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# Menu Commands ### File operations The following file formats are currently supported. For reading: MolMeccano (*.mlm) HyperChem (*.hin) SYBYL mol2 (*.mol2 *.ml2) Brookhaven Protein Data Bank (*.pdb *.ent) XYZ format (*.xyz *.xmol) For writing: MolMeccano (*.mlm) MDynaMix mmol (*.mmol) MDynaMix smol (*.smol) HyperChem (*.hin) Brookhaven Protein Data Bank (*.bdb *.ent) XYZ format (*.xyz *.xmol) Mlm is the native format of the system, which stores the molecular models as well as the fragments for chain molecule construction and torsion angles for conformational prototypes. Note that molecular mechanics manipulations and writing in the hin, mmol, and smol formats requires that the molecular mechanics type has been defined for each atom. Such types can be retrieved from mlm, hin, and mol2 files. The native mlm and HyperChem hin formats are supported for reading and writing. #### New Creates a new empty model and the corresponding graphical window. #### Open Create a new model from a file. #### Add The Add command is similar to the Open command except that it appends the file contents to the current model rather than to a new model. The previewed (gray) model appears immediately in the graphical window as dark spheres; however, it will be actually added only after pressing the OK button in the Add model panel, which converts its color to normal. The previewed model can be removed from the graphical window by pressing the Cancel button. Before pressing the OK button, the current model can be shifted in space using arrows. Note that only the current model can be shifted. Also, the molecules of the previewed model overlapping with the current one can be removed (’No overlap’ option). This can be useful when a box with a solvent is added to the model. Until the previewed model is appended by pressing the OK button, no operations (except the ’No overlap’ option) can be applied to it. Using this command is illustrated in A Typical Simulation Session in the Getting Started section. #### Pull on The Pull on command reads data from a file and overwrites the corresponding data in the model. This is convenient when several files store additional information about the same model. For instance, if we have a hin file with the information about molecular mechanics types of atoms and a xyz file with the coordinates obtained from an independent source, a complete model can be generated by reading the hin file (Open) and appending the coordinates from the xyz file (Pull on). Later, the resulting model can be stored as a hin file including both the atomic types and coordinates. The Pull on command should be used with caution. Make sure that the appended file describes the same model and that the atoms are listed in the same order as in the current model. #### Same folder If this option is checked, the same folder is offered to the user for reading and writing. Otherwise, the folders for reading and writing are independent and the user can open files from one folder and save them in another one by specifying the folders once. #### Save as … This command saves the active model in the selected format. If Auto is selected as the format, the model is saved in the format corresponding to the file extension. If the format is explicitly specified, the model is saved in a format and with the corresponding extension irrespective of the extension specified. #### Save This command saves the active model in the default format. #### Save All This command saves all models in the default format. #### With comments If this option is checked, additional information is included to saved files. It can be useful if the files are manually edited. In the mlm format, both the comments and a short description of the format are included. #### Exit This command exits the program. ### Edit #### Geometry This module measures the distances, angles, dihedral angles, and coordinates. It operates points in the three-dimensional space specified by Cartesian coordinates, positions of atoms, or positions of molecular centers-of-mass. The parameters can be both measured and altered by the user. Using the module is described in the Geometry editor section. #### Move model This command moves the whole model in space. Its panel also appears when the File > Add command is activated. This can be useful to separate the current and added models in space. Only the current model is moved. #### 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. #### Build crystal This command generates a spatial structure by replicating the model and placing the copies in the lattice cells. It can be useful to generate models of crystals and boxes with a solvent, which is exemplified in the Crystal builder section. #### Sequence 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 Sequence editor section. The Sequence editor manipulates residues contained in mlm files, which are stored in the Repository folder. The root folder contains several demonstration files of residues (used in the examples in this manual), which are not intended for normal work. The appropriate residue files are grouped in specialized sets such as Amino Acids, Nucleic Acids, etc. These sets are supplied separately from the main program. After purchasing a specialized set from Agile Molecule, the demonstration files can be removed. 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 Repository folder and its subfolders are considered as residues for the construction and are shown as buttons in the Sequence editor. 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:
@Table | Torsion_types
str | str | str | str | str | str
Type | Fine1 | Fine2 | Fine3 | Fine4 | Comment
Phi | C_amide | N_amide | C_alpha | C_amide |
Psi | N_amide | C_alpha | C_amide | N_amide |
This table specifies the φ and ψ angles for the polypeptide chain, which will be represented in the Sequence editor 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 Sequence 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 extreme 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:
@Table | Torsions
str | double | str | str
Type | Value | Res | Comment
Joint | 180 | 1 |
Phi | -140.53 | 1 |
Psi | 89.02 | 1 |
Joint | 180 | 2 |
Phi | 76.04 | 2 |
Psi | -129.7 | 2 |
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. #### Assign FF types 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. #### 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. ### Analyse #### Monitor This command opens the panel of monitors, which are used to keep an eye on the model status, e.g., during simulations. Double-clicking the desired monitor name opens a window with its properties, e.g., a plot. #### Information This command opens the Information panel, which includes the following sections:
Model | Information about the current model. Can be used to check the model before simulation.
Project | Brief information about all models in the project.
Session | Information about the main paths used in the current session.
Problems | Stores warning and error records in the current session.
Log | Shows the contents of the _log.txt file. This file stores the report of the current session: error messages, additional information about user actions, detailed information about calculations, debugging information, etc.
#### Geometry Same as in the Edit > Geometry menu. ### Compute #### Protocol Protocol is the main tool to organize computations in the system. It is a list of actions constitutively executed by the program. Protocol belongs to the whole project and can be applied to any model. The set of available protocols is shown in the central panel. It can be edited by changing the contents of the Protocols folder. A protocol can be executed from any step by selecting the desired item by mouse and pressing the Run button. The execution can be stopped by the Stop button. Each step can be executed by the combination of Tune and Start buttons. The Tune button makes all preliminary operations required for the corresponding step. The Start button executes this step. Actually, the Run button constitutively applies the Tune and Start combination to the protocol steps. Normally, the Run button is used to execute the desired protocol. The Start button is used in exceptional cases, since it is unsafe. If the Tune button was not pressed, the program behavior after pressing the Start button is unpredictable. Nevertheless, the Tune and Start combination can be very useful under particular conditions. If a protocol step uses an external program, the user can control its execution. Pressing the Tune button generates all files required for the external program execution, after which these files can be edited and the program can be started by pressing the Start button. This approach can be used to prepare tasks to be performed on remote computers. The protocol items (Length, T, P, and Comment) can be edited after double-clicking the corresponding cell. Both numeric values and units of measurement can be altered. Entering a unit of measurement after a numeric value forces the program to use the value in this unit. If a unit of measurement is entered (with no value), the previous value is converted to the new unit. Protocol changes have no effect on the protocol files and all changes are lost after the program is closed. The changes can be introduced by editing files in the Protocols folder. ### Help #### Contents This command shows the program documentation. By default, the documentation is stored at the program web site. For a local copy of the documentation in html or pdf formats contact with Agile Molecule.
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| Copyright 1996, 1999, 2005, 2007 by: Alexander Lyubartsev, Aatto Laaksonen, Alexey Nikitin. Department of Physical Chemistry, Stockholm University. All rights reserved. Copyright 2006, 2007 Agile Molecule. All rights reserved.