Workspace Preferences

These settings affect the appearance and behavior of selection-related actions in the Workspace.

Show predictive highlighting in Workspace

Highlight the atoms in the Workspace that would be selected (including undisplayed atoms) if you clicked at the current cursor position. The highlighting changes as you move the cursor.

Ignore Workspace click when giving focus to main window

Ignore any click in the Workspace when the main window does not have focus, and you are clicking on it to give it focus. Setting this preference prevents an unintended action from taking place when you happen to click in the Workspace to get focus in the main window. This preference is on by default. If the focus policy of your window manager puts focus in the main window without clicking (follows mouse), you might want to turn this option off.

These settings control the animation of changes to the view of the Workspace.

Animate view changes

When selected, this option enables animation of changes in the view: the structure changes from one view to another over a period of time, rather than instantly. View animation is done when an automatic change in view is made, such as spot centering, resetting the view, and fitting to the Workspace. The duration of the animation can be controlled by entering a value in the Duration text box.

Animation can be turned off if the distance over which the structure moves is greater than a given threshold, by selecting Limit animation distance, and entering the distance threshold in the Maximum distance text box.

If you select Non-linear animation, the animation starts slowly, speeds up in the middle, then slows down at the end. By default, animation is linear. If you are using animation for a smooth change between multiple views, linear animation may be preferable.

These settings apply when doing translation of the Workspace view.

Keep center of rotation fixed while translating

This option keeps the center of rotation in its current position relative to the view (i.e on the screen) when the Workspace structure is translated. When the option is deselected, the center of rotation moves with the structure when it is translated. This is the default.

Keep electron density centered while translating

When translating the Workspace structure, selecting this option ensures that the cube in which the electron density is displayed remains at the same place relative to the Workspace view. The effect is that the structure with its electron density appears to move through the cube. The size of the cube is set in the Surface Table panel.

Keyboard translation increment

Set the amount by which the Workspace is translated on each key stroke, when using the keyboard for translation. The amount is a percentage of the size of the Workspace.

These settings apply to rotation operations.

Sensitivity in rotation

Use the slider to set mouse sensitivity for rotation. Larger values result in faster rotation. The scale is from 1 to 500, with a default of 75.

Keep center of rotation fixed while translating

This option keeps the center of rotation in its current position relative to the view (i.e on the screen) when the Workspace structure is translated. When the option is deselected, the center of rotation moves with the structure when it is translated. This is the default.

Display center of rotation

Display a marker at the center of rotation. The marker is a set of three circles perpendicular to each other that indicate the orientation of the view.

Smoother local rotation

This option makes local rotation appear to happen smoothly. Turning it off can result in more jerky rotation, but may prevent rotation from continuing after the mouse has stopped moving.

Keyboard rotation increment

Set the amount in degrees by which the Workspace is rotated on each key stroke, when using the keyboard for rotation.

This section contains settings for trackpad gestures. There is only one setting, Pinch gesture sensitivity for zoom, which controls the rate at which zooming is done as you pinch.

These settings apply to translations or rotations, both global and local.

Keep center of rotation fixed while translating

This option keeps the center of rotation in its current position relative to the view (i.e on the screen) when the Workspace structure is translated. When the option is deselected, the center of rotation moves with the structure when it is translated.

Display center of rotation

Display a marker at the center of rotation. The marker is a set of three circles perpendicular to each other that indicate the orientation of the view.

Keep electron density centered while translating option

When translating the Workspace structure, selecting this option ensures that the cube in which the electron density is displayed remains at the same place relative to the Workspace view. The effect is that the structure with its electron density appears to move through the cube. The size of the cube is set in the Surface Table panel.

Include alternate positions in local transformations

When performing a local transformation on a set of atoms that include atoms with alternate positions, transform the coordinates for both alternatives. Deselect this option to transform the displayed location and not the alternate.

These options control the display of the dipole moment arrow in the Workspace.

