draw 

Draws a theta-degree arc in a plane perpendicular to the line pt1--pt2 starting at nDegreesOffset degrees rotation from reference point {ptRef} at a point fractionalOffset from pt1 to pt2. The SCALE parameter is used to set the diameter of the overall circle containing the arc; the DIAMETER parameter sets the diameter of the curved arc line itself. ARROW ARC adds an arrow head.

As above, but uses the plane as a reference to define a perpendicular axis.

Draws a straight (two-point) or curve (more than two-point) arrow. The keyword BARB indicates "fish-hook" half-arrows as for organic chemistry mechanisms involving radicals.

Draws an ARROW based on an array of points.

The DRAW command can be used to draw organic "mechanistic arrows." You need to specify two atoms, two bonds, an atom and a bond, or a bond and an atom. Atoms are identified using the keyword ATOM followed by an atom expression; bonds are identified using the keyword BOND followed by two atom expressions. For example: draw ID "arrow1" ARROW ATOM @1 BOND @1 @2, which draws a curved arrow from atom 1 (atomno=1) to the middle of the bond connecting that atom to atom 2. These drawn objects are then "connected" to the atoms, so if the atoms are not displayed, the arrow is not displayed either. Of course, individual arrows can be hidden independently of their associated atoms as well.

Draws the best boundbox through a set of atoms. The atoms can be given as one or more atomsets.

Draws the best line through a set of atoms. The atoms can be given as one or more atomsets.

Draws the best plane through a set of atoms. The atoms can be given as one or more atomsets.

Draws the currently defined boundbox. Note that by default this is a solid. To show just edges, use options MESH NOFILL.

Draws the (approximately) best box around the selected set of atoms, not necessarily oriented by the x,y,z axes. Note that by default this is a solid. To show just edges, use options MESH NOFILL.

Draws a boundbox with edges in the x, y, and z directions through a set of atoms, which may be given as one or more atomsets.

Draws a boundbox around the specified isosurface

Draws the best boundbox around he specified isosurface

Draws a circle with center at pt1 (which may be an atom expression) in the plane perpendicular to the line between pt1 and pt2. If pt2 is not specified, the circle appears in 2D and remains in the plane of the screen when the model is manipulated. Together, the SCALE and DIAMETER parameters set the overall size of the circle. If no DIAMETER is given and an atom expression is given for pt1, the default diameter is one that includes those atoms; otherwise the default diameter is 1.0 Angstrom. The circle will be filled to form a solid disk unless the MESH NOFILL option is given.

Draws a circle around pt1 in the indicated plane.

Draws a smooth curve through the given positions.

Draws a curve based on the array of points.

Draw CYLINDER creates a cylinder of the designated diameter. End caps can be set to closed/flat (FILL, the default) or open (MESH NOFILL).

For lines or mesh option. Draws a simple line with 1-pixel width.

For lines or mesh option. Draws a dotted 1-pixel line with alternating n on, n off pixels.

Draws a frame (an x,y,z axis set) at the given center with the given quaternion orientation. Quaternions are expressed using the quaternion() function within a math @{...} wrapper. For example, draw ID "q1" frame {0 0 0} @{quaternion(1,0,1,0)} draws a frame at the origin that has been rotated 90 degrees relative to the Y axis. (Jmol automatically normalizes the quaternion to q0=0.70710677, q1=0, q2=0.70710677, q4=0, which represents a 90-degree rotation about the Y axis.)

Draws a vector representing the local helical axis for the selected amino acid or nucleic acid residue, connecting it to the previous residue in its chain. The length of the arrow is the vertical height per residue.

Offsets an HKL plane from the origin by x.x Angstroms.

Alternative to HKL {1 1 1 x.x}

Allows for a hover label that appears whether or not drawHover is on.

Used for saving the hover label in a state.

Draws the portion of a plane that intersects the current boundbox based on a plane expression.

Intersects all types of boundboxes and unitcells with any type of plane or line.

Projects a unitcell or boundbox on any plane.

Extends the specified line to intersect a unitcell or boundbox

Draws the portion of a plane that intersects the current unit cell based on a plane expression.

Draws a set of line segments through the points. See also DRAW VERTICES.

Shortcut for DRAW * OFF; DRAW *xxx* ON. Hides all but the designated DRAW objects.

Draws a set of lattice points that are on a given plane; mostly for debugging. xxx can be an array [o a b c] or absent; plane can be PLANE or HKL and appropriate parameters.

Creates a four-vertex quadrilateral even if only three points are given.

Calculates and draws point group symmetry planes and axes for a symmetrical or nearly symmetrical molecule. As for calculate pointgroup, the calculation is carried out only on the currently selected atoms and is limited to at most 100 selected atoms. Parameters include specification of a subset to draw (Cn, C2, C3, C4, C5, C6, C8, Sn, S3, S4, S5, S6, S8, S10, S12, Cs, Ci) optionally followed by an index (for example, draw POINTGROUP C3 2 draws the second C3 axis only). A second option, SCALE x, allows adjusting the scale of the drawn planes and axes. The default scale of 1 puts the edge of planes directly through the outermost atoms. This command automatically sets perspectiveMode OFF so as to properly represent the planes and axes.

Calculates and draws point group symmetry, optionally allowing only a subset of atoms to be used, for example ignoring hydrogens with {!_H}. Also optionally allows the center to be set to a specific coordinate or atom.

Calculates and draws point group symmetry planes and axes for a polyhedron. One atom (one polyhedron) should be selected prior to this command.

Draws the crystal class symmetry operations for a space group

The POINTS option creates a set of points. For example, load $caffeine; draw POINTS [@5 @7 @12 @13 @1 @3].

