Maestro User Manual

Chapter 2: The Maestro Main Window

Schrödinger Software Release 2015-2 

30

Table 2.5. Sequence viewer shortcut menu items.

Menu Item 

Action 

Hide

 

Hides the sequence viewer. To redisplay it, use the 

Window

 menu. 

Color Scheme

 

Colors the sequence with the scheme selected from the submenu. Choose from 

None

, 

Color by Chain

, 

Residue Type

, 

Residue Property

, 

Secondary Structure

, 

Template ID

, or 

Proximity

 (sequence viewer only). 

Font Size

 

Sets the font size for the sequence viewer. Choose 

Small

, 

Medium

, 

Large

, or 

Huge

 from the submenu. 

View SSA

 

Shows or hides the secondary structure assignment for the sequence. 

Show Displayed 

Residues Only

 

Shows only the residues that are displayed in the Workspace.

Display Non-pro-

tein Molecules

 

Display non-protein molecules in the sequence viewer. Three lines are used, for 

ligands, waters, and ions.

Align by Residue 

Number

 

Aligns the sequences in the sequence viewer by residue number. (Does not affect 

the alignment of the structures.) This command enables gaps to be displayed in 

the sequence viewer.

Exclude Entry

 

Excludes the entry containing this chain from the Workspace. The chain is 

removed from the sequence viewer. If the entry contains multiple chains, all the 

chains in the entry are removed from the sequence viewer. 

Wrap Sequences

 

Wraps the sequence display so that long sequences are displayed across multiple 

lines with vertical scrolling rather than on a single line with horizontal scrolling.

Legend

 Opens 

the 

Sequence Viewer Legend

 dialog box, which explains the sequence 

color schemes. 

Preferences

 Opens 

the 

Sequence Viewer - Preferences 

dialog box, in which you can set the 

proximity cutoff. 

Save Image

 Opens 

the 

Save Sequence Viewer Image

 file selector, in which you can save an 

image of the sequence viewer to a file. The image format is determined by the 

extension that you choose. 

Export 

Sequences

 

Exports the sequences in the Sequence Viewer to a FASTA file. Opens a file 

selector to specify the location and the file name.

Help

 

Opens the Sequence Viewer help topic.

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Chapter 2: The Maestro Main Window

Maestro 10.2 User Manual

31

2.8

Mouse Functions

The Workspace has special uses for the middle and right mouse buttons. These are used on

their own and in combination with the 

SHIFT

 and 

CTRL

 keys to perform common operations

such as rotation, translation, centering, and zooming. The table below summarizes the standard

actions for a 3-button mouse with scroll wheel.

Table 2.6. Mapping of Workspace operations to mouse actions.

Mouse Button

Keyboard

Motion

Action

Left

click, drag

Select

Left

drag

Quick Torsion adjustment and adjust-

ment of distance, angle, dihedral 

Left

SHIFT 

click, drag

Toggle the selection

Middle

drag

Rotate about X and Y axes

Middle

SHIFT 

drag vertically

Rotate about X axis

Middle

SHIFT 

drag horizontally

Rotate about Y axis

Middle

CTRL 

drag horizontally

Rotate about Z axis

Middle

SHIFT + CTRL drag 

horizontally

Zoom

Right

click

Spot-center on selection

Toggle selection

Right

click and hold

Display shortcut menu

Right

drag

Translate in the X-Y plane

Right

SHIFT 

drag vertically

Translate along the X axis

Right

SHIFT 

drag horizontally

Translate along the Y axis

Right

CTRL 

drag horizontally

Translate along the Z axis

Middle & Right

drag horizontally

Zoom

Wheel

scroll Zoom 

In any adjust mode, do adjustment

Wheel

CTRL 

scroll

Adjust isovalue of electron density 

map (PrimeX)

In clipping planes window, move clip-

ping planes in opposite directions

Wheel

SHIFT 

scroll

In clipping planes window, move clip-

ping planes in the same direction

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Chapter 2: The Maestro Main Window

Schrödinger Software Release 2015-2 

32

Section 4.2 on page 64

 has more detailed information on changing the Workspace view. Mouse

and trackpad functions can be customized—see 

Section 13.3 on page 321

 for information

2.9

Shortcut Keys

Some frequently used operations in the main window have been assigned shortcut key combi-

nations. The default shortcuts, their functions, and their menu equivalents are listed in

Table 2.7

. Shortcut keys in the 

Project Table

 panel and the 

Plot

 panel are listed in the chapters

that describe those panels. In addition to the shortcut keys listed below, there are a set of keys

that can be used in either the Workspace or the Project Table. Most of these keys are for actions

in the Project Table—see 

Section 9.4.6 on page 192

 for more information. You can customize

the shortcut keys in the 

Customize Menus

 panel—see 

Section 13.2 on page 318

 for details. 

If 

Num Lock

, 

Caps Lock

, or 

Scroll Lock

 is enabled, the shortcut keys do not work. Some

shortcut keys might not work on non-English keyboards: for example, 

CTRL+=

 (full screen) on

German keyboards in the German locale or 

`

 (pick to select) on French keyboards in the French

locale. If this is the case, you can customize the shortcut keys for these functions.

Table 2.7. Default shortcut keys in the Maestro main window.

Keys

Action

Equivalent Menu Choice

B 

Pick bonds in the Workspace

CTRL+SHIFT+Z 

(



Z

)

Select the next defined adjustment of the 

current type for adjustment.

Edit 

→

 Adjust 

→

 Next Adjust-

ment

CTRL+SHIFT+A 

(



A

)

Select the previous defined adjustment of 

the current type for adjustment.

Edit 

→

 Adjust 

→

 Previous 

Adjustment

U 

Clean up the geometry of the Workspace 

structure or selected atoms.

Edit 

→

 Build 

→

 Clean Up 

Geometry

 

CTRL+C (C)

Copy the Workspace contents onto the clip-

board. Includes atoms, SMILES, and image 

at screen resolution.

Edit 

→

 Copy

 

CTRL+X (X)

Cut the atom selection (delete the selected 

atoms and put them on the clipboard)

Edit 

→

 Cut

 

DEL 

Delete the selected atoms 

Edit 

→

 Delete

 

CTRL+F (F)

Show or hide the 

Find 

toolbar

Edit 

→

 Find

 

X 

Mark or clear mark for the current entry, 

creating the 

Mark

 property if necessary.

Edit 

→

 Mark Target Entry

 

CTRL+V (V)

Paste atoms into the scratch entry

Edit 

→

 Paste

 

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