May 11 2023
[ Labeling | Atoms | Residues | Move | Variables | Sites | Label Color | Custom Labels | Undisplay Custom Label | Displaying Distances | Origin | Tethers | Dist/Restraints | Display Clash | Rainbow, Box and Ruler | Display Gradient ]
To add labels or display or undisplay pre-defined annotation:
To add new user-defined annotation:
Labeling options are contained within the Labels or Display Tab. In many cases clicking and holding a label button will allow you to view more options.
Select the atoms you wish to label (see display structure or selection toolbar).
To change the level of label detail:
To label residues:
To change the level of label detail:
To change the location of your residue label:
The +/- buttons on the side of the Residue and Atom buttons will shift the label. There are also other residue label move options available when you click and hold the residue label button. These options include Shift to Sidechain Tips, Shift to Calphas, and Restore Positions
To label variable angles (dihedral-torsion, planar and phase angle) the molecule needs to be converted into an ICM object.
To change the variable label style click and hold the variable atom label button as shown below.
Rings of varying diameter and color are superimiposed on rotatable bonds. Green rings with large diameter are considered less constrained than rings with small green rings. Red rings are highly constrained. When the Label Style/Energy option is selected the first number displayed represents the bond angle, the second the energy and the third the worst energy that could be achieved by rotating the bond.
To change the color of any label:
To generate a customized a label:
To edit or delete a label - right click on the label in the graphical display as shown below.
Undisplay Residue, Atom, and Variable Label Any label that is displayed can be undisplayed by selecting the region of the molecule related to the label and clicking on the corresponding label button in the labels tab. For example if you wish to undisplay an atom label - click the atom label button. If a label is displayed the coresponding button in the display tab will be shaded blue. When you delete the button will return to grey. 2D and 3D labels have an undisplay button (red cross on the button see customized label section).
Undisplay 2D or 3D label Click onthe undisplay label button in labels tab.
Within the labels tab there are tools for calculating and displaying distances. These tools can also be found in the Tools/Analysis menu.
To display distance between two atoms:
To find the distance from one atom to many:
The maximal and minimal distances can be selected by entering values in the boxes shown here (below) in the labels tab (previously called Advanced tab).
To change the color of the distance label
To display and undisplay the axis of the coordinate frame (origin):
A tether is a harmonic restraint pulling an atom in the current object to a static point in space. This point is represented by an atom in another object. Typically, it is used to relate the geometry of an ICM molecular object with that of, say, an X-ray structure whose geometry is considered as a target. Tethers can be imposed between atoms of an ICM-object and atoms belonging to another object, which is static and may be a non-ICM-object. You cannot create tethers in ICM-Browser, however, if the project that you have loaded contains tethers between two objects, then they can be displayed:
A distance restraint imposes a penalty function on the distance between two atoms in the same object. You cannot create distance restraints in ICM-Browser, however, if the project that you have loaded contains distance restraints, then they can be displayed:
To display a clash the file needs to be an ICM Object.
To (un)display a rainbow scale, box or ruler use the buttons shown below located in the Labels Tab.
This button is located in the display tab.
This option is described in detail in the language manual http://www.molsoft.com/man/icm-commands.html#display-gradient
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