• Show disk on positive end of arrow—Show a disk around the positive end of the arrow.
• Show positive and negative colors—Color the arrow with a color gradient from blue (negative) to red (positive).
• Show arrow from positive to negative—Show the arrow pointing from positive to negative ("chemists' convention"). Deselect this option to show the arrow pointing from negative to positive ("physicists' convention").

These options affect the adjustment of the clipping planes (the planes between which objects are displayed, and outside of which objects are hidden).

Adjust clipping planes when focusing on substructure

When focusing on a substructure that has been selected by one of the processes listed below, adjust the clipping planes to within the distance specified in the Clip to within text box.

• Selecting a residue in the residues table of the Density Fit panel (PrimeX)
• Selecting a rotamer in the Residues table of the Rotamers dialog box.
• Middle-clicking a residue selection in the Workspace sequence viewer (to zoom in to it).
• Finding any set of atoms using the Find toolbar.
• Fitting a ligand to the Workspace.

Zoom clipping planes with Workspace

Select this option to adjust the clipping at the same time as zooming in or out. The image in in the Adjusting the Clipping changes size when zooming, to reflect the new clipping planes settings. If it is deselected, the clipping planes are not adjusted when zooming, and the image in the clipping planes window stays the same size. This option is off by default.

Clip increment

Specify the increment by which the clipping planes are moved when you move them forward, backward, together, or apart (View → Move Clipping Planes). The increment is a percentage of the current width of the region between the clipping planes.

These settings allow you to change the font that is used for text that is displayed in the Workspace. You can choose the font and the point size, and make the text bold or italic. The fonts can be set for the following types of text:

• Atom labels
• Mesaurements
• Adjustments
• Properties

The font size is also changed by the Increase and Decrease items under Workspace → Fonts, or by the Font Size buttons in the Workspace Configuration toolbox.

These settings affect what happens when fitting to the Workspace is done.

Zoom clipping planes with Workspace

Select this option to adjust the clipping at the same time as zooming in or out. The image in in the Adjusting the Clipping changes size when zooming, to reflect the new clipping planes settings. If it is deselected, the clipping planes are not adjusted when zooming, and the image in the clipping planes window stays the same size. This option is off by default.

Enhance fog

Enhance the fogging depth cues when fitting to the Workspace.

Fit margin

Specify the margin in angstroms around the structures or selected atoms when fitting them to the Workspace.

These settings affect the display when zooming in and out in the Workspace.

Zoom clipping planes with Workspace

Select this option to adjust the clipping at the same time as zooming in or out. The image in in the Adjusting the Clipping changes size when zooming, to reflect the new clipping planes settings. If it is deselected, the clipping planes are not adjusted when zooming, and the image in the clipping planes window stays the same size. This option is off by default.

Minimum size of Workspace for automatic zooming option and text box

Set the minimum size of the Workspace in angstroms for automatic zooming, that is, zooming in that is performed as a result of other actions rather than user-initiated zooming. When this setting is on, zooming in stops when the distance across the Workspace either horizontally or vertically reaches the specified value. This option essentially imposes a maximum zoom level, so that there is a limit to the displayed length of bonds, and a single atom will (in general) never fill the screen. It guarantees that a defined amount of context will always be visible in the Workspace when zooming in.

These settings control how changes in the Workspace are saved to the project.

• Automatically—Maestro automatically saves any changes to entries in the Workspace to the project.

• When approved—Maestro determines when changes will be lost if they are not saved, and prompts you to save the changes. You must make a choice before proceeding.

• Only when specifically requested—Maestro never determines that changes must be saved. You must explicitly save changes or they will be lost. To save changes, click the disk icon in the status bar of the main window.

If Workspace changes are not saved automatically, you must save them explicitly by clicking the disk icon in the status bar , or choosing File → Save Workspace Changes .

These settings control the display of markers for periodic structures in the Workspace. The label depends on the profile: it is called Periodicity except for the Materials Science profile.

