Maestro User Manual

Chapter 2: The Maestro Main Window

Maestro 10.2 User Manual

23

2.4.3

The Workspace Toolbar

This toolbar contains buttons for some common Workspace operations, and buttons for

creating and managing scenes. 

2.5

The Status Bar

The status bar displays information about the contents of the Workspace or about a particular

atom, depending on where the pointer pauses. If the pointer is not over an atom, information

about the contents of the Workspace is displayed, in the format

Atoms:

sa/ma/na Entries:me/ne Res:nr Chn:nc Mol:nm Chg:n 

where the fields in the display have the following meanings:

Create Entry 

Create an entry in the current project using the contents of the Workspace. Opens a dialog box 

in which you can supply a title for the entry, and choose whether to create the entry from all 

atoms, the selected atoms, or the displayed atoms. If all the atoms in the new entry come from 

entries in the same entry group, the new entry is added to the same group, otherwise it is added 

to the ungrouped entries in the Project Table.

Menu equivalent: 

Workspace 

→

 Create Project Entry

.

Clear 

Clear the Workspace. Excludes all entries in the Project Table, and deletes the contents of the 

scratch entry, if there is one.

Menu equivalent: 

Workspace 

→

 Clear

.

Save Image 

Save an image of the Workspace to a file in TIFF, JPEG, or PNG format, in the 

Save Image

 

panel.

Menu equivalent: 

Workspace 

→

 Save Image

.

New Scene 

Create a new “scene”, which is a snapshot of part or all of the project, including the Work-

space content and display settings. Opens the 

New Scene

 dialog box, in which you can pro-

vide a description and choose which parts of the project to include in the scene.

Menu equivalent: 

Workspace 

→

 Scenes 

→

 New

.

View Scenes 

Enter a mode in which you view scenes. The 

Scenes

 toolbar is displayed in a bar at the bot-

tom of the Workspace, and the selected scene is opened. While you are viewing scenes, no 

changes are made to the project.

Menu equivalent: 

Workspace 

→

 Scenes 

→

 View

.

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Chapter 2: The Maestro Main Window

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24

If the pointer is over an atom, and the preference to show feedback on atoms is set, the status

bar displays the chain, residue number, element, PDB atom name, formal charge, and a user-

selected property, in the format 

atom:chain:residue number :(element) PDB :charge:"userchoice"

where the fields in the display have the following meanings:

If you are picking an object in the Workspace and you have the preference set, the index of the

object is displayed at the beginning of the status bar, in the format Pick: index. For example,

if you are picking molecules, the molecule number is displayed. 

The preferences to show feedback and the user-selected property can be set under 

Feedback –

Atoms

 in the 

Preferences

 panel—see 

Section 14.5.1 on page 358

. 

On the left of the status bar is a button that displays job status information. The text on the

button gives the number of jobs in the format 

Jobs: 

mj/nj, where mj is the number in the

project and nj is the total number. Clicking the button opens the 

Monitor

 panel. The tool tip for

the button displays information on the status of the first few jobs in the 

Monitor

 panel.

Atoms

Number of atoms in the Workspace: sa is the number selected, ma is the number

displayed, na is the total

Entries

Number of entries in the Workspace: me is the number displayed, ne is the total

Res

Number of residues nr in the Workspace

Chn

Number of chains nc in the Workspace

Mol

Number of molecules nm in the Workspace

Chg

Total charge n of the Workspace contents

atom 

Atom number in the Workspace

chain Chain 

name

residue

Residue name

number

Residue number and insertion code

element

Element

PDB

PDB atom name

charge

Formal charge of the atom

userchoice

Selected Project Table property

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Chapter 2: The Maestro Main Window

Maestro 10.2 User Manual

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2.6

The Sequence Viewer

The sequence viewer displays the sequence of the proteins that are included in the Workspace.

Each chain is displayed on a separate line. If a protein contains waters, ions, or ligands

2

, each

of these groups of molecules is displayed on a separate line. If the sequence is longer than a

single line, the entire set of lines is continued below the first set of lines (“wrapped”) by

default. (You can unset a preference if you want them to scroll horizontally instead.) The left

column of the sequence viewer displays a label for the sequence, in the format

row:pdbID_chainID, where row is the Project Table row number. The right column displays

the actual sequence as a list of single-letter codes, and also displays the secondary structure

assignment, if one is available.

The background colors of the sequences reflect the current coloring scheme for the alpha

carbon in the Workspace. Each residue in the sequence also has a tooltip that gives the residue

name, number, and insertion code.

If the protein has a secondary structure assignment, the assignment is displayed above the

sequence, using the following symbols:

• Helices are displayed as tubes, colored red

• Strands are displayed as arrows, colored cyan

• Loops are displayed as a gray line.

You can select residues in the sequence and perform actions on these residues. 

• To select a single residue, click the residue. 

• To add single residues to the selection or remove single residues from the selection, con-

trol-click the residues. 

• To select a range of residues, click the first and shift-click the last, or drag over the resi-

dues. If the sequence viewer is wrapped, you can drag over multiple rows to select resi-

dues in more than one row (but only in the sequence in which you started dragging). 

• To change the selection of a contiguous set of residues, hold down the 

CTRL

 key and drag

over the set of residues. The unselected residues are selected, and the selected residues

are deselected. This can be used to extend the selection or add a discontinuous sequence

fragment to the selection, for example.

The selected residues are highlighted in reverse video (as colored letters on a black back-

ground), and are marked in yellow in the Workspace. 

2.

These entities are defined by the corresponding ASL expressions. “Ligands” are defined by ligand detection set-

tings; “ions” are a small set of ionic species commonly found in or used with proteins.

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