Table of Contents
The scripting engine has been completely rewritten for Jmol Release 6. As of this writing it should be considered *alpha test* code. Please supply feedback in case of bugs and/or unexpected behavior and/or with feature requests. You can do this through the jmol home page http://jmol.sourceforge.net
Jmol supports the RasMol scripting language defined by RasMol. Information about RasMol can be found at http://www.openrasmol.org/. The current URL for full RasMol documentation is: http://www.openrasmol.org/doc/rasmol.htm.
The Chime web browser plug-in was based upon the RasMol source code. Various extensions were added, including additional scripting commands. Information about Chime can be found at http://www.mdlchime.com/ The current URL for extended chime scripting commands is: http://www.mdlchime.com/chime/chimerasmol.html.
Jmol currently supports many of the RasMol/Chime scripting commands. Our goal is to eventually provide full script support. This will provide a migration path for those who wish to move to an open source solution that supports a larger number of file formats on a wider variety of hardware platforms.
Please give us feedback on what features you use and that are currently no implemented. This will help us prioritize future development.
This documentation is autogenerated from the content on this website: http://www.stolaf.edu/people/hansonr/jmol/docs/.
Sets selected animation parameters or turns animation on or off. Note that there are four distinct animation types that can be employed using Jmol: (1) files may contain multiple stuctures that are "played" sequencially, (2) Gaussian output files may contain vibrational modes that can be animated, (3) scripts may be run through with delays and loops, and (4) the model may spin or move in a predefined way. The "animation" command only refers to method (1).
Syntax
Turns on or off animation.
Sets the animation direction to be from last frame to first frame.
Sets the animation direction to be first frame to last frame.
Sets the animation frames per second.
Go to a specific frame.
Overlay all frames.
Go to next frame
Go to previous frame.
Sets the animation mode to restart the sequence automatically when the last frame has played.
Allows for a time delay at the start and end of the loop.
Sets the animation to play once through and then stop (the default mode).
Sets the animation to play forward and back endlessly.
Allows for a time delay at the start and end of the palindrome.
Definitions
[frames-per-second]
is the animation rate -- (integer)
[time-delay1]
is the time in seconds to pause on the first frame -- (integer|decimal, >=0)
[time-delay2]
is the time in seconds to pause on the last frame -- (integer|decimal, >=0)
The Jmol commands select, restrict, define, center, and polyhedra take for parameters expressions that represent collections of atoms in one or more models. While this documentation does not attempt to define these expressions completely, several examples are given here. Note that the substructure() function takes a quoted smiles string for its argument. The first parameter of the within() function can be a decimal distance in Angstroms or one of the words group, chain, or model.
Examples:
select atomno=1;color purple;spacefill 600 select nitrogen;color yellow select [PRO];color green select within(5.0,[PRO]62) and not [PRO]62;color white select within(group,within(5.0,[PRO]));color yellow select substructure("[Fe][S]");wireframe 1.0
Shows the backbone of a protein or nucleic acid macromolecule by connecting the alpha carbons.
Syntax
Turns the backbone on or off
Backbone radius can be specified in angstroms using a decimal number (1.0, 2.0, etc.)
Definitions
[backbone-radius]
is the radius of the backbone -- (decimal, <=4.0)
Sets color of the background. For specifications, see color.
Syntax
Sets the background of the applet window.
Sets the background for the pop-up label box that appear when the mouse "hovers" over an atom. "NONE" results in there being no hover backgrounds. Operates globally, not on selected atoms.
Sets the background of the atom labels that appear with the "label" command. "NONE" results in there being no label background. Operates globally, not on selected atoms.
Definitions
[RGB-color]
is a name of a color or a red, green, blue color triple in decimal with commas, for example [255,0,255], or as a single hexadecimal number, for example [xFF00FF] (brackets included) -- (color name), [r, g, b], [xRRGGBB]
[color-or-none]
is (color name), [r, g, b], [xRRGGBB], NONE
Cartoons are the classic shapes the are used to depict alpha helices and beta-pleated sheets.