Unit cell settings

Make settings for the display of the unit cell in the Workspace. The Show settings allow you to display the unit cell boundaries, the lattice vectors, or both. You can adjust the with of the lines with the Line width slider, and you can set the color of the lines using the color button, which opens a color selector.

Polyhedrons settings

Make settings for the display of polyhedrons: set the color with the Polyhedron color button (which opens a color selector), and set the opacity with the Opacity slider.

Periodic Structure Tool settings

These settings are only present for the Materials Science profile, as the Periodic Structure Tool (Periodicity toolbox) is only available in this profile. See Workspace Tools for Periodic Structures for more information on this toolbox.

Default to recalculating connectivity for new periodic structures option

Set the default behavior for recalculating connectivity for new cells built using the Periodicity toolbox, and. If this option is selected, the default is to recalculate connectivity.

Bonds and Valences settings

These settings are only present for the Materials Science profile where they are used in the Periodic Structure Tool (Periodicity toolbox, see Workspace Tools for Periodic Structures) and the New Crystal Structure Panel.

Ignore atomic valences when calculating bonds option

When calculating the number of bonds (connectivity) between atoms in an inorganic structure for display purposes, ignore the atomic valence. If this option is not selected, the number of bonds is limited by the atomic valence (with a few exceptions, such as Na, Cl, and I, which can have 6 bonds).

There is one option: Rename crystal mate chains. If you want to generate unique chain names for the crystal mates, select this option. By default the crystallographically related copies have the same chain name as the original.

The settings in this section control features that relate to the graphics card or graphics libraries.

Note: OpenGL 1.2 is deprecated, and new graphics features are added only for OpenGL 2.1. If you are still using a graphics card that does not support OpenGL 2.1 you are strongly encouraged to obtain one that supports OpenGL 2.1.

Requested OpenGL level options

These options select the OpenGL library version that is used to draw objects in the Workspace. Two versions are available: 1.2 and 2.1. OpenGL 2.1 has features that are used to provide higher quality and improved performance of the rendering when using hardware graphics.

If you use -SGL when starting Maestro, the performance with OpenGL 2.1 is much slower than that of 1.2, because hardware acceleration is not being used. However, if you want a high-quality single image, for example, you can select 2.1.

The Best option selects the best available OpenGL level. OpenGL 2.1 is used if you have an NVIDIA or an ATI graphics card with OpenGL 2.1 support and the appropriate driver. OpenGL 1.2 is used if Maestro is started with the -SGL option on Linux, if Maestro is run over a network, or if OpenGL 2.1 is not available or is not adequately supported (as is the case with some cards that claim to support OpenGL 2.1). The version actually used is displayed below the options.

You must restart Maestro for the changes in the OpenGL level to take effect.

Full scene antialiasing option

Turn on full-scene antialiasing, which smooths the appearance of objects in the Workspace. Not all objects are smoothed, so you can use this in conjunction with the Antialiasing setting in the Effects settings for the smoothest result.

GPU-accelerated transparency option

Turn on the use of the depth peeling method for drawing of (semi-)transparent objects. This option can make drawing a lot faster and more accurate. Recommended for machines with a dedicated GPU.

This feature is on by default, but is disabled if you select OpenGL 1.2. You might want to turn it off if you see drawing errors in objects in the Workspace: this may indicate issues with your graphics card or its configuration, or other system-related issues or inadequacies.

Quality section

These settings control the quality of the molecular representation. The settings depend on the requested OpenGL level.

For OpenGL 1.2, the following settings can be made:

Use simplified representation when moving option

When a structure is being moved in the Workspace, display it at lower resolution than when it is at rest and in a simplified representation. This speeds up the operation on the structure. This option is off by default, but is turned on when you select the Performance rendering option.

Use thick lines for tubes when rotating

In the simplified representation, use thick lines (of the same thickness as the tubes) when rotating. This makes the simplified representation look a bit more like the normal representation. The default is to use wire frame representation for bonds in the simplified representation.

