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Preferences Panel |
This panel is used to set application-wide preferences. These preferences are preserved between Maestro sessions. Preferences are applied immediately, unless otherwise noted in the panel.
To open the Preferences panel, you can:
Choose Maestro → Preferences in the main window.
Press Ctrl+, (⌘,) in the main window.
The preferences panel is also opened at a particular tab by clicking the Preferences button or choosing Preferences from a menu in a number of panels.
Preferences are categorized into groups, and many of the groups are divided into subgroups. Several of the preferences are included in more than one group or subgroup, to make them easier to find. The groups and subgroups are listed in the tree structure on the right. To display the subgroups for a group, click the turner to the right of the group name. To display the preferences in a group or subgroup, click the group or subgroup name.
You can search for text in any of the preferences, tooltips, preference headings, or tree text. As you type text into tht Search text box, the tree is pruned to show only the parts that contain the text, and the groups are opened so that you can see the subgroups. To show the full tree again, click the clear button.
The preferences panel has a tree view of the preference groups and subgroups on the left in a scrolling pane. When a group or subgroup is selected, the settings for the group or subgroup are displayed on the right. Some settings are available in more than one subgroup. Below the tree is a search text field and button for clearing the text field.
You can search for text in any of the settings, their headings or their tooltips, or in the tree text, by entering the text into the Search text box. As you type, the tree is pruned to show only the groups and subgroups in which the text is found, and each group is opened. To show the full tree again, clear the text box by clicking the button next to it.
These options can be used to limit the number of commands stored, and therefore available in the Command Script Editor panel.
In this text box, you can specify how many items are displayed on the lists of recently used projects and recently imported files, which are displayed with Project → Open Recent and Project → Import Recent Structures.
Keep a record of operations on the project in the project annotations file. The record of operations is displayed in the Project Summary panel.
These settings determine some of the directories that are used by Maestro.
When you choose any of the options below, the current working directory is set to the specified location, and the option you select is stored as a preference. The current working directory is set to the specified location the next time you start Maestro.
Job files are written by default to the current working directory. File selectors display the contents of the current working directory when they are first opened in a Maestro session. Subsequently each file selector stores the last location you visted, and displays the files in that location when you open it again.
Thus, these options set the default by changing the current working directory immediately, on Maestro startup, and when a project is opened if the option is project-related.
If you change the current working directory explicitly after choosing one of these options, the new directory is used as the location for job files and the initial location for file selectors, rather than the choice you make from this set of options. For more information on changing the current working directory, see Changing the Working Directory.
In the descriptions below, the directory is called the default directory.
Note: If you choose an option for a directory that is inside the project, you should wait until any jobs launched from that project finish before you rename the project, or save the project if it is a scratch project.
Maestro's current working directory option—
Set the current directory to Maestro's initial working directory. When Maestro
starts, this directory on Linux is the directory from which Maestro was started;
on Windows and Mac it is the Schrodinger folder in your Documents
folder.
Parent of project directory—Set the
current working directory to the parent directory of the current project (the
directory that the project is in). Opening a different project or closing a
project (which opens a scratch project) sets the current working directory
again. For zipped projects, the parent directory is the directory that contains
the .prjzip file, rather than the temporary directory into which the
zipped project is extracted.
Jobs running with this setting are not lost if the project is renamed.
Project directory—Set the current working
directory to the top-level directory inside the current project. This is the
project-name.prj directory. This directory changes when a
new project is loaded, and the current working directory is reset to the new
project directory.
Jobs running in this directory will fail if the project is renamed. This includes saving scratch projects.
Project jobs directory—Set the current
working directory to the project's jobs subdirectory
(project-name.prj/jobs). This directory
changes when a new project is loaded or when a scratch project is opened, and
the current working directory is reset to the new jobs directory.
Jobs running in this directory will fail if the project is renamed. This includes saving scratch projects.
Other (specify below)—Use the specified directory as the current working directory. When using this option, you must enter the desired directory name in the Directory text box.
Specify the location of the custom directory to use in file selectors. The contents of this directory are displayed when you click the Custom icon in a file selector under Look in. There are two standard locations that you can select as the custom location, or you can choose your own location.
Maestro installation directory—Set the custom directory to the directory in the installation that contains the Maestro software and resources. The actual path is displayed in the tooltip for this option.
Maestro launch directory—Set the custom directory to the directory from which Maestro was started, on Linux, or the Schrodinger folder in your documents folder on Windows and Mac. The actual path is displayed in the tooltip for this option.
Other (specify below)—Specify the directory in the Directory text box.
Specify the location for the storage of temporary (scratch) projects. You can click Browse to navigate to the desired location. This directory should be large enough for your temporary projects, and for efficiency should be on a local file system. This location will be used for temporary projects the next time you start Maestro.
Two environment variables are used to determine a location for the scratch
project. If SCHRODINGER_TEMP_PROJECT is defined, the location it
specifies is used, and overrides the value set here. Otherwise if it is not
defined and a location is not set here, the location defined by TMPDIR is used. Failing any of these, the default is to use
the local application data directory, which on Linux is $HOME/.schrodinger/tmp, and on Windows is
%LOCALAPPDATA%\Schrodinger\tmp. If any of these directories is on
a file system with a limited amount of space, you should consider specifying
another location.
These settings control Maestro's default file suffix for five different file formats. A default suffix is automatically appended to a file name if that file name has no suffix. The default file suffixes are:
These settings control the appearance or layout of Maestro.
When the pointer is paused over a control, show information about the control in a box near the control after a short delay. The box is hidden after a period of time, or when the pointer is moved. This information in a box is known as a tooltip or balloon help.
Show the selected information in the title bar of the main window, after the application name (Maestro). The options are:
The order in which the information is shown is profile name, version number, directory.
