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5.5 Labeling and Annotation
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[ Labeling | Atoms | Residues | Move | Variables | Sites | Annotation | Label Color | Custom Labels | Undisplay 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:

5.5.1 Labeling


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.

5.5.2 Labeling Atoms


Select the atoms you wish to label (see display structure or selection toolbar).

To change the level of label detail:

5.5.3 Labeling Residues


To label residues:

To change the level of label detail:

5.5.4 Move Residue Label


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

5.5.5 Label Variables


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 and non-rotatable. 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.

5.5.6 Labeling Sites


To display and undisplay sites use the Toggle Site Label button shown below

To change the level of label detail:

NOTE: To create your own site labels see the Label Annotation section.

5.5.7 Annotation


To annotate a protein structure. Select the region you wish to annotate (see Selection Toolbar).

To change the detail (such as residue number) contained within the annotation.

To undisplay an annotation click on the site button in the Display tab.

To permanently delete an annotation.

To change the direction the arrow is pointing or move the arrow.

5.5.8 Changing Label Colors


To change the color of any label:

5.5.9 Customized Label 2D or 3D


To generate a customized a label:

To edit or delete a label - right click on the label in the graphical display as shown below.

5.5.10 Undisplay Customized Label


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.

NOTE: A label can also be deleted by right clicking on the label in the graphical display and selecting delete.

5.5.11 Labeling Distances


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).

NOTE: Distances can be displayed and undisplayed in the 3D labels section of the ICM Workspace. See image below.

To change the color of the distance label

5.5.12 (Un)display Origin


To display and undisplay the axis of the coordinate frame (origin):

5.5.13 Displaying Tethers


Theory

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:

5.5.14 Displaying Distance Restraints


Theory

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:

5.5.15 Display Clash


To display a clash the file needs to be an ICM Object.

5.5.16 Display Rainbow, Box, Ruler


To (un)display a rainbow key, box or ruler use the buttons shown below located i n the display tab.

5.5.17 Display Gradient


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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