The crosslinks command acts on pseudobonds, such as crosslinks from integrative hybrid modeling (IHM). See also: clashes/contacts, hbonds, distance, label
The top-level command sets pseudobond stick radius, number of dashes N, and/or color, where colorname specifies a single 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.
Usage: crosslinks histogram pseudobond-spec [ coordsets model-spec ]
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
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.
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 node context menu includes:
The background context menu contains the layout option.
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.