Markers and Links

• A marker is a pseudoatom, typically used to mark the position of some feature within volume data; markers are implemented as atoms, so actions that apply to atoms in ChimeraX also apply to markers: they can be specified in commands, selected, etc.
• A link is a connection between markers, analogous to a bond.
• A marker set is a model that consists of markers and links, analogous to an atomic model.

Markers and links can be created and adjusted with the mouse (see Marker Placement) or the marker command. Markers placed on volume series data are assigned a frame attribute with value indicating the associated time step within the series. Various other commands such as bumps, measure center, define centroid, and vseries measure may also create them to show the results of calculations.

Markers and links can be saved to and read from marker files. Markers and links are shown in the ball style when initially created with Marker Placement and when read from a marker file. They can also be saved to atomic-coordinate file types such as PDB, but may not be interpretable as molecules upon input (to any program). See also: MOLEonline channels, pseudobonds

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Marker Files

Marker file format (.cmm) is the same in ChimeraX as in Chimera. It includes marker set name(s), marker positions, marker notes, links, colors, and radii. However, ChimeraX does not save labels on markers as marker notes, and marker notes are not shown as labels when read from a file. Marker files can be opened and saved using the File menu or the commands open and save, respectively.

The format is actually XML, plain text that can be read or created by other programs or “manually” in a text editor. Libraries for parsing XML are available in many programming languages. The following marker file describes two markers connected by a link:

<marker_set name="marker set 1">
<marker id="1" x="-6.1267" y="17.44" z="-3.1338"  radius="0.35217"/>
<marker id="2" x="1.5395" y="16.277" z="-3.0339" r="0" g="1" b="1"
               radius="0.5" note="An example note"/>
<link id1="2" id2="1" r="1" g="1" b="0" radius="0.17609"/>
</marker_set>

The r, g, and b attributes are red, green, and blue color components, respectively, with possible values ranging from 0 to 1.

Extra XML attributes can be specified within the marker, link, and marker_set tags, as a mechanism for retaining information from or passing information to other programs. For example, the following marker description includes nr, ng, nb, and frame attributes:

<marker id="3" x="195.43" y="166.62" z="174.03" r="1" g="1" b="0" radius="5"
 note="cap domain" nr="1" ng="1" nb="0" frame="5"/>

The frame attribute is used for markers on volume series; it gives the associated time step for synchronized playback with vseries play. Whereas frame and radius are assigned as atom attributes and notes are currently ignored, the remaining XML attributes are not assigned as atom attributes but kept in a Python dictionary called marker_extra_attributes. These extra attributes are remembered in sessions and included when a marker file is saved.