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Sequence Form

Figure 4.14: The Sequence form

This form is used to list the amino acid residue sequence of protein molecules, and to select residues from the sequence list for highlighting in the 3-D structure in the main VMD window. When residues are selected in the main VMD window, the corresponding residue is highlighted in the sequence list in this form. Color-coded structure and B-factor information are displayed for each residue.

Sequence information

The Sequence form contains a large vertical listing of the residue sequence of a loaded protein molecule. The Molecule pop-up menu control chooses which molecule to display the sequence of, the current 'top' molecule is displayed the first time the Sequence form is opened. The name and molecule number of the sequence displayed is shown in the title frame of the Sequence form.

For each residue displayed, the form lists: residue number, residue name/code, and chain letter. If no chain is specified, chain letter is set to ``X''. To the right of this are two color coded columns, ``B value'' and ``struct''. ``B-value'' shows the contents of the B-value (temperature factor) field. The ``struct'' field shows secondary structure, select Help:Structure Codes from the form menu for an explanation of the single letter codes in the color key.

Selecting residues from the Sequence form listing

Click anywhere in the vertical listing to highlight one residue. Click and drag to highlight multiple residues, shift-click to add a single residue to the current selection, shift-click and drag to add multiple residues to your selection. Highlights appear as thick yellow ``Bonds'' representations, these can be changed or turned off.

Selecting residues by clicking on the 3-D structure

Use the Mouse menu to enter ``Pick Atom'' mode (or press ``1'', the standard keyboard shortcut). Click on any protein atom and its residue will highlight, and the sequence list will scroll to display this residue. Shift-click works the same way, but adds to the current selection. Note that if the zoom factor is smaller than 1.0, the single-residue sequence highlight will be shorter in height than a full line of text. Once the Sequence window has been opened, any ``Pick'' will create or add to selections, until highlighting is turned off.

Sequence Zooming

Larger proteins contain thousands of residues, too many to display in a linear text list all at once. The sequence form can only list about 40 text lines; to work with a protein of more than 40 residues use the scroll bars to scroll through the long list, or use the Zoom controls to fit the data from a long list into a small space.

The Zoom slider, and the Fit all, Every Residue buttons, zoom in and out of a long sequence list to allow viewing and selecting from the entire list all at once. To represent more than 40 residues on the form, the text list seems to ``skip'' residues, but selections, highlights and color-coded data are still active for all residues.

By setting the Zoom slider to a value smaller than 1.0, or by pressing the Fit all button, more or all of the sequence information for a large protein can be seen at once. To show a text line for every residue in the sequence (zoom factor = 1.0), click on the Every Residue button. The Zoom slider can be dragged with the left mouse button (to re-scale sequence smoothly) or it can jump to a given value by clicking along the slider track with the middle button (this is useful to work more quickly with very long sequences).

For a multi-thousand residue protein with Fit all selected, hundreds of residues can be selected at once, and trends in B-value and structure across the entire protein sequence can be detected. In the screen-shot above, a section of 70 residues with lower B-values than surrounding sequence is selected, by dragging a rectangle around the green stretch in the B-value column.

Other controls include:

Turn off highlighting / Change highlight style

After first being opened, the sequence form will always try to highlight at least one residue in the structure of a selected molecule. To turn this representation off completely for a given molecule, find the representation in the Graphics form which the Sequence form has created (set to ``Bonds, ColorID 4'') and set the style to ``none''. To change highlighting style, find the Graphics form representation, then change it to your preferred style and coloring. The representation on the Graphics form remains consistent after the first time the Sequence form has displayed the molecule. This selection of this representation will be changed whenever the sequence form selection changes.


next up previous contents index
Next: Tracker Form Up: Description of each VMD Previous: Render Form   Contents   Index