Maestro User Manual

Chapter 8: Labeling and Annotating the Workspace

Schrödinger Software Release 2015-2 

162

8.2

Labeling Atoms

Labels are useful tools for building, identifying, and analyzing molecular structures since they

can be used to display any combination of predefined information or user-specified text. For

instance, you might want to display atom numbers so that you can retype a specific atom, or to

pick atom pairs for superposition, inclusion in a set, or measurement.

Atom labels are persistent. The labels are stored as part of the entry, and are restored when an

entry is excluded from then included in the Workspace. However, labels that are dependent on

the numbering in the Workspace, such as Molecule Number, may change because they are rela-

tive to the Workspace, not the entry. 

User Text 

Change the user-defined text in the atom label on the picked atom. If the atom does not have a 

label, a label is added. A dialog box opens, to enter the text and choose whether to replace the 

entire label or replace the text in the label. 

Feedback 

Display information about a single entry, termed the “target” entry, in the top left corner of the 

Workspace. 

Menu equivalent: 

Workspace 

→

 Single-Entry Feedback

.

Highlights 

Create, modify, delete, or apply highlights to atoms in the Workspace. Opens the 

Manage 

Highlights

 panel. 

Menu equivalent: 

Workspace 

→

 Highlights.

Quick Highlight 

Add a highlight to picked atoms with the current highlight settings.From the button menu you 

can choose a structural unit for picking to highlight; open the 

Atom Selection

 dialog box to 

select atoms to highlight; or open the 

Manage Highlights

 panel to make highlight settings. 

Add Caption 

Add a caption to the Workspace. Opens the 

New Caption

 dialog box, in which you can type in 

the text, and set the caption background, font, and text color. 

Menu equivalent: 

Workspace 

→

 Add Caption

.

Show Cap 

Show or hide the Workspace captions. 

Increase Fonts 

Increase the size of all the Workspace fonts (atom labels, measurements, adjustments, cap-

tions, highlights, feedback).

Decrease Fonts 

Decrease the size of all the Workspace fonts (atom labels, measurements, adjustments, cap-

tions, highlights, feedback). 

---

Chapter 8: Labeling and Annotating the Workspace

Maestro 10.2 User Manual

163

Labels can be set up and applied in the 

Atom Labels

 panel. To open the 

Atom Labels

 panel,

choose 

Workspace 

→

 Atom Labels

 or choose 

Composition

 from the 

Label All

 or the 

Pick to

Label 

button menu.

Labels can be constructed from a variety of atom, molecule, residue, chain, and entry proper-

ties, including element, charge, stereochemistry, atom and residue names and numbers, and

also user-defined atom and entry properties. By default, the 

Element

 and 

Atom number

 atom

properties are in the label.

Figure 8.1. The Atom Labels panel.

To add properties to the label composition, click 

Add

, and select the properties in the 

Add Label

Fields

 dialog box. The 

Atom Properties

 and 

Entry Properties

 tabs have lists of properties that

you can select. You can filter and sort the entry properties. Click 

OK

 to add the selected proper-

ties to the label composition.

To remove properties from the label composition, select them in the 

Fields

 list, and click

Remove

. To remove all properties, click 

Remove All

. 

To show or hide properties in the label, but keep them in the list for easy access, check or clear

the check box for the properties. This allows you to keep the properties that you want to use

most often for labels available, but quickly change the displayed label. 

---

Chapter 8: Labeling and Annotating the Workspace

Schrödinger Software Release 2015-2 

164

Figure 8.2. The Add Label Fields dialog box, Atom Properties tab (left) and 

Entry Properties tab (right).

The properties are added to the label in the order they appear in the 

Fields

 list. You can change

this order by selecting properties in the list and dragging them to the desired position in the list.

The property values are separated by spaces in the label.

When you have finished composing the label, choose 

Add labels (replace

) from the 

Pick to

option menu to begin adding labels. 

To select the atoms for the chosen labeling action, use the standard picking tools in the 

Label

atoms

 section. Labels are added to atoms that do not have labels, and existing labels are

replaced on atoms that already have labels. The labels are applied only at the time you perform

the labeling action, and do not change if you change the composition. If you want to update all

labels with the new composition, click 

Update Existing Labels

. 

If you want to remove labels, you can do so by selecting atoms or you can remove all labels. To

select atoms to remove labels, choose 

Clear labels

 from the 

Pick to

 option menu, then use the

standard picking tools in the 

Label atoms

 section. To remove all labels, click 

Clear All Labels

.

---