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Main Window Molecule List browser

The Main window 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 or fixed in place (e.g., prevented from being affected by mouse rotation commands). The window contains controls to change the status of the molecules individually or in groups.

The browser displays information about each molecule. A unique integer ID is assigned to each molecule by VMD when it is loaded. The Molecule is the file name which contained the topology information. Atoms shows the number of atoms in the molecule, and Frames gives the number of frames associated with the file.

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:

Changing the Molecule's Status

The status of a given molecule can be changed by selecting the molecule in the browser and double-clicking the appropriate flag. Only one molecule can be top at any one time, so the previous top molecule will change status when another is toggled.

Saving Trajectory Frames

Using the Save Coordinates... 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 Save 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 Save button in the browser, the file will be written without further confirmation. See the section on the atomselect writexxx command for information on how to write atom coordinates for an atom selection in a PDB file.

Deleting Trajectory Frames

You can delete frames from memory through a dialog box. To bring it up, start by selecting a molecule and choosing the Delete Frames... from the Molecule menu, or by double-clicking on the Frames column for that molecule in the Molecule Browser. On this is done, choose the range of frames you wish to delete with the First and Last controls, and then press the Delete button. There is no confirmation of deletions.

The Stride control allows you to keep some frames in the range using the specified interval. For example, if your range contains 10 frames labeled 0 through 9, and you use a stride of 4, the frames numbered 0, 4 and 8 will be kept. A stride of 0 (zero) implies that all frames will be deleted.

Deleting a Molecule

The Delete Molecule menu item deletes all the 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.

GUI Shortcuts

There are a few useful mouse-based shortcuts that can be used in the Molecule List browser. Here is a list:

next up previous contents index
Next: Main Window Animation Controls Up: Description of each VMD Previous: Main Window   Contents   Index