Display the toolbar buttons as icons only, text only, or icons and text with text beside the icon or under the icon. Clicking the Apply to All Toolbars button changes the style for all the toobars. You can set the style for individual toolbars from the shortcut menu for the toolbar.
Set the font, size, and style for the text. The Regular settings control the fonts in all the application panels: headings, button labels, menu items, and so on. The Text editing settings control the fonts in all places where you can edit text (text boxes, tables, and so on). The Project Table settings control the fonts for the text that is displayed in the column headings and the table cells in the Project Table. The Toolbar buttons settings control the fonts for the text that is displayed on toolbar buttons.
An example of the font size is given under each option menu. You must restart Maestro to apply the new fonts.
Control the docking, location, and choice of panels.
This option allows panels to be docked into the Workspace. Most of the panels other than those on the Applications or Tasks menu are dockable. This option is selected by default. If it is not selected, when you open these panels, they are opened outside the Workspace and cannot be attached to the Workspace (docked).
Specify the location to place the docked panels. They can be docked in either the main window, or in a floating window, named Docked Panels.
When a dialog box opens, center it on the current pointer position. If you turn this option off, the dialog box is displayed at its last displayed location (or its default location if it has not been displayed).
Show all panels in front of the main window, and ensure that they do not go behind the main window.
Select the default interface to use for homology modeling, when choosing Tasks → Homology Modeling or Applications → Prime → Homology Modeling. The options are:
Select the information that is shown or saved when Maestro quits.
Display the Quit panel when quitting Maestro, which provides an opportunity to cancel the quit operation.
Display a warning if a PyMOL session launched from Maestro is still running when quitting Maestro. Quitting Maestro also forces termination of this PyMOL session, so the warning enables you to save any work done in PyMOL before Maestro quits and closes PyMOL.
Save the panel layout (size, location) of all panels that have been opened in a Maestro session in a resource file when Maestro quits. The layout is read the next time Maestro is started. You can also save the layout by choosing Window → Save Layout.
Write a log of commands used in the Maestro session to the log file specified in the text box. The log file is written to Maestro's working directory. This information can be useful to Schrödinger support staff when responding to any problem you report.
These options affect the behavior of Maestro when projects are opened or closed.
Select options for Maestro actions related to opening projects.
Store the name and location of the last project opened in Maestro, and reload it when you restart Maestro.
Open the Project Table panel when you open a project.
Open the Entry List panel when you open a project.
Select options for Maestro actions when closing a project.
When closing a scratch project, show the Save Scratch Project dialog box, which gives you the choice of saving the project with a name, discarding it, or canceling the operation that closes the project. This dialog box is shown if you explicitly close the project (Project → Close), or open another project or quit Maestro with a scratch project open.
When closing a project, turn off the setting to reapply the Workspace Style when the Workspace changes (the Reapply button on the Style toolbar).
These settings can be used to make a daily automatic backup of the project that is open in your Maestro session, to control the number of backups (either automatic or manual), and to receive notification of the status of a backup. For more information on project backups, see Backing Up and Restoring Projects.
Select this option to request an automatic daily backup of the current project. The following options can be set for the backup:
Schedule the backup for the specified hour (on a 24-hour clock).
Choose an option for checking on the success of the backup. The options are:
Select this option if you want email notification with details of the backup. If you select this option, you must fill in the information or make choices for the following settings:
Full name of the SMTP mail server used to send email notification.
Port to use for the SMTP mail server.
Type of security to use for email. Choose from None, STARTTLS, or SSL/TLS.
Full email address of the user account from which email notification is sent.
If sending email requires a password, specify it in this text box.
Note: The password is not encrypted. If this is a concern, you
should choose an account that does not require a password to log on to the mail
server, and choose None from Security option menu.
Full email address of the user account to which email notification is sent.
Select this option to limit the number of backups.
Specify the maximum number of backups to save. This option is only available if you choose to limit the number of backups. When the number of backups exceeds this limit, the oldest backup is removed. This means that you must have space for one more backup than the number set, as the new backup is written before the oldest backup is removed.
Select an option for when to display a notification dialog box when a backup finishes. The choices are Never, Only when an error occurs, and Always.
Specify an alternate location for backups, by clicking Browse and navigating to the desired location. The location is shown in the text box when you click Choose in the directory selector that opens. When you first set an alternate backup location, the Alternate backup location option under Store new backups in is automatically selected, so that the new backup location is used.
Specify where to store new backups. You can choose from Same directory as project (the default), or Alternate backup location, to use the location you specified.
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.
These settings control how structures are imported. Some of them are duplicated in the Import panel.
If the structure file has other data associated with it, such as volume
data for surfaces, the data can be imported into the project and associated with
the relevant entries, by selecting this option. The mapping of the data to the
entries is done in a file with the suffix .smap. This option is
selected by default.
When importing from a .cms file, import only the first structure. There is no need in this case to use the Start and Total text boxes.
Select this option to read alternate locations from a PDB file. If deselected, the coordinates for the atoms with the highest occupancy are read, and the rest are ignored. You can display alternate locations from the Workspace menu.
After importing a structure from a PDB file, open the Protein Preparation Wizard panel, so that the protein can be prepared for other applications.
When importing a PDB file, color the structure by the status of the conversion. See Color-Based Error Reporting Scheme in the PDB Conversion and Converters topic for information.
When a pose viewer file (_pv.mae[gz]) is imported, perform
the setup in the Project Table for viewing poses. See Viewing Poses for more information.
Specify the property to be used as the title in Maestro:
Select this option to clear the Workspace before opening the new file, and display in the Workspace the structures specified with the Include in Workspace option menu. If this option is not selected, the new structures are added to the current project and the Workspace remains as it is.
