The Molecule List browser

   

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.