Moving resolution slider

Specify the resolution to use for the structure when it is moving, on a scale from 1 to 50. Lower numbers mean lower resolution (lower quality).

Resting resolution slider

Specify the resolution to use for the structure when it is at rest, on a scale from 1 to 50. Lower numbers mean lower resolution (lower quality).

For OpenGL 2.1, the following settings can be made:

Use faster sphere-drawing method option

Use the faster method for drawing spheres. This method provides up to 20% speedup when there are many spheres in the Workspaces, such as for a protein in CPK representation. It is not used when perspective is enabled.

Restore Defaults button

Restore the default values for OpenGL level and quality.

These settings control the lighting effects on objects in the Workspace. There are two sets of controls, one for each light source, each of which has the following features. The second light is not available with OpenGL 1.2.

Light direction display

The light direction control allow you to pick the direction of the selected light. To change the direction, click the desired location on the red ball, or drag the yellow spot to the desired location.

Use light option

Select this option to use the selected light. Deselecting this option disables the controls for the light.

Ambient slider and text box

Set the ambient value with the slider, or enter the value in the text box. This is the relative intensity of the (ambient) nondirectional light.

Diffuse slider and text box

Set the diffuse value with the slider, or enter the value in the text box. This is the relative intensity of diffuse reflection (reflection that has the same intensity in all directions).

Specular slider and text box

Set the specular value with the slider, or enter the value in the text box. This is the specular reflection intensity ("shiny" reflection of the light source)

Restore Defaults button

Restore the settings to their default values.

The materials tab contains controls for the definition of the appearance of the objects in the Workspace.

Edit material for option menu

Select the object whose material appearance is to be customized.

Presets buttons

These four buttons, Metallic, Plastic, Rubber, Wood, set values of the properties that control the appearance of the selected object. They are not available with OpenGL 1.2.

Property sliders

These sliders allow you to set the five properties of the material:

• Ambient—intensity of ambient (nondirectional incident) light. Not available with OpenGL 1.2.
• Diffuse—intensity of diffuse (nondirectional) reflection of light. Not available with OpenGL 1.2.
• Specular—intensity of specular (directional) reflection of light
• Emission—light emission intensity of the object
• Shininess—size and brightness of specular highlight (larger value gives a smaller and brighter highlight)

Each property has a slider and a text box. You can use either of these controls to set the property value.

Restore Defaults button

Restore the settings to their default values.

The 3D settings contain controls for use of stereo and perspective.

Stereo section

The settings in the Stereo section allow you to switch between the stereo viewing methods and make settings for those methods. Stereo display only applies to the Workspace—none of the Maestro main panel tools or other panels are displayed in stereo. You might want to use full-screen mode when you are viewing structures in stereo, which you can turn on and off with Ctrl+= (⌘=), or by choosing View → Full Screen and using ESC to exit.

You can also adjust the alignment depth to shift objects that you want to see more clearly in stereo toward the plane of the screen.

The stereo method and settings persist across Maestro sessions.

Swap stereo images option

Select this option to swap the images for the right eye and the left eye. This is useful to resolve synchronization problems with hardware stereo. It applies also to the software stereo methods, and has the effect of swapping cross-eyed and wall-eyed stereo.

Method option menu

Select a stereo viewing method from this option menu. There are five stereo viewing options, three of which are software implementations and do not require special hardware, and the other two are hardware stereo methods. The software methods can be used on any computer, and displayed remotely. The hardware methods can usually only be used locally.

• Wall-eyed—In the "wall-eyed" stereo viewing method, the eyes focus on both displayed images at once, instead of focusing at a central point. One difficulty that may arise when using this stereo viewing method is that it is difficult, if not impossible, to achieve the stereo effect when the images are more than the inter-ocular distance apart, or about 2.5 inches. Structures more than 2.5 inches wide will therefore need to be resized and repositioned using the Size factor and Separation factor sliders. The height of the molecule is not critical for stereo viewing. Any height less than the window height is acceptable.