Select this option to fit the structures that are displayed in the Workspace on import to the Workspace size. This option is enabled by default, because structures might not be centered around the coordinate origin, and therefore would not be visible in the Workspace until a fit to the Workspace was performed.
This option menu allows you to include in the Workspace the first imported structure, all imported structures, or none of the imported structures. By default only the first imported structure is displayed.
When you import structures, they can be added to the Project Table as entry groups. This option menu allows you to create a group for each file with multiple structures (the default) or for all files, to create a single group for all files, or to import structures without placing them in an entry group (None option). This choice applies whether you are importing from a single file or from multiple files. If you choose to create a single group for all imported files, you can provide a name in the Group name text box.
Select this option if you want to map properties in an imported SD file to existing properties in the project other than SD properties. You can also choose whether to modify the mapping each time you import an SD file (Always) or not to use a mapping (Never). If you choose to modify the mapping, the Map Properties dialog box opens on import. Choosing Never is the same as deselecting the main option.
This group contains settings for the project table itself.
These settings control the display of properties in the Project Table and the general display of the table.
These options mainly determine what is shown in the table.
These options control which new properties are shown in the Project Table when new entries are added.
These options determine how numeric and textual values are justified in the table cells. The options for each type of data are Left, Center, and Right. By default, numeric values are right-justified, which is generally equivalent to aligning numbers on the decimal point, because real properties are generally displayed with a fixed number of decimal places. Text is aligned left by default.
These options affect the order in which sorting is done when the property used to sort the table is a string. This preference applies to other tables and lists in Maestro as well as the Project Table.
Alphanumerically—Sort strings with
upper-case letters before lower-case letters and lower-case letters before
numbers. A sequence of digits is treated as a single number for the purpose of
the sort. This allows a sequence of strings that have increasing values of the
numerical part to be sorted in ascending numerical sequence, while the rest is
treated as a string. For example, if the sequence of strings was
ligandn, where n ran from 1 to 100,
ligand10 would follow ligand9, and
ligand100 would follow ligand99. In ordinary string
sorting, ligand10 would follow ligand1,
and ligand100 would follow ligand10.
Alphabetically—Sort strings in case-insensitive alphabetic order, with numbers preceding letters ("dictionary order"). No special treatment is given to sequences of digits.
When the pointer pauses in the Row column, show the structure as a 2D image in a tooltip.
Specify the default number of decimal places to be displayed for real-valued properties. This value is applied as the default value when new properties are created, whether manually or when importing from a file or a spreadsheet.
You can change the number of decimal places for properties in the Set Decimal Places dialog box, which you open by choosing Property → Columns → Decimal Places in the Project Table panel. In this dialog box you can also choose to use E notation (e.g. 1.0e-02) for properties.
Add padding of the specified number of pixels to either side of the column when using the commands that fit the columns to the data (Table → Columns → Fit to Data).
These two options determine the location of the vertical scroll bar. It can be placed on the left of the table or on the right.
These settings control the colors used in the Project Table. Each of the color settings show the color and have an edit button to change the color. Some of the colors are optional, others are always applied. The optional colors are only applied in place of the default color.
Set the color for unselected rows.
Set the color used for selected entries (rows), both inside and outside entry groups.
Set the color used for the group row when some but not all of its entries are selected.
Set the color used for the group row when all of its entries are selected.
Set the color used for the standard (default) columns in the fixed area. This color is only applied if the option is selected.
Set the color used for the nonstandard columns in the fixed area (columns that you move to the fixed area). This color is only applied if the option is selected.
Set the color used for the row number column (Row). This color is only applied if the option is selected.
Set the color used for the column heading row (Row). This color is only applied if the option is selected.
Use different shades of the colors for odd and even rows in the table.
Draw a horizontal line at the bottom of each row to mark the boundary between rows.
These buttons reset the colors. Default sets the colors to the default values. Classic sets the colors to those used in Suite 2011 (Maestro 9.2) and earlier.
These settings control behavior related to entry groups. There is only one setting, Warn when deleting entry groups, which posts a warning dialog box when an empty group is about to be deleted. The default is not to post the warning.
These settings affect the appearance and behavior of picking actions in the Workspace (click or right-click).
Select this option to make the system beep for each successful pick in the Workspace.
Choose a small, medium, or large picking cursor. The sizes are in pixels
Select this option to display a shortcut (context-sensitive) menu when you right-click in the Workspace. You can set the time-delay for displaying this menu by entering a value in the Delay before showing menu text box.
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.
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.
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.
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.
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.
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.
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 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.
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.
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.
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 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.
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.
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.
These options affect the adjustment of the clipping planes (the planes between which objects are displayed, and outside of which objects are hidden).
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.
Select this option to adjust the clipping at the same time as zooming in or out. The image in in the clipping planes window 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.
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:
The font size is also changed by the Increase Fonts and Decrease Fonts buttons on the Labels toolbar.
These settings affect what happens when fitting to the Workspace is done.
These options control when an automatic fit to the Workspace is performed. The fitting only applies when you include entries in the Workspace: it does not apply to entry exclusion or to the results of job incorporation.
Select an option for the atoms that should be fitted to the Workspace when an automatic fit is done, from All atoms or Ligands. If you have multiple ligands, all ligands are included in the fitting procedure. The fitting itself is done to the displayed atoms of the selected target, and does not include undisplayed atoms.
Select this option to adjust the clipping at the same time as zooming in or out. The image in in the clipping planes window 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.
Fit the structure to the Workspace after each fragment addition in Grow mode. If this option is deselected, no change of zoom is made when growing, and an addition can place the grow bound outside the display area, so that it is no longer visible. You then have to translate the molecule to see the grow bond.
Enhance the fogging depth cues when fitting to the Workspace.
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.
Select this option to adjust the clipping at the same time as zooming in or out. The image in in the clipping planes window 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.
