The clip command controls clipping planes. Up to four planes can be active:
If given without arguments, clip acts like clip front 0. The command clip off or ~clip turns off all clipping planes, whereas clip list reports the locations of any active clipping planes. Whether planar caps should be shown for clipped surfaces can be controlled with a preference setting and/or the surface cap command. Clipping plane positions can be adjusted interactively with the mouse . See also: view, cofr, vr
Each plane can be activated or turned off individually; specifying an offset activates a plane if it was not already active. Offsets are in physical distance units (generally Å), with positive values increasing away from the viewer for the near/far planes. The offsets are relative to the position reference point, if given. Otherwise, offsets are relative to the current positions of the planes, or (if a plane is newly activated) the center of the bounding box of displayed models. The position of a plane is forgotten when it is turned off.
The position reference point can be given as x,y,z (three values separated by commas only), an atom-spec, or any of the other standard point specifications.
The axis option sets initial front/back plane orientation as perpendicular to x, y, z, or any of the other standard vector specifications. The default orientation is perpendicular to the line of sight (screen Z).
The screen coordinate system (X horizontal, Y vertical, Z in/out of screen) will be used to interpret position and axis coordinates unless a reference model is specified with the coordinateSystem option.
Usage: clip model model-spec [ on | off ]
The clip model command is used to turn off front/back clipping for specific models, allowing per-model clipping. It does not apply to near/far clipping. Boolean values (true or false) can be used as well as on and off.
For example, the protein in structure 1g74 has an oleic acid residue OLA in an interior pocket. The following commands show the protein surface, activate front clipping for all models, and then turn it off for the atomic model (#1) while leaving it in place for the molecular surface (#1.1):
clip front 0 position :ola
clip model #!1 false
hide ~:ola target ar
style :ola ball
If the cap on a clipped surface is shown, it may be useful to color it by attribute, map, or zone, perhaps with transparency. The Protein-Ligand Binding Sites tutorial includes an example of coloring a clipped surface by the MLP.