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Color Menu

The first item of the menu is always grayed, and reminds the user what will be colored. It can be either Backbone+Sidechain (default), Backbone, Sidechain, or Ribbon, depending on the status of the pop-up located above the color boxes in the Control Panel.

These menus will affect all residues of the current layer. You can restrict their action to the selected groups only by simultaneously helding down the control key. Note also that you can act on all layers by invoking them with the shift key held down.

  • CPK
    Restore default atom colors for the current layer.
  • RMS
    To be active, this menu requests that at least two proteins have been loaded, superimposed, and that a structural alignment has been generated. At this point, each amino-acid of the active protein will be colored accordingly to its RMS backbone deviation from the corresponding amino-acid of the reference protein (the first loaded). Dark blue means good superposition whereas red means bad superimposition. By default colors provide from a fixed scale, but you can choose a relative scale where the best RMS is dark blue, and the worse RMS is red by enabling the appropriate item of the preferences menu.
  • B-factor
    The molecule will be colored accordingly to its temperature factor, from dark blue for low B-factor to red for high B-factor. In the case of a model returned by Swiss-Model, red means reconstructed. The highest B-factor of any backbone atom is attributed to all backbone atoms, the same is true for sidechains. By default colors provide from a fixed scale, but you can choose a relative scale where the best RMS is dark blue, and the worse RMS is red by enabling the appropriate item of the preferences menu.
  • Custom Scale
    This will access a list of submenu resulting from parsing the file 'customcolor.txt' which is located in the 'usrstuff' folder coming with the distribution. This file can be edited and new color lists can be very easily defined. Simply provide a the title of the menu you want to add and then red,green,blue values for each amino acid type. Save the file, and use the update menu list of the Swiss-PdbViewer custom color submenu to make it available.
  • Secondary Structure
    A secondary structure detection will be performed imediately before coloring helices in red and strands in yellow. The rest of the structure is colored in grey. These default colors can be changed in the preferences.
  • Selection
    This will simply colour selected residues in cyan and non selected residues in dark grey. This is useful to quickly highlight the spatial position of some residues compared to the rest of the protein.
  • Layer
    Each layer will be coloured with its own coulour.
  • Chain
    Each chain of the current active layer will be coloured with its own colour. Ideal to have a look at the arrangement of multimeric proteins.
  • Alignment Diversity
    This menu is only enabled when at least two proteins have been loaded. To have meaningful results, it is also necessary to align the proteins. The alignment color will reflect the residue conservation at each position, using a color gradient from dark blue (conserved) to green to red (divergent)
  • Accessibility
    Each amino acid is colored by its relative accessibility. Maximum accessibility is defined as beeing the accessible surface of an amino-acid X in a pentapeptide GGXGG in extended conformation. This is only an approxiamtive scale, but perfectly sufficient to differentiate core amino-acids from surface ones. Dark blue color is attributed to completely buried amino-acids, whereas red color is attributed to amino-acids with at least 75% of their relative surface accessibility accessible.
  • Threading Energy
    Color each residue of the protein accordingly to its energy computed by a mean force potential computed from a "Sippl-like" mean force potential [ref. 7]. Dark blue means that the energy is low, hence, that the specific residue is happy with its environment, whereas a red color means that the threading energy is high, and that the residue is a little less happy with its envovironment. Use this with caution.
  • Force Field Energy
    Each residue is colored accordingly to its energy (computed with a partial implementation of the GROMOS force-Field). You can choose what kind of interaction you want to compute (bond, angles, improper, electrostatic...) and you can ask for a full text report where detailed energy of each residue is given. Blue means low energy, while red means high energy. Colors are automatically scaled from the lowest to the highest with a color gradient blue-green/green-red. This is especuially useful during refinment of a structure as you can color by bond and angle deviations only and this will identify distorted parts of the protein.
  • Protein Problems
    Note: This menu will affect the color of the backbone and of the sidechain separately irrespective of the 'Color act on...' current setting.. Residues with peptide bonds too long will be colored in pink, while the rest of the protein is colored in grey. This is very useful during modelling. In addition, the backbone of residues with phi/psi angles laying in "forbidden" zones will be colored in yellow (except GLY that are ignored) and Prolines whose backbone will be colored in red. Also, the sidechains of residues capable of H-bonding that are not participating in any H-bond with other residues are colored in orange. Finally, Clashes will also be computed and displayed in pink dotted lines. Residues with clashes will be selected.
  • Other Color
    This will color all the groups with the same color. It is functionnaly equivalent to an option-click (right mouse button for PC users) on any color box f the control Panel; or to a SelectAll followed by a click on the "color" text of the Control Panel header.
  • Backbone Color
    Backbone colors will be copied to the sidechains or ribbon colors, depending on the status of the pop-up located above the color boxes in the Control Panel. This item is grayed when the coloring acts on backbone color.
  • Sidechain Color
    same for sidechain colors.
  • Ribbon Color
    same for ribbon colors.