Chimera Commands Index

mclip [ model-spec  options ]

~mclip [ model-spec ]

The mclip command controls per-model clipping. See the video mini-example. See also: surface, sop cap, volume, clip, movie-related commands

The model-spec can be a specific model number or range of model numbers (preceded by #), or simply # or the word all to indicate all models. Mclip without any arguments also clips all of the models. A more complicated model-spec can be used to clip a surface model but not the molecule model with which it shares a model number, for example:
mclip "#0 & ~ @"
The command ~mclip disables per-model clipping for the specified models, or if none are specified, all models.


Option keywords for mclip can be truncated to unique strings, and their case does not matter. Synonyms for true: True, 1. Synonyms for false: False, 0. A vertical bar “|” designates mutually exclusive options, and default settings are indicated with bold.

Initial defaults apply when per-model clipping is first turned on for a given model. Thereafter, a plane's last specified position and orientation are its defaults (even if the plane was subsequently turned off).

coords local | screen
Whether axis and origin coordinates should be interpreted in the local (input model coordinates) or screen (viewing) frame of reference. In the screen frame of reference, the x axis is horizontal in the plane of the screen, the y axis is vertical in the plane of the screen, and the z axis is normal to the screen. In the local frame of reference, the axes rotate along with the model.
axis x | y | z | x,y,z
Orient the clipping plane perpendicular to the specified axis or vector in the indicated frame of reference. Numerical coordinates x,y,z (separated by commas but not spaces) can be used to define a vector of any length pointing in any direction.
origin center | x,y,z
Place the clipping plane at the specified origin plus any offset and stagger along the axis. The origin can be set to the center of the model's bounding box (initial default) or specified with numerical coordinates x,y,z in the indicated frame of reference.
offset  distance
Offset the clipping plane along the axis by distance in physical units of length (default 0.0, can be positive or negative).
stagger  spacing
When clipping multiple models, locate the clipping plane for the lowest-ID model as specified by origin (or match) and offset, but additionally offset each successive model's plane by spacing in physical units of length (default 0.0, can be positive or negative). Staggering or otherwise offsetting the clipping planes of multiple surfaces avoids display of an irregular mosaic of colors where two or more surface caps coincide.
flip true | false
Whether to flip the plane 180° to hide the opposite part of the model.
match  plane
Position the clipping plane to match plane (overrides axis and origin):
slab true | false
Whether to show a slab of the model instead of all parts to one side of the clipping plane (initial default false). Slab width can be specified with thickness.
thickness  slabwidth
Set slab thickness to slabwidth in physical units of length (initial default 5.0).