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The ePlayer allows you to view in succession the structures associated with selected entries. By carefully selecting entries to be included in the Workspace, and then selecting an entry to be used as a reference, you can use the ePlayer to visualize structure relationships such as ligand-receptor docking. You can also run a script on each entry as it is displayed. To use the ePlayer, you must have a project open with at least one entry selected. The ePlayer can be oper- ated from the toolbar or from theePlayer menu.

8.6.1

ePlayer Modes

The ePlayer has two modes, Continuous mode and Step mode. In Step mode, you manually advance the ePlayer to show each new entry structure. You can use the Next andPrevious

buttons on the toolbar, or theNext andPrevious items on theePlayer menu.

To go to the beginning or the end of the entry list, use theGo to Startor Go to Endtoolbar buttons orePlayer menu items.

In Continuous mode the ePlayer automatically displays all selected entry structures in sequence. You can play through the structures once, or you can loop over the series by repeating the sequence of structures in the same direction, or by reversing the direction. These options can be selected from theLoopsubmenu of theePlayermenu or theLoopbutton menu on the toolbar.

If you choose None, the ePlayer displays the selected structures once in the direction you choose and stops.

If you chooseSingle Direction, the ePlayer displays all selected structures in sequence, then loops back to the first structure and redisplays the entire series until you click another ePlayer directional button.

If you selectOscillate, the ePlayer displays all of the selected structures in the forward direc- tion, then in the reverse direction, and repeats this sequence until you click another ePlayer

Figure 8.9. The ePlayer Options panel.

8.6.2

ePlayer Options

TheePlayer Optionspanel provides access to controls for the ePlayer and extra actions that can be performed during play. To open theePlayer Optionspanel, chooseOptionsfrom theePlayer

menu. The panel has three sections: general options, options for superimposing structures, and options for running a script.

General

You can adjust the speed at which the ePlayer moves through the specified structures by entering a value in seconds in the Speed text box. This is the time that each structure is displayed in the Workspace. The default is zero seconds per entry, which means that the speed of play is limited only by the speed of rendering of the structures.

In Continuous play mode, the structures are only temporarily displayed in the Workspace. By default, any changes in the structure are also temporary. However, you can save changes during play by selectingSave workspace at each step.

Superimpose Entry

One instance in which you may find the ePlayer very helpful is in superimposing entries onto each other or onto a reference structure. For instance, when viewing ligands, you might want to view them superimposed on a receptor. You can do this by fixing the receptor in the Workspace but selecting only the ligands.

If you choose On Previous Entry, each entry is superimposed on the previous entry in the series. If you chooseOn Reference Entry, you must specify a reference entry, either by typing

its name in theReferencetext box, or clicking theChoosebutton and choosing an entry from the list. The reference entry can be any entry, but to view it during play, you must fix it in the Workspace.

If you choose to superimpose structures inStepmode, the project synchronization mode that you have selected in thePreferencespanel is applied. If you have chosenAutomaticallyfor the synchronization mode, superimposing structures changes the coordinates of the structures involved. If you do not want to save the coordinates that result from using the ePlayer, choose

Only When Specifically Requested for the synchronization mode.

InContinuousmode, coordinate changes that result from superposition are saved to the project only if you have selectedSave workspace at each stepin theGeneralsection.

Run script at each step

In addition to superimposing structures, you can execute a command script when each struc- ture is displayed. If you choose Current Script, the script that is currently loaded in the

Command Script Editorpanel is executed for each structure. You can open this panel and edit the script by clickingEdit. If you chooseFrom File, you can choose the file that contains the command script you want to execute. This script is not loaded into theCommand Script Editor

panel, but is stored temporarily.

Note: You should not include in your script any command that operates on all selected entries, or that changes the inclusion state of the entries.