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.
Allow periodic boundary conditions to be added to the model.
This module creates molecular lattices.
Using this module is described in the Build crystal
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
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
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.
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
Once specified, they are stored throughout the program session and can be
applied to generate any model. Such conformational prototypes are used in the
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
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.
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.
is a panel with examples of nanocarbon structures. (For demonstration purposes.)
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.
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.
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.
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.