/* ligand_sampling_boxes.mdl" */
/* Five transparent boxes are
created in which to sample free ACh and Ch concentration (book Fig. 4.6A). A box is simply a special case of a polygon
list object, with 6 quandrangular faces.
By definition, boxes are created with the front side of all 6 faces on
the outside of the box. Although it is
not illustrated here, effector sites can be added to box objects just as for
polygon mesh objects. In that case,
however, each selected box wall is automatically bisected to form 2 triangles,
each of which then is tiled using standard barycentric subdivision. If the box wall and resulting triangles are
long and thin, the effector tiles will also be long and thin, and visualization
of effector sites will show molecules in apparent linear arrays. If, on the other hand, triangles and
effector tiles are nearly equilateral, visualized effector sites will appear
realistically positioned in hexagonal arrays.
This is one factor to consider in choosing between a polygon list and a
box object if effector sites will be used (see Stiles et al., 2000, for further
details). */
sampling_box_1 BOX {
CORNERS = [ -0.05,-0.015,-0.015 ], [
-0.02,0.015,0.014 ] /* A box is initially defined simply by a "lower-left-front" vertex
and an "upper-right-back" vertex, and the corresponding "FRONT", "BACK",
"LEFT", "RIGHT", "TOP", and "BOTTOM" faces are filled in and lie parallel to
the xz, yz, and xy axis planes.
Thereafter, the box template may be scaled, translated, and rotated in
space to any arbitrary position, and one or more faces may be removed. */
FULLY_CLOSED = YES /* Would be set to NO if any
faces had been removed. Since the box
is fully closed, all diffusing molecules can be detected as they enter and
exit, and this allows enclosed molecules to be counted. */
TRANSPARENT {
LIGAND = ACh
ELEMENT = ALL_ELEMENTS
}
TRANSPARENT {
LIGAND = Ch
ELEMENT = ALL_ELEMENTS
}
}
sampling_box_2 BOX {
CORNERS = [ -0.015,-0.06,-0.06 ], [ 0.015,0.06,-0.029 ]
FULLY_CLOSED = YES
TRANSPARENT {
LIGAND = ACh
ELEMENT = ALL_ELEMENTS
}
TRANSPARENT {
LIGAND = Ch
ELEMENT = ALL_ELEMENTS
}
}
/* The contents of the 2 box
templates above are copied (multiple times) into one metaobject named
"all_sampling_boxes", which then is instantiated in the main mdl file
"rat_nmj.main.mdl". */
all_sampling_boxes OBJECT {
box_1 OBJECT sampling_box_1 { } /*
"sampling_box_1" above is copied as is, i.e., no geometric transformation is
applied. */
box_2 OBJECT sampling_box_1 {
TRANSLATE=[0.07,0,0] } /* "sampling_box_1" is copied again and then moved 0.07 microns in
the direction of the positive x axis to a new position. */
box_3 OBJECT sampling_box_1 {
TRANSLATE=[0.035,0.035,0] } /* copied and moved in the positive x and y directions. */
box_4 OBJECT sampling_box_1 {
TRANSLATE=[0.035,-0.035,0] } /* copied and moved in the positive x and negative y directions. */
box_5 OBJECT sampling_box_2 { } /*
"sampling_box_2" above is copied without geometric transformation. */
TRANSLATE=[0.0005,0,0.01032] /* A
final adjustment of position is applied to all five subobjects. */
}