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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.


Creates a new empty model and the corresponding graphical window.


Create a new model from a file.


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 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 models can be shifted in space using arrows. Also, the overlapping molecules 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.

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.


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.


This command exits the program.


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