The Joint values of 180° can be omitted since it is the default value.

Free drawing

This module is designed to draw molecules on screen using a mouse. It is described in the Molecular drawing section. Note that, when the Draw panel is open, the right mouse button is used to draw atoms and bonds rather than to select objects.

Nano

is a panel with examples of nanocarbon structures. (For demonstration purposes.)

Strip

This command removes hydrogen atoms nonexistent in terms of the current force field. Such atoms are assigned to the molecular mechanics type '0'. This operation is unsafe, since removed atoms cannot be restored. It is recommended to save a model copy before this operation.

Force field

This command associates the user-selected force field with the model. In this case, the Fine types are used to define the molecular mechanics type of each atom. New partial charges should be set for atoms if they were specified for the selected force field in the @Table MM_types. Note that the association of atomic types with a particular force field does not mean that this field is available in the program. Such association makes sense if the constructed model is to be used in some other program, where the desired force field is available.

Detect bonds

This command tries to define chemical bonds in the model based on the distances between atoms. It is rarely used since chemical bonds are commonly defined. After reading a file with no bonds specified (xyz, pdb), this command is automatically invoked. Sometimes it can fail, for instance, if the model includes substantially overlapping atoms. In this case, the user can try to solve the problem and then to execute the command manually. The command can be useful for models retrieved from a manually created file.

Detect molecules

This command defines molecules in the model assuming that sets of chemically bound atoms are molecules. It is commonly used after the Detect bond command to coordinate the model.