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Command: crosslinks

crosslinks  pseudobond-spec  [ radius  r ] [ dashes  N ] [ color  color-spec ]

The crosslinks command acts on pseudobonds, such as crosslinks from integrative hybrid modeling (IHM). See also: pbond, clashes/contacts, hbonds, distance, interfaces, label

The top-level command sets pseudobond stick radius, number of dashes N, and/or color. Only whole numbers of dashes are accepted, with 0 indicating solid sticks. Currently, odd numbers are rounded down to give an even number of dashes.

The following subcommands perform plotting and other analyses:

Any pseudobond-spec can be used: model numbers of pseudobond models or the atomic models containing them, sel to indicate the current selection, hbonds, etc. For IHM data, it is typically the model number of a sphere model, in which spheres are pseudoatoms and the pseudobonds between them represent crosslinks or other restraints.

Histogram by Length

Usage: crosslinks histogram  pseudobond-spec  [ coordsets  model-spec ] [ bins  N ] [ minLength  X-start ] [ maxLength  X-end ] [ height  Y-max ]

A histogram of lengths can be shown for either a collection of pseudobonds within a given structure, or for a single pseudobond across the frames of a trajectory specified with the coordsets option. See also: coordset, select by pseudobond length, measurements

Crosslinks with lengths ranging from minLength X-min to maxLength X-max (set by default to include all observed lengths) are tabulated into the specified number of histogram bins N (default 50). The height setting allows truncating tall bars to prevent them from overwhelming the histogram, or conversely, to leave extra space above the tallest bar to give the same vertical scaling between multiple histograms for purposes of comparison (the default is to accommodate the counts observed, without truncation).

Passing the cursor over bars in a multiple-pseudobond histogram shows just the pseudobonds of the corresponding length, temporarily enlarged (thickened) by a factor of three. In a histogram for a single pseudobond across a trajectory, passing the cursor over a bar shows just the trajectory frame (coordinate set) in which the pseudobond has the corresponding length.

The histogram context menu includes:

Chain-Chain Network Diagram

Usage: crosslinks network  pseudobond-spec 

Chains crosslinked by the specified pseudobonds can be depicted in a 2D network diagram. In the diagram, nodes (circles) represent groups of atoms (chains in an atomic model or sets of spheres within a sphere model) and edges (lines) are drawn between nodes where the corresponding groups are crosslinked. Nodes are labeled with the number of intrachain pseudobonds, edges with the number of interchain pseudobonds. Node colors match the colors of the groups when the diagram is created. Clicking a node selects the corresponding atoms.

Various parts of the diagram have different context menus. The background context menu includes:

The node context menu also includes:

...whereas the edge context menu includes:

Minimize Inter-Model Crosslinks

Usage: crosslinks minimize  pseudobond-spec  [ moveModels  model-spec ] [ iterations  N ] [ frames  M ]

A simple optimization can be performed in which whole models are moved as rigid bodies to shorten inter-model pseudobonds. The minimized quantity is the sum of squares of the lengths. Models to move can be restricted with the moveModels keyword and are repositioned (in memory, not in the display) once per iteration, with multiple iterations (default 10) converging toward a minimum. In the display, movement from the initial position to the final position will occur over a total of N frames (default 1).

Intra-model crosslinks are not affected.

UCSF Resource for Biocomputing, Visualization, and Informatics / November 2023