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:

**crosslinks histogram**- plot as histogram by length**crosslinks network**- plot as chain network diagram**crosslinks minimize**- move models rigidly to minimize lengths

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:crosslinkshistogrampseudobond-spec[coordsetsmodel-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:crosslinksnetworkpseudobond-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

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

**Select [**- select the corresponding chain (same as simply clicking the node)*chain*]**Lay out to match structure**- redraw diagram with orientation similar to the current 3D structure (including repulsion to prevent node overlaps in the diagram)

The **background** context menu contains the layout option.

Usage:crosslinksminimizepseudobond-spec[moveModelsmodel-spec] [iterationsN] [framesM]

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 2017