  To use the Wall-Eyed stereo viewing option, stare past the screen as if focusing on an image far beyond it. This tactic tricks the eyes into focusing in a plane beyond the screen. When performed correctly, wall-eyed viewing produces three images, with the center one being a 3D combination of the two outer ones.

• Cross-Eyed—This stereo method is difficult and is not advised for stereo viewing novices, since inadvertently viewing the cross-eyed image wall-eyed will result in the molecule being inverted along the z-axis. This can produce inaccurate depth information, particularly when the wire molecular representation is being used.

• Hardware—Technically, this is quad-buffered hardware stereo. It requires a suitable monitor, with a refresh rate greater than 100 Hz, a graphics card that supports quad-buffered stereo, and 3D glasses. A warning is displayed if the hardware does not support stereo and this option is selected. This option is not available on Mac platforms, which do not in general support hardware stereo.

  There are other specialized viewing devices that can be used with this method.

• Interlaced—This hardware method requires a monitor that supports interlacing, and 3D glasses. Interlaced stereo works on all supported platforms if the hardware is available. A warning is displayed if the hardware does not support stereo and this option is selected.

• Anaglyph—This stereo method uses color filters to display the two images. To use it, you must have glasses with one red and one cyan filter. The stereo image is perceived in full color, though the red colors tend to be somewhat dull. You can use the Type option menu to brighten the image (Half Color), which is harder on the eyes, or to keep the duller red colors (Reduced Fatigue) to relieve eye fatigue. This option menu is only displayed when you choose anaglyph stereo.

• Chromadepth—This stereo method uses false coloring to represent depth, and requires glasses designed for chromadepth stereo.

Size factor slider

Use this slider to reduce the size of the displayed structure to better facilitate cross-eyed or wall-eyed viewing.

Separation factor slider

Use this slider to decrease the distance between the left and right stereo images. This feature eases cross-eyed and wall-eyed viewing. The Separation factor slider becomes available once the displayed structures have been resized with the Size factor slider (see above).

Eye separation slider

Use this slider to adjust the stereo viewing angle, which governs the amount of depth perceived in stereo. The stereo viewing angle increases roughly in proportion to eye separation, and increases with perspective scale (decreases in nearly inverse proportion to viewing distance). The slider should generally be positioned near the center of the range, to correspond to a "normal" adult inter-ocular distance of 2.5 inches and viewing distance of 24 inches. Use smaller values for smaller inter-ocular distance or larger viewing distance, or to reduce the side-effects of larger stereo angles, such as clipping and double images. Use larger values for larger inter-ocular distance or smaller viewing distance, or to increase the amount of perceived depth.

Reducing this parameter can help stereo perception with interlaced stereo on certain monitors.

Perspective settings

The Perspective feature helps facilitate 3D viewing by scaling the apparent size of objects according to their z-axis depth (making more distant objects appear smaller, as in normal viewing).

Display in perspective option

To use perspective, select this option. Perspective is enabled by default.

Perspective scale slider

Adjust the amount of perspective, which relates to the viewing distance, with this slider. Here, perspective scale is the ratio between the actual size and the projected size of an object placed 0.7 feet behind the display screen. This has a corresponding viewing distance,

view_dist = (0.7 ft) / (perspective_scale - 1)

For a known viewing distance,

perspective_scale = 1 + (0.7 ft / view_dist)

Therefore, for a normal viewing distance of 2 feet,

perspective_scale = 1 + (0.7 ft / 2 ft) = 1.35

To get a stronger depth cue, using exaggerated perspective, you can use larger perspective scale values.

When perspective is in use, the viewing volume indicator (shown in green in the Adjusting the Clipping) takes a trapezoidal shape that reflects the perspective scale.

Alignment depth slider and text box

This slider translates the region of molecule space bounded by the front and back clipping planes. This appears to move objects within that region, in or out (along the z-axis), relative to the screen. Smaller alignment depth values place the displayed objects farther from the viewer (farther behind screen). Larger values place objects closer to the viewer (farther in front of screen).