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 options control the enhancement of the depth view using approximate ambient occlusion, which takes into account the ambient lighting blocked by nearby atoms. It is applied only to atoms in the CPK representation. For a similar effect with ambient occlusion applied to the whole Workspace, use the Ambient occlusion option in the Effects tab of the Appearance panel.
Turn on or off the enhancement of depth viewing.
Use this slider to change the amount of depth enhancement applied.
Adjust the grid size for the ambient occlusion calculations. A larger grid includes more atoms, which is desirable when there are large pockets in a protein structure, for example. However, this also makes the calculation slower.
Restore the default values for the depth factor and cutoff.
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 Project → Save Workspace Changes.
These settings control the display of markers for periodic structures in the Workspace.
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.
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.
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.
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, 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.
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 tab of the Appearance panel for the smoothest result.
These settings control the quality of the molecular representation. The settings depend on the requested OpenGL level.
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.
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.
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).
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).
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 the default values for OpenGL level and quality.
These settings control how sequences are displayed. They are also available on the Sequence viewer shortcut menu.
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.
Show the secondary structure assignment for the sequence.
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 in the sequence viewer. Three lines are used, for ligands, waters, and ions.
Set the distance cutoff for the sequence viewer proximity color scheme.
When displaying residues within a given distance of the currently displayed atoms, select this option to display nonpolar hydrogens. By default only polar hydrogens are displayed.
These settings control the atom information that is shown in the status bar when you pause the pointer over an atom.
Display selected properties in the status bar when the pointer is over an atom in the Workspace: number of atoms, entries, residues, chains, molecules, and formal charge, followed by a user-selected atom-level property.
When picking in the Workspace, show the index of the object that is being
picked (atom, molecule, ...) as the first item in the Status Bar, in the format
Pick: index.
This noneditable text box shows the property that is displayed. To choose the property, click Select to open a property selector. This is the last property in the atom feedback. The default for this property is the entry title.
Click this button to save the settings in this panel as preferences that apply to all projects. The default is that the settings apply only to the current project.
These settings control the properties that are displayed in the Workspace for a target entry.
Display project properties for a single entry, termed the "target" entry, in the top left corner of the Workspace. The target entry is the entry defined by the following conditions:
If none of these conditions is met, there is no target entry, and no feedback is displayed. The symbol in the In column of the Project Table is red for the target entry.
Select this option to include the names of the properties along with the property value, in the form name:value.
Choose a combination of font, size, and weight for the text shown in the Workspace from the option menus. The available fonts are those installed on your system.
Set the color for the text shown in the Workspace by clicking on the button and choosing a color. The button displays the current color.
List of properties to display in the Workspace for the target entry. You can select properties in the list to delete with the Delete button. To add properties to the list, click Add and select the properties in the property selector dialog box that opens. The default properties displayed are the entry title and the PDB ID.
Click this button to save the list of properties as preferences that apply to all projects. By default, the property selection applies only to the current project.
The option in this tab, Show job status feedback in Workspace, shows the status of the last job submitted from the current project in the top left corner of the Workspace, in the format jobname:status
These settings control the appearance and placement of atom and bond labels.
Choose a combination of font, size, and weight for labels from the option menus. The available fonts are those installed on your system. Only four styles are supported: Normal, Bold, Italic, and Bold Italic. The font size is also changed by the Increase Fonts and Decrease Fonts buttons on the Labels toolbar.
Enter a single character for the separator between properties of labels. Default is a space.
Select this option to include the name of the property in the label,
separated from the value by an equals sign. For example, atom number is
displayed as:
anum=3
Select this option to display one-letter residue names. Only the common (naturally occurring) residues have one-letter names; the rest are labeled "X".
When displaying element labels, use the isotope symbols for hydrogen (H, D, T). This option is on by default.
Specify the horizontal distance from the atom or bond midpoint to the left edge of the label.
Specify the vertical distance from the atom or bond midpoint to the bottom of the label.
Select this option to display labels even when the atoms themselves are hidden. If this option is deselected, bond labels are hidden if one of the atoms in the bond is hidden.
Select an option for the color of the atom labels:
Color bonds with the displayed color. Click the color square to display a color palette, then select the color, or click Advanced to open the Choose Color dialog box in which you can choose from a wider range of colors.
This group of settings controls the display of measurements in the Workspace.
These settings control how many decimal places are displayed for measurements of distances, angles, and dihedrals.
These settings control the font and border used to display measurements.
Choose a font, a point size, and make the font bold or italic (or both). The font size is also changed by the Increase Fonts and Decrease Fonts buttons on the Labels toolbar.
Select this option to draw a border around the measurement text in the background color. The default is to use a transparent background (no border).
These settings control the color of the measurement markers. The color buttons open a color selector, which you can use to select a new color for the marker type.
Set the width of the lines drawn to represent measurements, in pixels.
This group of settings controls the display of non-bonded interactions in the Workspace: hydrogen bonds, halogen bonds, contacts, and pi interactions.
These settings are used to set the criteria for defining hydrogen bonds, halogen bonds, and contacts.
These settings control the cutoffs that define a hydrogen-bond (H-bond). Hydrogen bonds are defined by relations between four atoms: the donor hydrogen atom (H), the donor atom (D) bonded to H, the acceptor atom (A), and another neighbor atom (B) bonded to A, D–H...A–B. The following must be true for a valid hydrogen bond:
The default values used by Glide and those used in Maestro are different.
Specify the maximum distance from the H atom to the acceptor atom for an H-bond to be identified. The Maestro default is 2.8Å; the Glide default is 2.5Å.
Specify the minimum D–H...A angle for an H-bond to be identified. The Maestro default is 120°; the Glide default is 90°.
Specify the minimum H...A–B angle for an H-bond to be identified. The Maestro default is 90°; the Glide default is 60°.
