Main Form Molecule List browser

The Main, form shows the global status of the loaded molecules. Any number of molecules may be displayed by VMD simultaneously. Each molecule can separately be hidden from view, fixed in place (e.g., prevented from being affected by mouse rotation commands). The form contains controls to change the status of the molecules individually or in groups.

The browser at the center displays information about each molecule. The Name is the file name which contained the topology information, followed by a unique integer ID which is assigned to each molecule by VMD when it is loaded. Atoms shows the number of atoms in the molecule, Frames gives the number of timesteps associated with the file, and Source is either File or Remote, reflecting whether the information was acquired from a file or a remote simulation.

Next to each molecule is a set of status flags, which indicate the current Status of each molecule. Each molecule has the following characteristics, which can be on or off:

• Top (T)
  Top indicates the default molecule used in the text commands when nothing is specified for the mol text command. It is also used in some forms (like Graphics and Animate) to determine certain values. There can be only one top molecule at a time.

• Active (A)
  Several commands and actions in VMD operate on many molecules. These commands, unless specifically specified otherwise, will do their action for all the active molecules.

• Drawn (D)
  If a molecule is Drawn then it is being displayed in the graphics display window. This is useful for temporarily hiding a molecule from view without deleting it.

• Fixed (F)
  Fixed molecules do not undergo rotation, translation, or scaling. Note that while it may seem that one molecule has been moved relative to another, the difference is only apparent. The internal coordinates do not change when a standard rotation is applied by using, for example, the mouse. It is possible, however, to change the coordinates of atoms in a molecule, using the text command interface, and by using the atom move picking modes.

Changing the Molecule's Status

The status of a given molecule can be changed by selecting the molecule in the browser and pressing the toggle that controls the appropriate flag. The active, drawn, and fixed status values can be changed for several molecules at the same time by selecting several molecules before pressing the toggle. However, only one molecule can be top at any one time, so Make Top can only be applied to one selection. Pressing one of the All ... or No ... buttons either sets or unsets corresponding flag on all the loaded molecules.

The Single A/D/T button makes the selected molecule active, displayed, and top. It also resets the scene so the given molecule roughly fills the screen. It is a quick way to switch from viewing one molecule to another when it is desirable to only show one molecule within the graphics display window at a time.

Saving Trajectory Frames

Using the `Save Trajectory' menu item, you can write trajectory frames to a file in one of several file formats including PDB, DCD, Amber CRD, etc. This feature may be used to write out a new trajectory in a single file after assembling many frames from different sources (such as PDB CRD, DCD or Gromacs files, or even from a remote simulation). You can also use this, in combination with the molecule file browser as a way to make PDB files from a DCD/CRD trajectory.

You can either save the entire stored trajectory, or a slice of the data by using the Amount chooser. Then select the appropriate output file type in the File Type chooser, and press the Write button in the bottom right corner. This brings up the file browser, which you can use to enter the new filename. Once you press the Write button in the browser, the file will be written without further confirmation. See section on atomselect command for information on how to write atom coordinates for an atom selection in a PDB file.

Deleting Trajectory Frames

This provides a way to delete frames from memory. First, choose the frames you wish to delete with the Amount chooser and (possibly) the frame skip controls, then press the Delete button. There is no confirmation of deletions.

One problem with this mechanism is there is no way to delete every frame except for those given by the frame skip. You can get around this by writing the skip selection to a CRD/DCD file, deleting all the frames from memory, then reading the skip back in from disk.

Deleting a Molecule

The Delete button deletes all selected molecules. There is no prompt verifying the deletion, so take some care. If a deleted molecule was the top molecule, a new top molecule will be set from the remaining structures.