Maestro User Manual

Chapter 4: Viewing the Workspace

Maestro 10.2 User Manual

73

zoom in and out in the Workspace. If you deselect this option, the top view stays the

same, regardless of what happens in the Workspace. Translation in x and z moves the dis-

played structures. 

• Clipping planes: These are horizontal lines that mark the planes where the graphical

image is clipped. The lower line marks the plane that is closest to the viewer, and the

upper line marks the plane furthest from the viewer. 

The planes can be moved by dragging the horizontal lines. To move both planes in the

same direction, hold down the 

CTRL

 key and drag one of the planes or use the scroll

wheel. To move both planes in opposite directions, hold down the 

SHIFT

 key and drag

one of the planes or use the scroll wheel. You can use the keyboard to move the planes

closer together (

F

), further apart (

G

), towards you (

=

), or away from you (

-

), in small

increments. These actions are also available from 

View

 

→ 

Move Clipping Planes

.

The clipping planes are adjusted if you select 

Adjust clipping planes when focusing on a

substructure 

under 

Workspace 

→

 Clipping Planes

 in the 

Preferences

 panel (see

Section 14.4.8 on page 351

) and you do one of the following:

• Select part of a structure and perform a fit-to-Workspace.

• Perform a fit-to-ligand.

• Middle-click a residue in the sequence viewer to zoom in on it.

• Select a residue in the residues table of the 

Density Fit

 panel (PrimeX)

• Select a rotamer in the 

Residues

 table of the 

Rotamers

 dialog box.

• Find a residue with the 

Find 

toolbar.

• Viewing volume indicator: This is a green box that represents the viewing volume. As

you zoom in on the structure, the box shrinks. If you have perspective enabled, the view-

ing volume box is trapezoidal, with the small side at the bottom.

Clipping can be applied to fit objects in the Workspace, by choosing 

To All Atoms

, 

To Selected

Atoms

, or 

To Ligand

 from the 

Move Clipping Planes

 submenu of the 

View

 menu. This feature

can be used to reset the clipping without changing the zoom. 

Clipping can be applied selectively, as well as to all graphical objects. To choose what clipping

is applied to, right-click in the clipping planes window and make your choice from the shortcut

menu that is displayed. The choices are:

•

All

—Apply clipping to all objects (structures and surfaces). Clipping planes are drawn as

horizontal orange lines, and can be adjusted by dragging.

•

Surfaces

—Apply clipping to surfaces but not to structures. There are four clipping

planes: front, back, left, and right. These planes are drawn as horizontal and vertical pur-

ple lines, and can be adjusted by dragging.

---

Chapter 4: Viewing the Workspace

Schrödinger Software Release 2015-2 

74

•

Surfaces to selected atoms

—Apply clipping to the surfaces using a cube centered on the

selected atoms. For example, you might select just the ligand in a ligand-receptor com-

plex, and the surface will be clipped to a cube that contains the ligand. The outline of the

cube is displayed in cyan. You can resize the cube by dragging horizontally.

•

Selected atoms

—Apply clipping only to the selected atoms. For example, you could

select the receptor in a complex, and leave the ligand unclipped. Clipping planes are

drawn as horizontal cyan lines, and can be adjusted by dragging.

4.7

3D Viewing

Maestro provides several tools to enhance the 3D appearance of complex structures. These

tools include stereo viewing, perspective, fogging distant atoms, and depth cues. They are

described in the sections that follow. Most of the tools are in the 

3D

 and 

Fog

 tabs of the

Appearance

 panel, which you can open by choosing 

View 

→

 3D Options

 or 

View

 

→ 

Fog

 

→

Settings

.

4.7.1

Stereo Viewing

Maestro provides two kinds of stereo viewing method: software stereo and hardware stereo.

Software stereo can be run on any computer, and can be run across a network or with remote

display software, such as NX or Remote Desktop. It usually involves displaying both images

on the screen simultaneously, and relies on focusing or simple devices to view the stereo effect.

Hardware stereo requires some special equipment—a specialized monitor or graphics card, or

both, and 3D glasses. It can usually only be viewed locally. 

Two software stereo methods are available. In the first, two images are displayed simultane-

ously on separate parts of the screen, and the stereo effect relies on focusing your eyes so that

the images appear to merge into a single image. Two variants of this method are available:

“wall-eyed”, in which the left eye looks at the left image and the right eye looks at the right

image (focusing at a very long distance); and cross-eyed, in which the left eye looks at the right

image and the right eye looks at the left image (focusing at a very short distance). Neither of

these variants needs any special hardware, though a device for screening out one image for

each eye may be useful. The default variant is wall-eyed. 

The second software stereo method is anaglyph stereo, in which the images are superimposed

and are drawn with color filters, red and blue-green. To view the stereo effect, you need a pair

of glasses with the appropriate color filter for each eye. The images have full color, but the red

colors are not as true as when you do not view in stereo. 

---