Click Glide or Maestro to set the defaults for the three criteria to those for Glide or Maestro.
These settings control the cutoffs that define a halogen bond. Halogens can act as donors or acceptors. As an acceptor it interacts with a hydrogen, so it is like a hydrogen bond but with its own characteristics. As a donor it interacts with an electronegative element in a similar way to hydrogen, but again with some differences.
Halogen bonds in which the halogen acts as donor are defined in a similar way to hydrogen bonds, by relations between four atoms: the donor halogen atom (X), the donor atom (D) bonded to it, the acceptor atom (A), and another neighbor atom (B) bonded to A, represented as D–X...A–B. The following must be true for a valid donor halogen bond:
Halogen acceptor bonds likewise have relations between the donor H atom (H) and the atom bonded to it (D), the halogen acceptor (X) and the atom bonded to it (B), D–H...X–A. The following must be true for a valid acceptor halogen bond:
Specify the maximum distance from the halogen atom to the other atom for a halogen bond to be identified. This value is independent of whether the halogen atom acts as an acceptor or a donor.
Specify the minimum D-X...A angle or D-H...X angle for a halogen bond to be identified. This angle can be set independently for halogens as donors and halogens as acceptors.
Specify the minimum X...A–B or H...X–A angle for a halogen bond to be identified. This angle can be set independently for halogens as donors and halogens as acceptors.
Specify the maximum H...X–A angle for a halogen bond to be identified when the halogen acts as an acceptor.
These settings define the distance ratios for contacts and allow the exclusion of certain types of contacts from consideration as contacts.
Contacts are classified into three types: good, bad, and ugly. The criteria are based on the following formula:
C = D12 / ( R1 + R2)
where D12 is the distance between atomic centers 1 and 2, and R1 and R2 are the van der Waals radii of atomic centers 1 and 2. C must be monotonically increasing for each of the contact types, that is C(ugly) < C(bad) < C(good). The default values are:
good 1.30 bad 0.89 ugly 0.75
A contact is considered to belong to a particular type if the value of C is less than the cutoff value (but greater than any smaller cutoff value). Any distance ratio larger than the Good cutoff is not considered a contact.
Specify the ratio C that define Good, Bad, and Ugly contacts.
These options control whether certain atom pairs are considered to be in contact or not.
H-bonds—Do not consider the hydrogen and the acceptor atom in a hydrogen bond to be in contact. This option is on by default.
1,4 interactions—Do not consider pairs of atoms that are conected by a sequence of 3 bonds to be in contact. Intra-ring contacts are always excluded. This option is off by default.
These settings control the color and line width of the non-bonded interaction markers, whether any interactions are displayed while adjusting or transforming structures, and if so, which interactions are displayed.
These buttons opens a color selector, in which you can choose a color for the markers. There is one button for each marker type.
Set the width of the lines drawn to represent the markers, in pixels.
Select this option to display selected interactions while adjusting structures or transforming structures. The interactions are updated dynamically as you perform the adjustment or transformation. The interactions to display can be selected from the options given below this option.
This group of settings controls the display of surfaces in the Workspace.
These options set the default appearance for new surfaces, which includes surfaces created directly in Maestro, and surfaces created on import of volume data into Maestro that have no information on appearance settings.
Set the default transparency of the front surface and the back surface.
Link the Front surface and Back surface sliders, so that they are both adjusted together, and are set to the same value.
Choose between Solid, Mesh, and Dot for the default surface style. Only Solid is affected by the value of Transparency. Mesh and Dot are always drawn fully opaque. The default style is not applied to surfaces that have a predefined style (such as PrimeX and SiteMap).
Set the default colors for surfaces from the standard Maestro color set from these option menus. Standard surfaces have only one sign for their volume data. Paired surfaces are those whose volumes have both positive and negative values, such as molecular orbitals. The remaining surface types are for representation of electron density maps in PrimeX.
Darken the shade of the color used for a surface by its depth relative to a smooth surface. This preference applies to newly created surfaces, and can be overridden by an option in the Surface Display Options dialog box.
Specify the intensity of the darkening effect, on a scale from 0.0 to 1.0, where 1.0 applies the full effect, and 0.0 is equivalent to turning off the effect. Setting this value is useful when the cavities are deep.
Open the Manage Surfaces panel when surfaces are created.
These settings control the appearance or behavior of all surfaces or surfaces of a particular type. The Global contour settings section and the Angle-dependent transparency option are only present when the OpenGL level is 2.1 (see Graphics settings), as this level is required for the rendering.
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 Manage Surfaces panel.
When zooming in and out, selecting this option allows the width of the lines in the mesh representation to be scaled appropriately. The Min and Max text boxes provide the means to specify the minimum and maximum scaling factor that should be used for the mesh. The scaling factor is applied to the mesh width set with the Mesh width slider.
Set the width in pixels of the lines in the mesh representation of the surface. Scaling of the mesh width is applied to this value.
Vary the transparency of transparent surfaces according to the surface normal, from maximum transparency when the surface normal is perpendicular to the screen, to opaque when the surface normal is parallel to the screen. The maximum is affected by the transparency slider in the Surface Display Options dialog box.
Draw depth-enhancing contours on the edges of surfaces and when an edge is in front of another part of the surface by more than a defined distance.
Set the thickness of the contour (in angstroms).
Set the minimum distance that an edge of the surface must be in front of other parts of the surface for the contour to be drawn.
Set the color of the contour, by clicking the Edit button, and the intensity of the contour color with the Intensity slider and text box. The intensity is the fraction of the contour color that is mixed with the surface color when drawing the contour.
These settings determine how surfaces are rendered when they are rotated, which affects the performance of the operation, usually at the expense of quality.
