ChimeraX Settings (Preferences)

The ChimeraX Settings dialog is listed in a standard platform-dependent location in the menu (for example, Favorites... Settings on Windows and Linux, UCSF ChimeraX... Preferences on a Mac) and contains sections:

Background
Clipping
Distances
Labels
Log
Startup
Toolshed
Trackpad
Web Access
Window

The buttons at the bottom of the dialog can apply to just the currently shown section or to all sections of the Preferences dialog (depending on the Buttons below...  option):

• Save – save the current settings
• Reset – replace the current settings with the initial (“factory”) defaults
• Restore – restore values that were saved previously
• Help – show documentation

Several other preferences do not appear in this dialog, but in separate interfaces.

ChimeraX preferences are stored as multiple files in a standard platform-dependent location:

• ~/Library/Application Support/ChimeraX/  on Mac
• ~/.local/share/ChimeraX/  on Linux
• C:\Users\<user-name>\AppData\Local\UCSF\ChimeraX\  on Windows

The location can be reported with command:

info path user unversioned config

Preferences files are named according to the modules to which they apply, and are not created until nondefault settings are saved.

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Background

• Background color – a color well that can be clicked to choose the color interactively (initial default ). See also: set bgColor

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Clipping

See also: clip, surface cap

• Cap clipped surfaces – whether to cap surfaces when they are sliced by clipping (initial default true)
• Cap mesh surfaces – if capping is on (the previous setting is true), whether to show caps for mesh surfaces (initial default false)
• Cap subdivision factor – fineness of triangulation (initial default 1.0), which affects appearance when the cap is multicolored, such as by map value or by zone. Higher values give finer triangulations, and the minimum value is 0.0.
• Mouse clipping enables – which type of clipping planes are enabled by the clip mouse mode
  • scene planes (initial default) – those which reorient with the scene (front/back)
  • screen planes – those which remain fixed parallel to the screen (near/far)

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Distances

Settings for distance-monitor pseudobonds are saved instantly (without clicking Save). The decimal-place and angstrom-symbol options also apply to H-bond pseudobonds when labeled by distance. See also: Distances, H-Bonds, mousemode, selection context menus

• Color – a color well that can be clicked to choose the color interactively (initial default )
• Decimal places – distance-label places after the decimal (initial default 3)
• Number of dashes (initial default 9)
• Radius (initial default 0.1 Å)
• Show angstrom symbol (Å) – whether to include the Å symbol in the distance label (initial default true)

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Labels

• 3D label height (Å) – for 3D labels, the default height in distance units (initial default 0.7); can also be set with the command label defaultHeight
• 3D model label height (Å)
• Balloon-help specifier style – format/type of identifying information shown by pausing the cursor over an object in the main window (see the identify object mouse mode)
  • command line – command-line specifier (for example, /B:21@OD1)
  • serial number – atom serial number (for example, 126)
  • simple (initial default) – chain ID (preceded by slash), residue name, residue number, atom name (for example, /B ASN 21 OD1)
  Model number will be included when multiple models are present. This setting is also the default style for atom logging by the H-Bonds tool and the hbonds and clashes/contacts commands (see their namingStyle options).
• Label missing-structure segments in models with ≤ N chains (initial default 4) – label missing-structure pseudobonds with the number of biopolymer residues that they represent, according to PDB SEQRES information or the mmCIF equivalent, depending on the number of chains in the atomic model (initial default 4 chains; 0 would indicate no missing-segment labels regardless of model size). The chain limit can be adjusted temporarily (without changing this preference) by using the label missing command.

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Log

The Log echoes commands and shows messages and other information. See also: log

• Errors shown in dialog (initial default true) – whether error messages in the Log should also generate a separate dialog window
• Raise log when logging occurs (initial default false) – whether to show the Log (bring to front if tabbed behind another panel, or reopen if closed) whenever some action or message adds to its contents
• Warnings shown in dialog (initial default false) – whether warning messages in the Log should also generate a separate dialog window
• Restoring session clears log (initial default true) – whether to clear the current contents from the Log before populating it with the contents from a session that is being restored

