NMR Models/Animation

Introduction with Examples
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Below are the technical documentation and specifications for Protein Explorer's Animation capabilities.

Initially, all models are shown at once, overlayed, as thin backbone traces, colored by group. Ligand is shown spacefilled for all models. This display can be restored with the [All] button.

  [Animate]: Animated "Movie" of Models

Each time the [Animate] button is pressed, a new animation window is opened, obeying the current settings, including zoom and the orientation established by prior dragging on the molecule with the mouse, the display and color scheme selected with the radio buttons, the model list and "always show" model (if any), and the script in the box (which may be edited). Multiple animation windows can be opened concurrently, with different displays or color schemes, etc. The animation windows can be resized without crashing (unlike the main PE window, but toggle animation off first). An animation window can be saved as an html file, which can be played back in Netscape without running PE.
The [Animate] button opens a new window in which the models are played as a "movie". The "movie" shows each model, one at a time, in numerical order. The menu-specified Delay is inserted between each model, except that the first and last models are shown for 0.5 sec. These 0.5 sec delays at the ends can be removed by unchecking the Ends checkbox. The animation is bidirectional by default, but unchecking the Bidirectional checkbox will produce a forward unidirectional animation loop. The animation is generated using the script in the box, which is normally generated by the radio buttons, but can be manually edited.

The animation shows all models in numerical order unless a subset of the models has been entered in the Model List slot.

If the PDB file in the Protein Explorer session was loaded via Internet from the Protein Data Bank, the animation window will re-load the PDB file via Internet. It will be faster if the session uses a copy of the PDB file saved to local disk. (Because PDB files obtained via Internet from the Protein Data Bank are specified as a query parameter on the URL, the 2nd request does not come from cache. If the PDB file is a static file on a remote server, the 2nd request does come from cache.)

  DISPLAY and COLOR control.

Radio buttons can be used to select among several displays and color schemes, such as Cartoon and Structure. Clicking a radio button automatically generates a new script in the script box below the radio buttons, and then re-displays the models using that script. The display and color scheme chosen affect the images produced by all other controls on this page. The script in the box can be edited.

  [Model+]: Displaying Individual Models

Pressing the [Model+] button will display model 1. Pressing it again will display model 2, and so forth. When the model number reaches the actual number of models loaded (or specified in the Model List slot), pressing the [Model+] button again will return to 1 automatically. The [-] button moves similarly through the models but in decreasing numeric order.

If model numbers have been entered into the Model List slot, the [Model+] and [-] buttons obey this list, in the order specified.

It is also possible to type any model number into the model number box (just to the right of the [Model+] button). After entering the number, when you click anywhere outside this box (such as on a blank white area) the specified model will be displayed.

  [Water], [Ligand] Buttons

While displaying one model at the "NMR Models/Animation" page, [Water] and [Ligand] buttons work only on the one model selected. However, after you press [Back] to go to a different page (so the "NMR Models/Animation" page is no longer visible), the [Water] and [Ligand] buttons will operate on whatever models are currently selected. At QuickViews, the buttons always operate only on model 1.

  [All]: Displaying All Models Overlayed

To display all models overlayed, press the [All] button. The display and color scheme obey the script in the box, which is specified by the radio button settings (or can be manually edited). All models will be displayed unless a subset has been entered in the Model List slot.

When one model is shown using the [Model+] button, disulfide bonds are shown. Disulfide bonds cannot be shown when the [All] button is pressed due to a bug in Chime.

  Always Show One Model in Black

The purpose of this option is to compare a single selected model with the other models, showing each pair in turn. For example, enter "1" into the "Always show model" slot and then click on any blank white area outside the slot. Model 1 turns black and all other models are shown in the current display and color scheme designated by the radio buttons. Now press the [Model+] button repeatedly to cycle through the models, one at a time. Each model is shown overlayed with model 1 for comparison.

To cancel this option, simply delete the number in the "Always show model" slot and then click on any blank white area outside the slot.

The black "always shown" model does not show disulfide bonds.

If you have manually edited the script in the box, Always show model .. black will be ignored. It is possible, of course, to include commands in the customized script that always show one model in black, but this can be tricky (see Custom Scripting NMR Models/Animation for details).

  Model List

When a list of model numbers is typed into this slot, the [Model+], [All], and [Animate] buttons will use this list instead of displaying all of the models present in the PDB file. The [Model+] and [Animate] buttons will follow the list in the order given, which allows models to be displayed in an order different from their numbers. Numbers in the list should be separated by commas and/or spaces. These examples are valid lists:

  13, 7, 9, 22, 23
  13 7 9 22 23
A model list can be used in conjunction with an Always show model number, which need not be a member of the list.

When the model list is deleted, the buttons will return to displaying all models present in the PDB file.

  Manually editing the script

Press the [?] button closest to the radio buttons for instructions.