Color Menu

The first item of the menu reminds the user of the color setting in effect, which is determined by the status of the triangular pop-up menu located above the color boxes in the Control Panel window. The choices there are backbone+sidechain (default), backbone, sidechain, ribbon, residue label, and surface.

By default, a Color Menu selection colors all residues of the active layer, but:
... Control-select colors only selected residues.
... Shift-select colors all layers.
... Control-shift-select colors selected residues in all layers.

A standard orderly palette of 20 colors is used below (*) whenever a range of values must be colored (providing 5% increments on a 0 to 1 scale). By convention, blue is at the low extreme, green is intermediate, red is at the high extreme.

CPK: Colors atoms in the topmost layer with standard Corey-Pauling-Koltun values, eg, blue for nitrogen. These conventions can be changed in the color submenu of the preference menu.

Residue Polarity (Type): Colors basic amino acids in blue, acidic in red, polar in yellow, and hydrophobic in grey. These default colors can be changed in the color submenu of the preference menu.

*RMS: Colors by root mean square values. Two or more proteins must have been loaded, superimposed, and aligned. The active protein layer is colored according to its RMS backbone deviation from the corresponding amino acid of the reference protein (the first loaded). Dark blue means good superposition, green so-so, red bad. Twenty orderly colors are provided in 5% increments from an absolute RMS scale. However, colors can be scaled to RMS values at hand using the checkbox in the general submenu of the preference menu. The palette itself cannot be changed.

*B-factor: Colors backbone and sidechain separately by uniform temperature factor (roughly spatial uncertainty; column 11 of a pdb entry, often 0.00). The highest B-factor of any backbone atom is assigned to all backbone atoms, and so on for sidechains. In the case of a model returned by Swiss-Model, red means reconstructed (in analogy to high B-factor). By text editor search-and-replace, the B-factor column of a pdb entry can be used to color-code any user-defined property, for example evolutionary conservation.

Secondary Structure: Colors alpha helices red, beta strands yellow, the rest in grey. These default colors can be changed in the color and ribbon submenus of the preference menu. Swiss-PdbViewer overrides secondary structure calls in the pdb entry with its own secondary structure detection scheme, but assignments can be changed in the edit menu. The secondary structure should be recalculated (tools menu) if phi/psi angles are adjusted.

*Secondary Structure by Order: Colors alpha helices and beta strands in order of appearance from blue to red using the 20 orderly colors palette. This can be helpful in displaying linear sequence non-adjacency in beta sheets or within a large protein.

Selection: Colors residues selected in the control panel in cyan, others as dark gray, to quickly highlight the spatial position of these residues relative to the rest of the protein.

Layer: Colors each layer distinctly, helpful when two or more layers are superimposed. The default palette cannot be changed, but layers can be recolored individually in the control panel. 32 layers are currently supported.

Chain: Colors each chain of the top layer distinctly, helpful with subunit arrangements in multimeric proteins. The default palette cannot be changed , but chains can be recolored individually in the control panel.

*Alignment Diversity: Colors according to degree of conservation at each residue of a primary sequence alignment using the same 20 orderly colors of the RMS and B-factor palette (blue: most conserved, red: least conserved). Dayhoff's PAM 250 matrix (no choice) is used to score residue conservation, with the average rescaled between 0 and 1. Alignments are manipulated in their own window.

*Accessibility: Colors each amino acid by its relative surface accessibility to solvent, relative to maximum accessibility possible in the extended pentapeptide GGXGG environment. This differentiates core amino-acids from surface ones. Using the 20 color scaling palette, blue is assigned to completely buried amino-acids and red to surface accessible amino acids (75% or more).

*Threading Energy: Colors each residue of a protein accordingly to its energy as computed by a Sippl-like mean force potential [ref. 7] using the 20 color palette. Dark blue represents low energy (residue happy with its environment); red color means that the threading energy is high (residue unhappy with its envovironment). Treat as a useful approximation.

*Force Field Energy: Colors each residue accordingly to its energy (computed via a complete implementation of the Gromos96 force-field in vacuo at pH 7.0) . User chooses computed interaction (bonds, angles, improper values, electrostatic, ...) and whether a full text report is wanted. Blue is low energy, red high energy. Intermediate energies are scaled with the standard 20 color palette. Coloring by bond and angle deviations during structural refinment helps identify distorted parts of the protein.

Backbone Problems: Highlights residues having problematic structural attributes, useful in modelling or detecting pdb entry anomalies.

... Peptide bonds too long -- pink.
... Phi/psi angles in "forbidden" zones -- yellow (not applicable to glycine).
... Prolines with bad Phi angle -- red.

Color All: Colors all residues with a user-selected pop-up color, overriding the control panel pop-up menu setting. This command is functionnaly equivalent to option-click (right mouse button for PC users) on any color box of the control Panel or to SelectAll followed by a click on the "color" text of the Control Panel.

Use Backbone Color: Copies backbone colors to the sidechains or ribbon, depending on the status of the pop-up located above the color boxes in the Control Panel.

Use Sidechain Color: Copies sidechain colors to the ribbons or backbone, depending on the status of the pop-up located above the color boxes in the Control Panel.

Use Ribbon Color: Copies ribbon colors to the sidechains or backbone, depending on the status of the pop-up located above the color boxes in the Control Panel.