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Startup

• Custom presets folder – where to look for user-defined presets in the form of ChimeraX command files (.cxc) and/or Python files (.py). Although “presets” are generally intended to be display settings, in practice any ChimeraX commands could be used. The presets will be named by filename, excluding the format suffix. Those directly in the specified folder will be in category Custom, and those in first-level subfolders will be in categories named according to the folder names. Any underscores in file/folder names will be converted to spaces. Folders can be named to create new categories or to place custom presets in the already existing (built-in) categories. Presets can be applied by choosing them from the Presets menu or with the preset command. See also: alias

  For example, putting the command file kyte-doolittle_hydrophobicity.cxc into your custom presets folder will create menu item: Presets... Custom... Kyte-Doolittle Hydrophobicity, the ChimeraX version of the “hydrophobicity surface” Chimera preset. See also: coloring by residue type, setattr, color byattribute, mlp , attribute assignment examples, amino acid hydrophobicity

• Execute these commands at startup – ChimeraX commands to execute when the Command Line Interface is first started within a session. See also: alias, name, color name

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Toolshed

The Toolshed is the web repository of ChimeraX bundles. It can be shown from the menu (Tools... More Tools) or with the toolshed command. The command can also be used to list, install, or remove bundles, and to control how the toolshed manages bundle information.

• New version check interval – how often to check for a newer version of ChimeraX
  • every day
  • every week (initial default)
  • every month
  • never
• Toolshed update interval – how often to check the Toolshed for updates to installed bundles as well as for new features (commands, file formats) available from bundles that the user does not have installed. This connection occurs at startup but asynchronously, i.e., without slowing down the startup process or subsequent use of ChimeraX.
  • every day
  • every week (initial default)
  • every month
  • never

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Trackpad

• Trackpad gestures to rotate and move (initial default on) – whether to respond to trackpad multitouch gestures (currently Mac only): two-finger rotation, three-finger translation, pinch-zoom, and four-finger “scrolling” (for which the initial default is zooming, see mousemode). With this option on, Magic Mouse scrolling will not work properly after a trackpad has been used.

  Otherwise (Mac with this option off and on other platforms' multitouch trackpads), two-finger drag performs the “scrolling” action. Regardless of the multitouch setting, touchpad click-drag alone and with modifier keys perform the actions of left, middle and right mouse buttons (details...).

• Trackpad sensitivity – sensitivity to trackpad multitouch gestures; with a factor of 1.0 (initial default):
  • a 6-cm two-finger drag rotates 360°
  • a 6-cm three-finger drag translates across the full width of the graphics window
  Other actions scale accordingly:
  • sensitivity of two-finger twist (rotation around Z axis) is 6 times that of two-finger drag (XY rotation)
  • sensitivity of pinch-zoom or four-finger zoom (translation along Z axis) is 3 times that of three-finger drag (XY translation)

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Web Access

Proxy settings are needed to allow users at certain sites to fetch data over the web; these settings should be the same as for web browsers.

• HTTP proxy host [ hostname ] port [ number ] (initial default 80)
• HTTPS proxy host [ hostname ] port [ number ] (initial default 443)

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Window

• Default tool side – on which side of the main window to dock tool panels when they first appear (overridden for tools with previously saved positions):
  • left
  • right (initial default)
• Initial overall window size – startup size of the overall ChimeraX window (including any tools present at startup, not just the graphics window)
  • last used (initial default)
  • proportional – as a percentage of screen width and height
  • fixed – width and height in pixels
  • maximized – screen width and height (different from fullscreen in that the title bar is retained)
• Resize graphics window on session restore – whether to restore the graphics window size of a session along with its contents; if this option is off (initial default), the graphics window will not resize when a session is restored. This setting can be overridden with the open command resizeWindow option. See also: windowsize
• Tool windows start undocked – whether tools (other than those launched at startup) should open in the undocked and undockable state; initial default off

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Other Preferences

Some preferences do not appear in the main ChimeraX Settings dialog, but can be accessed through context menus, other dialogs, or commands. Examples include:

• Generic tool-interface preferences: autostart, panel dockability, etc. (see also ui)
• Tool-specific preferences:
  • Command History – whether to list typed commands only; number of commands to remember
  • Log – whether command links should be executable or show help
  • Sequence Viewer – several aspects of appearance and contents
  • Toolbar – Home tab customization
• Function key assignments

Some tools have settings that are “sticky,” automatically saved in the preferences and presented to the user upon later uses of that tool. Examples: H-Bonds, Modeller Comparative