This simple POLYGON option creates a polygon from a list of points. For example, load $caffeine; draw polygon [@5 @7 @12 @13 @1 @3].

This POLYGON option draws one polygon based on an array of integers (the "face") and an array of points that the indices of the face point to. The array of points is optional and defaults to {*}.xyz.all. For example,

  load $p4
  x = {*}.find("*1**1","map")
  draw ID p4r polygon @{x[1]} color red
  draw ID p4b polygon @{x[2]} color blue
  draw ID p4y polygon @{x[3]} color yellow
  draw ID p4g polygon @{x[4]} color green

This POLYGON option draws one or more polygons based on a set of vertices and a set of faces. This capability allows drawing any number of flat triangular (not quadrilateral, but read on...) faces with or without edges around each face. The description is somewhat like that for PMESH files and involves (a) giving the number of vertices, (b) listing those vertices, (c) giving the number of faces, and (d) listing the faces with a special array syntax. Each face is described as an array indicating the three (0-based) vertex indices followed by a number from 0 to 7 indicating which edges to show a border on when the mesh option is given:

0	no edge
1	edge between first and second vertex
2	edge between second and third vertex
4	edge between third and first vertex
3, 5, 6, 7	combinations of the above.

For example: draw POLYGON 4 {0 0 0} {1 1 1} {1 2 1} {0 5 0} 2 [0 1 2 6] [0 3 2 6] mesh nofill. The points and faces can be provided as arrays: draw POLYGON @points @faces mesh nofill, where in this example, points is an array of the four points, and faces is [[0 1 2 6] [0 3 2 6]].

This POLYHEDRON option creates a set of polygons, collectively forming (possibly) a polyhedron from an array of arrays of indices (that is, an array of faces) and an optional array of points, which defaults to {*}.xyz.all. For example, load $caffeine; draw POLYHEDRON @{{*}.find("*1****1||*1*****1","map")} fills in the 5- and 6-membered aromatic rings with a colored surface. load $p4; draw POLYHEDRON @{{*}.find("*1**1","map")} fills in the faces of tetrahedral tetraphosphorus. The faces need not be wound correctly.

Draws vectors for the previously selected residues representing the quaternion frame and rotational axis for each residue. The parameters for this command are the same as for plot quaternion or the quaternion command. Vectors are named based on the axis (x, y, z, q), residue number, and chain.

Draws curved arrows marked with PHI and PSI angles in planes perpendicular to the N-CA and CA-C bonds of the selected amino acids, respectively.

Creates a DRAW object based on DRAW object $id, which must be of POLYGON type, that is slabbed based on a plane definition. For example: draw p4 polygon 4 {0 0 0} {0 3 0} {3 3 0} {0 3 3} 2 [0 1 2 0] [2 3 0 0]; draw p4 slab $p4 PLANE @{plane({0 0 0}, {5 0 0})}

Draws the symmetry elements of the representative set of symmetry operations (the operations generally given in a CIF file) for the current space group.

Draws symmetry elements of the representative operations of the current space group, including all translations of those operations that intersect with the unit cell. Essentially a 3D interactive "space group diagram."

Draws symmetry elements of all representative operations for which the specified atom (in the current model only) is invariant except for lattice translation. If the atom is in a general position, nothing is drawn. For example:

load =ams/marcasite 1 packed
draw spacegroup @3
-x,y,z mirror plane
x,-y,-z C2 axis
-x,-y,-z Ci: 0 0 0

Draws the i-th operation for which the specified atom (in the current model only) is invariant except for lattice translation. If the atom is in a general position, nothing is drawn. For example:

load =ams/marcasite 1 packed
draw spacegroup @3
x,-y,-z C2 axis

Draws a graphic representation of a crystallographic space group symmetry operation. Operations include simple rotations, screw rotations, rotation-inversions, mirror planes, and glide planes, Either a number (for one of the model's symmetry operations) or a string indicating a Jones-Faithful operation may be used. The position may be an atom expression may be a point. If a point, it can be expressed either as a cartesian coordinate or a fractional coordinate (using a "/" in at least one position -- for example, { 1/2 0 0}. The ID of the draw command is prepended to the drawn object IDs. For example, draw ID "s1" SYMOP "x,1/2-y,z" {1/2 1/2 1/2}. See also the Jmol Crystal Symmetry Explorer.

Draws the symmetry relations between any two atoms or groups or any two positions in space. For example, draw SYMOP {molecule=1} {molecule=2}.

Draws the symmetry relation associated with the specified symmetry operator between any two atoms or groups or any two positions in space. For example, load =ams/quartz 1 packed;draw symop 2 @1 @3.

Draws the nth symmetry operator for special positions, where multiple symmetry operations relate two positions in space. For example, load =ams/quartz 1 packed;draw symop @1 @3 1.

Draws the given array of symmetry operations (1-based) for atom 1.

Draws the symmetry operation targeting a given normalized lattice offset, where {0 0 0} is always into the unitcell [0, 1).

Draws the symmetry operation associated with the given 4x4 matrix, which most likely comes from a variable, for example here the symmetry operation that is the product of two other symmetry operations: draw SYMOP @{symop(11)*symop(14)}.

Draws the currently defined unitcell. Note that by default this is a solid. Default rendering for UNITCELL is MESH NOFILL.

Draws a set of lattice points, including lattice centering; mostly for debugging; possibly useful

Draws the currently defined unitcell along with colored axes.

This option is similar to ARROW, and accepts two points. The first point is the origin; the second is of the form {dx,dy,dz}, indicating a vector to the next point rather than the point itself.

See also:

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