Adjust clipping to preserve depth cues option

This option determines whether the front and back clipping planes should be automatically adjusted to preserve the eye separation while displaying in stereo and to preserve the perspective scale (corresponding to viewing distance) when displaying in perspective. When this option is enabled, perceived depth is maintained but some objects may be clipped, especially when zooming in (in which case, you may also want to adjust the alignment depth). If Adjust clipping to preserve depth cues is deselected, then the stereo and perspective settings are automatically adjusted in order to preserve the front and back clipping planes. Then, objects are not clipped more in front and back when zooming in, but are effectively flattened (reducing their perceived depth). These automatic adjustments are not permanent, but are done whenever the current 3D settings cannot be used to display, in an acceptable manner, the entire region between the front and back clipping planes.

These settings allow you to apply some special effects to the Workspace.

Fog settings

The Fog feature helps facilitate 3D viewing by providing emphasis on the parts of the structure that are closest to you. Closer parts of the molecule appear in the pure currently selected atom color, and more distant parts appear to turn gray and finally disappear into the background. Fog can be useful when hardware-assisted stereo viewing is not available, but it is also helpful when used in conjunction with stereo viewing.

Display fog option menu

Select the conditions under which fogging is used.

• Automatic—Turn fog on if there are more than 40 atoms in the Workspace.
• On—turn fogging on for all atoms
• Off—turn fogging off for all atoms

Display fog on atom labels option

Apply fogging to atom labels as well as to atoms.

Method option menu

This option menu contains three fogging gradient types: Linear, Exponential, and Exponential Squared. Currently, only the Linear method should be used when displaying in perspective.

Linear Start and Linear End sliders

The Linear Start and Linear End sliders allow you to increase or decrease the range of available colors created by fog gradations. Linear Start moves the plane that defines the fog boundary that is closest to the screen. Linear End moves the fog boundary that is behind the structure. There is a finite number of gradations, and if there is empty space, some of them are wasted.

Density slider

This slider allows you to increase the contrast of colors created by the fogging feature. Closer portions of the structure will appear even brighter and more distant ones will more quickly converge on the background color.

Effects settings

These effects are calculated for the full screen for each pixel, and require OpenGL 2.1. The effects can be turned on and off using the checkboxes. The available effects are as follows:

Antialiasing option

Smooth the edges of objects so they don't appear jagged. This effect does not antialias semi-transparent objects. The Full-scene antialiasing preference (under Workspace – Graphics) does, but it does not antialias spheres and cylinders (balls and sticks). For the smoothest edges, use both the preference and the screen effect.

Ambient occlusion option and sliders

Enhance the perception of depth by taking into account the ambient lighting blocked by other objects. This option is available for any structure, but is most useful for large structures in CPK representation and with molecular surfaces.

You can set the intensity of the darkening effect with the Intensity slider and box. The intensity is represented as a percentage, with 0 corresponding to no effect.

You can also change the range of the effect, with the Radius slider. Any screen object within the specified radius of a pixel is considered to occlude the pixel. Thus, the smaller the radius, the more local and "sharp" the effect, At a very small radius, the effect is like outlines.

Outlines option and controls

Add a thin outline to objects in the Workspace. The color of the outline can be set by clicking the Color button and choosing a color in the color selector that opens. The new color is shown on the color button. The width of the outline in pixels can be changed in the Width box, from 0 to 10.

Cartoon shading option and controls

Use cartoon shading, in which the color or shading is done in steps rather than continuously. You can specify the number of steps in the Steps box, which can take values from 2 to 10.

These settings control how sequences are displayed. They are also available on the Sequence viewer shortcut menu.

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.

Display SSA

Show the secondary structure assignment for the sequence.

Align by residue number

Align the sequences in the sequence viewer by residue number. (Does not affect the alignment of the structures.) This option enables gaps to be displayed in the sequence viewer.

Display non-protein molecules

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

Proximity cutoff

Set the distance cutoff for the sequence viewer proximity color scheme.