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Command: marker

The marker command adds or modifies markers and links, nonatomic representations used for marking and measurement that are generally handled in the same ways as atoms and bonds. It is the command implementation of the Marker Placement tool and associated mouse modes with icons in the Markers tab of the Toolbar

See also: hkcage, define centroid, measure center, the tape measure mouse mode

Creating Markers and Links
Changing Markers and Links

Example commands:

marker #2 position 16.06,-9.172,116.5 color yellow radius 1
marker change #2:3 position 2.021,-29.09,121 color blue radius 2
marker link #2:1,2
marker segment #2 10.75,4.667,116.5 to 12.79,-17.44,111.2 color yellow radius 1
mark delete #2 linksOnly true
marker delete #2:3

Creating Markers and Links

Usage: marker  marker-model  position  point-spec  [ radius  r ] [ color  color-spec ] [ coordinateSystem  model-spec ]
Usage: marker link  markersradius  r ] [ color  color-spec ]
Usage: marker segment  marker-model  position  point-spec1  toPosition  point-spec2  [ coordinateSystem  model-spec ] [ radius  r ] [ color  color-spec ] [ label  label-text ] [ labelHeight  h ] [ labelColor  color-spec | default ]
Usage: marker connected  surface-spec  [ radius  radius ] [ color  color-spec ] [ markers  marker-model ]
Usage: marker fromMesh  surface-spec  [ edgeRadius  stick-radius ] [ color  color-spec ] [ markers  marker-model ]

The marker command creates a new marker. The marker-model and point-spec arguments are required. The marker can be added to an existing marker model or added as a new model, and each marker has its own residue number, assigned starting with 1. The resulting model ID and residue numbers can be used to specify markers and their associated links in commands (analogous to atoms and their associated bonds), such as to change or delete them with the marker command. Links can be specified by their endpoint markers or directly by selection and the word sel. Model numbers are shown in the Model Panel, and residue numbers in the identifiers that pop up when the cursor is paused over an item in the main window.

A point-spec can be given as x,y,z (three values separated by commas only), an atom-spec, or any of the other standard point specifications; x,y,z values are interpreted in scene coordinates unless a different coordinateSystem (reference model number) is given.

The marker link command adds a link between the two specified markers. For both markers and links, the default radius is 0.5 Å and the default color is yellow

The marker segment command creates two markers and a link between them, optionally labeled with the specified label-text. The default labelHeight is 1.0 Å and the default labelColor is default (meaning white or black depending on the window background color). See also: label

The marker connected command adds a marker at the center of each connected piece (blob) of the specified surface(s). Parts of the surface hidden with surface dust, surface zone, or volume zone are not marked and are not used to determine connectivity. When the command is used on volume series surfaces, the markers are assigned a frame attribute with value indicating the associated time step within the series. This allows synchronization during playback with vseries play. The markers option allows adding the new markers and links to an existing marker model. See also: measure blob

The marker fromMesh command creates markers and links (shown as sticks) from a surface mesh, which can only be shown as lines. The edgeRadius option sets stick radius (default 1.0 in physical distance units). In this case, the color default is the same as the surface model, where each marker gets the corresponding vertex color and each link (stick) is assigned the average color of its two endpoints. See also: hkcage, shape, volume

Changing Markers and Links

Usage: marker change  marker-spec  [ position  point-spec ] [ coordinateSystem  model-spec ] [ radius  r ] [ color  color-spec ] [ markers  true | false ] [ links  true | false ]

The marker change command changes the specified marker(s) and their associated links. The position option applies to markers only. The color and radius settings apply to both markers and links unless one or the other is excluded with markers false or links false. Markers and links can also be adjusted in the Marker Placement tool, with size and color commands, or with the mouse .


Usage: marker delete  marker-spec  [ linksOnly  true | false ]

The marker delete command removes the specified marker(s) and their associated links, or just the links if linksOnly true is used. Alternatively, individual markers can be deleted with the mouse and marker models can be closed with the close command.

UCSF Resource for Biocomputing, Visualization, and Informatics / November 2021