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 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.
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.
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