These three options (Solid, Mesh, Dot) control how surfaces are drawn while they are being rotated. Choosing mesh or dot surfaces may result in quicker rotation.
These three options (When rotating, Always, Never) allow you to choose when low-quality transparency is used for display of surfaces. Low-quality transparency speeds up the redisplay of surfaces after rotation, at the expense of surface display quality.
These three options (When in interlaced stereo, Always, Never) allow you to choose when to use a random pattern for low-quality transparency. The regular pattern does not produce good results for interlaced stereo. This option is primarily intended for use with interlaced stereo to improve the appearance of transparent surfaces.
The settings in this group control various aspects of the generation of 2D structures, which are displayed in a number of places.
Display the 2D structure only for molecules that have no more than the specified number of atoms.
Scale down images by at least this amount, relative to the size of the cell or display area. This cutoff can be used to prevent small molecules from appearing on a much larger scale than large molecules. Set this factor to 1 to fit the image into the cell.
Point size of the font used for the atom labels in the generation of the image.
Margin around atom labels, in pixels.
Width of bond lines in pixels for image generation.
Width of wedge bonds in pixels for image generation.
Space between bond lines for multiple bonds in pixels for image generation.
Color the atoms by element in the 2D images.
Show all hydrogens, rather than leaving them implicit. Nonpolar hydrogens are always displayed.
Display a C for each carbon atom, rather than leaving them implicit.
These settings define what is classed as a ligand in Maestro; in particular
they define the ligand ASL expression.
In this section you can specify criteria for detecting ligand molecules.
Enter the minimum number of atoms that a valid ligand molecule can have in this text box. Default: 5.
Enter the maximum number of atoms that a valid ligand molecule can have in this text box. Default: 130.
Select this option to allow molecules that are small ions (less than 10 atoms) to be considered as ligands. This option is deselected by default.
Select this option to allow molecules that consist only of amino acids to be considered as ligands. This option is selected by default.
In this tab you can specify molecules that are not to be considered as ligands, by means of their residue code, which is usually 3 letters, but can be any length from 1 to 4 letters. The tab contains a table and tools to add and delete residues.
This column contains a checkbox for each residue. When the box is checked, the residue is excluded from consideration as a ligand. By default all residues are excluded.
This column lists the residue code for various common residues, such as cofactors and ions. The column is noneditable.
This column lists a description for each residue. The column is noneditable.
In this text box, enter the residue code of a residue that you want to add to the table.
Click this button to add the residue entered in the Residue to add text box to the table. An error is posted if the residue name is more than 4 characters long.
Click this button to delete the selected residues from the table.
In this tab you can specify residues that may validly be part of a ligand. Molecules that contain any of the listed residues are considered ligands. The residue codes are usually 3 letters, but can be any length from 1 to 4 letters. The tab contains a table and tools to add and delete residues. The table is empty by default.
This column contains a checkbox for each residue. When the box is checked, the residue is permitted to be part of a ligand.
This column lists the residue code for residues to be included as allowed in ligands. The code must correspond to a known residue code: there is no facility for defining custom residues.
This column lists a description for each residue. The column is noneditable.
In this text box, enter the residue code of a residue that you want to add to the table.
Click this button to add the residue entered in the Residue to add text box to the table. An error is posted if the residue name is more than 4 characters long.
Click this button to delete the selected residues from the table.
This button resets the settings to the defaults. It removes any residue codes added to the table and restores any default residue codes as well as redoing the settings.
These settings define actions that are taken when building structures.
This tab allows you to set preferences that control the inclusion of hydrogens, adjustment of bonds and zoom level in building operations, and several other related settings.
The use of united atom types can cause problems for users who do not want implicit hydrogen atoms in their structures, such as Jaguar users. United atom types with implicit hydrogens are assigned by default when hydrogens are deleted from heavy atoms. If this option is cleared, united atom types are never assigned when atoms and bonds are explicitly deleted, atoms are retyped, or structures are drawn freehand. Instead, the atom types remain unchanged, or explicit radical types are assigned if they are available. United atom types are used regardless of this option if a hydrogen treatment that requires united atom types is applied, or when reading in a structure file (such as a PDB file) that does not have explicit hydrogens present.
When atom types are changed, bond lengths are automatically adjusted to give a "reasonable" bond length. This behavior is undesirable if the geometry is already correct (such as from a crystal structure) and it is only necessary to change the atom types. Clearing this option prevents the adjustment of bond lengths.
The number of hydrogen atoms is adjusted by default to maintain a normal valence during formal charge, bond order, or retyping changes. This behavior is not always desirable, and can be prevented by clearing this option.
When deleting an atom, terminally attached atoms can be deleted or retained.If this option is selected, they are deleted. For example, if you delete the carbon atom of a methyl group, the hydrogen atoms attached to the methyl group are also deleted if this option is selected. If you delete the middle carbon atom in propane, the two hydrogens attached to this atom are deleted, but the carbon atoms are not because they are not terminal atoms.
Fit the structure to the Workspace after each fragment addition in Grow mode. If this option is deselected, no change of zoom is made when growing, and an addition can place the grow bound outside the display area, so that it is no longer visible. You then have to translate the molecule to see the grow bond.
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.
When determining which atoms are bonded together to form molecules, consider atoms that are joined by zero-order bonds to belong to the same molecule. This option is selected by default.
These settings determine which method is used for cleaning up the geometry, which you can do by pressing U or by choosing Edit → Build → Clean Up Geometry. There are two choices:
These settings can also be made from the Clean up button on the Build toolbar.
Freeze the atoms that are not selected in the Workspace when geometry cleanup is done with the built-in minimizer. By default, atoms within 5 Å of the selected atoms are restrained with a moderate restraint, and atoms within 5 Å of these atoms are restrained with a much tighter restraint, while the rest of the atoms are frozen. This option does not affect cleanup with the UFF minimizer.
