Protein Feature Accent supplemental information

The Protein Feature Accent tool window is organized into 4 sections:

• Control Panel
  In this area are buttons for navigation within the Jmol window, and other controls for the look, orientation, and coloring of the molecule(s) displayed in the window.
• Jmol applet window This is the graphical display section. The Jmol viewing window offers all of the Jmol java applet‘s interactive features. Among these are:
  You can click and drag with the mouse to rotate the molecule, and use your mouse wheel (shift-drag in Safari) to zoom the image. You can also mouse-over to show residue/atomic information, and double-click on pairs of atoms to measure distances and angles.
  Right-click (Windows) or control-click (Mac) in the Jmol window to open the Jmol menu, which provides access to many other options.
  In some browsers, you may need to click on the applet window to 'activate' it, before these mouse-accessed features will work.
  For more information about the Jmol applet, visit www.jmol.org.
• Sequence View
  This section displays, at the least, the amino acid sequence of the 'main' molecule chain displayed in the Jmol window, aligned with a reference sequence appropriate for the organism. If you provide a sequence or an aligned set of sequences to the tool, your sequence(s) will be aligned with these sequences, and the resulting alignment will be presented here. There are also controls here to show or hide the model sequence, the reference sequence, and/or the sequence(s) provided by the user.
  This section is interactive, in the sense that you can use your mouse or other pointing device to select portions of the model sequence, and the selected amino acid residues will be 'highlighted' in the graphic in the Jmol window. Please note that the only selectable sequence in the alignment is the one from the model, since this sequence corresponds directly with the residues shown in the graphic.
• Highlighting
  In this section are controls pertaining to the sequence highlighting facility of the Protein Feature Accent tool. Here you can choose among options for how highlighting behaves in the graphic. The residue numbers of the currently highlighted residues are listed in this section. You may also type in lists of residues and have these highlighted, providing an alternative to the sequence selection method. There is also an option to highlight residues that are 'near' the residues you type in, and you can specify what 'near' means in terms of distance. Finally, if the model loaded contains multiple 'chains', i.e., sequences, a panel of checkboxes here will let you show or hide each chain individually in the Jmol window.

How to type residue lists
A set of residues can be typed in the 'Highlight residue numbers' box using the following rules:
You can indicate an interval of residue numbers, i.e., residue numbers 112 through 123, using a dash: '112-123'.
Separate residues can be indicated with a comma-separated list: '240, 256, 258'. Spaces after commas are fine.
These two formats can be combined: '112-123, 240, 256, 258'.

Glycosylation sites
The Protein Feature Accent tool identifies potential N-linked glycosylation sites (also called sequons or PNGs) that match the Nx[TS] motif, where 'x' can be any amino acid except proline. The asparagine (N) α-carbon is marked in the graphic. For a more complete analysis of glycosylation sites in your protein sequence set, try the N-GlycoSite tool.

See also Gavel & Heijne, 1990, Zhang, et al, 2004

Carbohydrate glycosylation structures
For certain structure files, such as the SIV gp-120 protein structure 2BF1, full glycosylation structure information is present. In these cases, an option to display these carbohydrates is offered. Note that for two of the display styles, 'cartoon' (the default view) and 'rocket', these carbohydrate structures do not appear. They reappear when the view is switched to one of the other display styles.

Alignment entropy color scheme option
When you submit an alignment to the tool, the Shannon entropy is calculated for each alignment column. This information can be visualized on the Jmol graphic by selecting the 'entropy' option under the menu labeled 'pick color scheme'. Zero- and low-entropy residues are colored a 'cool' color (e.g., blue-green), and higher entropy residues are shown in shades of yellow, orange, and red. Residues for which an entropy cannot be calculated (for instance, residues which correspond to an all-gap column in the alignment sequences you provide) are colored a distinctive 'cold' color (e.g., dark blue).

PDB model file upload option
You can upload a Protein Data Bank model file and the tool will display your model instead of one of our stored protein models. The tool will extract and display the protein sequence from the PDB file you provide, and you can highlight residues in the graphic by selecting them as usual. If you provide a sequence or an aligned set of sequences, the tool will align the PDB file sequence to your sequence(s) and display the alignment.