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.
Restore default atom colors for the current
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.
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
- 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.
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.
Each layer will be coloured with its own coulour.
Each chain of the current active layer will be coloured with its
own colour. Ideal to have a look at the arrangement of multimeric
- 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)
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
- 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.