In this group, you can set preferences for job monitoring, job names, structure checking, job incorporation, and retention of job files.
These settings affect how and where jobs are started.
Minimize the changes to the Workspace and the Project Table from job monitoring and incorporation. With this option selected, the Project Table selection is not changed on job incorporation, and the Workspace is only changed if job incorporation changes an entry that is displayed in the Workspace. Structure monitoring is turned off, but you can still display the Monitor panel and monitor job progress.
Proteins that have been prepared by the Protein Preparation Wizard from Suite 2012 on are marked with a Maestro property. When you start a job with a protein that does not have this property, a dialog box is posted to warn you that the protein does not appear to have been prepared. You can choose to continue and mark the protein as prepared, or cancel the job. Proteins prepared with the Protein Preparation Wizard in releases prior to Suite 2012 do not have this property, and will be regarded as possibly unprepared.
To prevent the display of this dialog box, deselect this option. Proteins will then be accepted regardless of their preparation, but will not be marked as prepared.
Display a warning dialog box when a job is started or its files written with the same name as an existing job. If the job is run with the same name, the existing job files are overwritten. Deselect this option if you want to overwrite files from existing jobs without displaying a warning. If the existing job is still running, the files will not be overwritten, regardless of this setting, and a warning is displayed.
Allow Prime to use the BLAST web site to perform a BLAST search. This option allows you to run Prime Structure Prediction without having a local copy of the BLAST database. If your query structures are proprietary, you should not select this option.
When running jobs on a remote host, run the driver for that job on the
remote host as well. This option is useful if you are running on the Cloud, as
the driver must run on the remote host. Note that some jobs, such as Glide,
Prime MM-GBSA, and Induced Fit Docking, rely on the driver running locally and
using the local file system (-LOCAL) to ensure that jobs are
restartable. Running these jobs on the remote host will prevent restarting.
When the job is run, print debugging output. This option is useful when running jobs for analysis by Schrödinger technical support. It is not stored between Maestro sessions.
These settings control the display of monitoring information and its frequency.
Set options for monitoring behavior:
Start monitoring—Start monitoring jobs when they are submitted. If this option is disabled, jobs will not be monitored, but they will be incorporated if your preference for incorporation does not include monitoring (see under Incorporation settings).
Open Monitor panel—Open the Monitor panel when a job is started. This option does not apply to wizard-like workflows, where the job status button can be used to open the Monitor panel. By default, the Monitor panel is not opened when a job is started.
Update the job status and related information for unfinished jobs that are listed in the Monitor panel at the specified frequency. If you have chosen to incorporate jobs automatically or when approved, jobs that are not being monitored may be incorporated during the status update, if their status changes to "completed".
Set the interval at which the status of a monitored job is updated, by clicking one of the arrow buttons, or specifying a time interval in the text box. This is the frequency with which information on the monitored job is updated, not the frequency with which status information is updated in the Monitor panel.
Update the job status information shown on the Job toolbar for application panels and the Jobs button on the status bar in the Workspace at the specified frequency.
Show the job status as a button on the right end of the Workspace status bar. The button shows the number of active jobs in the project and the total number of active jobs. The tooltip for the button gives information on various job categories, listing up to three in each category. Clicking the button opens the Monitor panel. The frequency with which this status is updated can be specified in the Update every N seconds text box.
These settings control what happens to jobs and files when the jobs finish.
Set options for the incorporation of jobs that have finished and are ready for incorporation:
Only when monitored—Jobs are only incorporated when you monitor them in the Monitor panel.
When approved—You are prompted to incorporate a job when it finishes and is ready for incorporation. If you choose not to incorporate, you must monitor the job to incorporate it. If you subsequently select another option, you must restart Maestro for the option to take effect on jobs that you chose not to incorporate.
Automatically—Jobs that are ready for incorporation are incorporated automatically. Maestro is unavailable while the job incorporates. This is the default behavior.
A progress dialog box is displayed while jobs are incorporated, and you must wait until incorporation is complete before you can do anything in Maestro. Incorporation is only done for jobs from the current project. If you change projects, the option you select applies to the new project.
Set options for the retention of job files for products that involve a wizard-like workflow. By default, these files are deleted on incorporation of the results.
CombiGlide—Keep job files for the Combinatorial Screening workflow.
Phase—Keep job files for the Develop Pharmacophore Model workflow.
Prime—Keep job files for the Structure Prediction workflows (Comparative Modeling and Threading).
These settings affect the directories used when running jobs.
When you choose any of the options below, the current working directory is set to the specified location, and the option you select is stored as a preference. The current working directory is set to the specified location the next time you start Maestro.
Job files are written by default to the current working directory. File selectors display the contents of the current working directory when they are first opened in a Maestro session. Subsequently each file selector stores the last location you visted, and displays the files in that location when you open it again.
Thus, these options set the default by changing the current working directory immediately, on Maestro startup, and when a project is opened if the option is project-related.
If you change the current working directory explicitly after choosing one of these options, the new directory is used as the location for job files and the initial location for file selectors, rather than the choice you make from this set of options. For more information on changing the current working directory, see Changing the Working Directory.
In the descriptions below, the directory is called the default directory.
Note: If you choose an option for a directory that is inside the project, you should wait until any jobs launched from that project finish before you rename the project, or save the project if it is a scratch project.
Maestro's current working directory option—
Set the current directory to Maestro's initial working directory. When Maestro
starts, this directory on Linux is the directory from which Maestro was started;
on Windows and Mac it is the Schrodinger folder in your Documents
folder.
Parent of project directory—Set the
current working directory to the parent directory of the current project (the
directory that the project is in). Opening a different project or closing a
project (which opens a scratch project) sets the current working directory
again. For zipped projects, the parent directory is the directory that contains
the .prjzip file, rather than the temporary directory into which the
zipped project is extracted.
