Structure Window : Style Commands

• Edit global style
  • Rendering styles
  • Coloring styles
• Favorites
• Rendering shortcuts
• Coloring shortcuts
• Annotate

Edit global style

Edit the global drawing style that applies to all structures. (To change the style of specific residues, see the Annotate item below.) This brings up the style editor panel. You will see the changes take effect immediately if the Apply after each change option is on; otherwise, changes will only occur when you click Apply or Done. The settings chosen here will be saved and restored automatically when you write your data out to a file. There are three tabbed panes in the style editor:

• Settings tab: these items control rendering and coloring of the various structural elements. The columns in this panel are:
  • Group: which atoms or objects are controlled by each row.
  • Show: whether these items should be displayed, and for backbones, what type of backbone is drawn. Trace is alpha carbon or phosphate only; Partial shows all backbone atoms that make a linear chain.
  • Rendering: what shapes are used to draw these elements. See the descriptions of rendering styles below.
  • Color scheme: how these items are colored. See the descriptions of coloring styles below.
  • User color: press these buttons to select any color to use when Color scheme is set to User selection. On PC and UNIX, the background color of these buttons will be the color selected.
• Labels tab: controls if and how residues are labeled.
  • Spacing: labels are drawn every N residues.
  • Type: one or three letter residue names are used.
  • Numbering: Sequential means residues are numbered in order starting from one; From PDB will use residue numbers from the original PDB file (which may be ordered arbitrarily).
  • Contrast: if selected, white labels are used if the background is a dark color, and black labels otherwise.
  • Termini: label the ends of the chains. For example, the N terminal residue of chain B will be labeled "N (B)".
  • Metal ions: whether to put the element symbol in the center of transparently-drawn metal ions.
• Details tab: controls sizes of the various rendered objects. These numbers are in units of Angstroms, except for Space fill size which is a scale factor applied to the van der Waals radius of the element. For example, you can change the relative radii of atoms and bonds in a Ball and Stick model by adjusting the Ball radius and Stick radius items..

Rendering Styles

Both the style editor and the rendering shortcuts offer a variety of drawing styles. Here are descriptions of the available choices:

• Wire worm: a curved thin line that is drawn through only the alpha carbons (or phosphates) of the backbone.
• Tube worm: like wire worm, except a thick tube is drawn instead.
• Wire: bonds between all atoms are drawn as straight thin lines.
• Tube: bonds between all atoms are drawn as thick tubes.
• Ball and stick: bonds are drawn as thick tubes, and atoms are represented by spheres.
• Space fill (sometimes called CPK): atoms are drawn with larger spheres proportional to their van der Waals radii. No bonds are drawn.
• With/without arrows: this is a special style that applies only to the objects that represent protein helices and strands, and controls whether or not arrowheads are used to indicate the N-to-C direction of the protein backbone.

Coloring Styles

Both the style editor and the coloring shortcuts offer a variety of color schemes. Coloring schemes typically control how atoms are colored; bonds are colored according to the colors of the atoms at each end. Here are descriptions of the available choices:

• Element: colors by atomic element.
• Object: each structure object - one MMDB/PDB entry - is assigned a different color.
• Molecule: each molecule - one chain or heterogen or solvent - is assigned a different color.
• Domain: each domain in a chain is assigned a different color.
• Secondary structure: for protein chains, distinguishes helix, strand, and coil with different colors.
• Temperature: uses a traditional temperature color cycle (blue - green - yellow - red - white) to indicate relative temperature factors for each atom, where blue is lowest and white highest temperature.
• Rainbow: uses a ROYGBIV color cycle along each chain from N to C (or 5' to 3').
• Charge: for proteins, draws positively charged residues in blue, negative in red, and neutral in gray.
• Hydrophobicity: for proteins, uses a standard hydrophobicity scale to draw the most hydrophobic residues in red, to the least hydrophobic (most hydrophilic) in blue.
• User selection: a solid color of the user's choice.
• Sequence conservation: these schemes are all used to color sequence alignments in different ways based on sequence conservation.
  • Aligned: aligned residues are all red.
  • Identity: columns of identical residues are red, others blue.
  • Variety: columns with the lowest number of different amino acids represented are colored red, and highest variety columns are blue.
  • Weighted variety: similar to variety, but scaled by a standard BLOSUM62 substitution score so that columns of most strongly conserved residues are more red.
  • Information content: scales color according to the information content of each column, where a higher score is more red.
  • Fit: colors each residue according to how well it "fits" in the column it is in (based on residue-to-PSSM score). A residue colored red has a high substitution score given the other residues in that column; a blue color indicates a low score.
  • Block fit: similar to fit except residues are colored by blocks and ranked by the sum of residue-to-PSSM scores. The highest scoring blocks in the entire alignment are red, the lowest blue.
  • Normalized block fit: similar to block fit except scores are normalized within each column of aligned block; the highest scoring row in a given block column is red, the lowest blue.
  • Block row fit: Similar to normalized block fit excpet scores are normalized across each sequence row; the highest scoring block of a given sequence will be red, the lowest blue.

Favorites

Rendering shortcuts

Coloring shortcuts

Annotate

This panel allows you to annotate a structure by defining different styles - rendering, coloring, and labeling - to specific sets of residues. This could be used, for example, to emphasize the amino acids that comprise the active site of a protein, in a figure for a publication.

To create a new annotation, simply highlight the residues and molecules you would like to include in the annotation. They can be from any number of different chains or even PDB structures. Then bring up this panel and click on New. You will be prompted for a short name and a longer description, and the edit style button will bring up the standard style editor - except that the style for only the highlighted residues is changed.

You can have any number of style annotations defined. The annotations you have created are listed in the Available area. By default, a new annotation is always turned on. The Displayed area shows which annotations are visible; to turn an individual annotation off, simply select it and click on Turn off, and to redisplay it again, select it and click Turn on.

The bottom row of buttons are operations you can do on whichever annotation is currently selected. Highlight will cause the residues and molecules associated with the annotation to become highlighted. Edit allows you to change the annotation's name, description, and style definition. Move can be used to change the location of the annotation - simply highlight the residues and molecules you would like to move the annotation onto, then press this button. Delete will remove the annotation completely.

If annotations cover overlapping regions of residues, then the style associated with the annotation at the top of the Displayed list is the one that is shown in the overlapping area. If you would like instead for another overlapped style to be displayed, select that annotation and press Move up until that style is at the top of the Displayed list. Similarly, you can lower the annotation's order by pressing Move down.