Jobs running with this setting are not lost if the project is renamed.
Project directory—Set the current working
directory to the top-level directory inside the current project. This is the
project-name.prj directory. This directory changes when a
new project is loaded, and the current working directory is reset to the new
project directory.
Jobs running in this directory will fail if the project is renamed. This includes saving scratch projects.
Project jobs directory—Set the current
working directory to the project's jobs subdirectory
(project-name.prj/jobs). This directory
changes when a new project is loaded or when a scratch project is opened, and
the current working directory is reset to the new jobs directory.
Jobs running in this directory will fail if the project is renamed. This includes saving scratch projects.
Other (specify below)—Use the specified directory as the current working directory. When using this option, you must enter the desired directory name in the Directory text box.
When a job finishes, create a zip file of the temporary directory that the job used to write files needed for the job (the job directory), and copy it back to the job launch directory. The zip file is not automatically unzipped. This option can be useful if you need to debug a job that fails, and keep the files, or to use the files for some other purpose. Normally, these files ("scratch files") are deleted and the directory is removed when the job finishes.
This option sends the -SAVE option to Job Control. It is not
saved across Maestro sessions, but it is initialized from the
SCHRODINGER_SAVE_JOBDIR environment variable.
When a job is run, use the launch directory as the temporary location to write files needed for the job, and leave the files in place when the job finishes. If the job launches subjobs, the subjobs might not use this directory for their working directory: the behavior depends on the application. If the subjobs do not write to the launch directory, you can set the Copy archived job directory to the launch directory when job finishes option to copy back the subjob temporary directories. Note that in this case, the files that are local already are not archived in a zip file.
This option sends the -LOCAL option to Job Control. It is not
saved across Maestro sessions.
These options control the default representation of atoms and bonds.
This option menu allows you to set the default representation to one of the five representations: Wire, Thin tube, Tube, Ball & Stick, or CPK. Selecting one of these choices from the menu sets the representation used for new atoms that are built or imported. If you import a file in Maestro format and it includes graphical information, the representation saved in the file is used rather than the defaults.
This option menu allows you to set a default color scheme for atoms and bonds. For some color schemes (which usually include the word Custom), a color option menu is displayed below the schemes option menu, so that you can choose the custom color. This option menu has a list of allowed colors. For a description of the standard color schemes, see Color Schemes.
The Wire representation has a range of options for the style, representation of bonds, and display of bond orders.
If you want the wire width to scale as you zoom in, select Scale wire width. You can adjust the minimum and maximum wire (line) width in the Min and Max text boxes. The values are given in pixels, and there are limits on how much you can change these values that are determined by the OpenGL implementation on your computer.
Set the width of wire in pixels.
The Style settings control how color is applied to bonds.
These options control when bond orders are displayed. Multiple bonds are displayed as multiple lines or multiple tubes, and zero-order bonds are displayed as dashed lines.
The Automatic option displays bond orders at high zoom, when the portion of the displayed structure that is visible in the Workspace is less than 20 Å across. If you zoom out, bond order display is turned off, and if you zoom in again, bond order display is turned on again when the display meets the criterion given.
These options request smoothing of the graphical display of the bonds. When Show bond orders is on, those bonds that are drawn with widths greater than one are not smoothed.
This section has a set of options for the display of bond orders, and sliders for setting the diameters of the tubes and spheres used in these three representations.
These options control when bond orders are displayed in Tube and Ball & Stick representations. The Automatically option displays bond orders at high zoom, when the portion of the displayed structure that is visible in the Workspace is less than 20 Å across. If you zoom out, bond order display is turned off, and if you zoom in again, bond order display is turned on again when the display meets the criterion given.
The Tube radius and Thin tube radius sliders set the radius of the tubes in angstroms.
The Ball percentage slider sets the percentage of the van der Waals radius of the atoms that is used to determine the size of the spheres. The Stick radius sets the radius of the sticks in angstroms.
The CPK percentage slider sets the percentage of the van der Waals radius of each atom that is used to determine the size of the spheres.
Restore the default values for the atom and bond representation.
These settings control the defaults for display of ribbons.
Set the quality of the ribbon rendering. The choice controls the smoothness of the ribbons.
Use a lower-quality ribbon representation when translating or rotating. You might want to set this preference if translation or rotation of structures is slow when ribbons are displayed, to improve the speed.
Select this option to create a smooth color transition on the ribbons between residues.
Select an option for coloring the interior of helices (and ladders). The two options are to use gray for the inside, or the same color as the outside, which is determined by the color scheme.
Set the width of ribbons in angstroms.
Set the thickness of ribbons in angstroms.
Set the width of strands in angstroms.
Set the thickness of strands in angstroms.
Set the width of thin tubes in angstroms. These tubes are used in Cartoon and Thin Tube representation.
Set the width of thick tubes in angstroms. These tubes are used in CA Trace Tube and Thick Tube representation.
Set the width of the rungs of the ladder for DNA and RNA. The sides of the ladder are controlled by the ribbon settings.
Select an option from this menu to determine which of the atoms that are associated with the ribbons are displayed or hidden when a ribbon is created. This option only affects the initial visibility; the normal atom display controls can be used to change the visibility of these atoms. The options are:
These options do not affect atoms that are not associated with the ribbons, such as ligands, cofactors, and water molecules.
Restore the default values for ribbon representation.
This group of settings controls the generation of SMARTS patterns from selected atoms. There is one set of options, for including notational elements in the SMARTS pattern:
Include the formal charge on an atom in the SMARTS pattern.
Include the number of substitutents that are attached to each atom in the SMARTS pattern.
Examples of the notation with the option selected are given next to the label.
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