Syntax
Definitions
[cartoon-radius]
is the radius of the cartoon elements -- (decimal, <=4.0)
Sets the center of rotation to be the center of the set of atoms defined by the atom expression. This is calculated as the mean value of the coordinates of the selected atoms along each of the respective axes. If no atoms are selected then the center is set to the center of the bounding box (the default).
Syntax
Recenters the model on the default center.
Centers the model on the specified atom set.
Definitions
[atom-expression]
is any expression that evaluates to a set of atoms -- (atom-expression)
Examples:
select [CYS]32 center selected
The color command takes several forms, depending upon the type of object being colored: an atom object, a bond object, a chemical element, or a model object. In addition, you can set the default color of any chemical element individually. This section of the guide discusses each of these in turn:
Sets the color of atom-related objects (atoms, backbone, cartoons, dots, labels, meshribbon, polyhedra, rockets, stars, strands, trace, and vectors).
Syntax
Sets the previously selected atom set to a color based on a particular color scheme. Note that to color a specific set of atoms, you MUST select that set first, then use use the color command. You cannot script, for example, "color *.N? green".
Sets the color of atom-related objects based on a previously selected atom set to a specific color, a color scheme, or back to its default color (CPK), or to inherit the color of its associated atom (NONE). (In the case of "color atom", CPK and NONE both revert to the default color.)
Definitions
[color-scheme]
is to color based on a scheme. (CPK and NONE are synonymous here) -- (color name), [r, g, b], [xRRGGBB], AMINO, GROUP, CHAIN, FIXEDTEMPERATURE, FORMALCHARGE, MONOMER, PARTIALCHARGE, RELATIVETEMPERATURE, SHAPELY, STRUCTURE, CPK, NONE
[atom-associated-object]
is an object related to an atom -- ATOM, BACKBONE, CARTOON, DOTS, LABELS, MESHRIBBON, POLYHEDRA, RIBBONS, ROCKETS, STARS, STRANDS, TRACE, VECTORS
Three types of bonds are distinguished by Jmol for coloring purposes: regular bonds, disulfide bonds, and hydrogen bonds. Each can be colored independently, and hydrogen bond colors in proteins can take on a special coloring scheme based on their connectivity.
Syntax
Colors selected bonds a specific color or resets them to inherit the color of their associated atoms.
Colors disulfide bonds a specific color or resets them to inherit their color from their associated atoms.
Colors hydrogen bonds a specific color or resets them to inherit their color from their associated atoms.
Colors hydrogen bonds specifically in proteins based on how many residues one end is from the other. Note that to get this effect, one must first execute "hbonds ON" and then issue "color hbonds TYPE". The colors assigned are based on the number of basepairs between the interacting H atoms. This TENDS to indicate secondary structure, but is not perfect.The correlation between color and offset are as follows:
Definitions
[color-or-none]
is (color name), [r, g, b], [xRRGGBB], NONE
You can use the 'color' command to specify customized default colors that are used for elements. [default Jmol element colors] color carbon limegreencolor hydrogen [x32CD32];These changes are not molecule-specific; they will continue in effect even if new molecules are loaded. However, in a page with multiple applets, each applet will have its own set of element colors.If you choose to use this feature, you should consider encapsulating your favorite colors into a script and then executing that script as a subroutine. For example:script LoadMyFavoriteColors.txt;load foo.xyz;load bar.xyz;Note:
Syntax
Definitions
[element-name]
is to color specific elements such as CARBON or HYDROGEN -- (element name)
[RGB-color]
is a name of a color or a red, green, blue color triple in decimal with commas, for example [255,0,255], or as a single hexadecimal number, for example [xFF00FF] (brackets included) -- (color name), [r, g, b], [xRRGGBB]
Sets the color of various objects (axes, boundbox, echo, hover, measurements, pmesh, and unitcell).
Syntax
Definitions
[model-object]
is AXES, BOUNDBOX, ECHO, HOVER, ISOSURFACE, MEASUREMENTS, PMESH, UNITCELL
[RGB-color]
is a name of a color or a red, green, blue color triple in decimal with commas, for example [255,0,255], or as a single hexadecimal number, for example [xFF00FF] (brackets included) -- (color name), [r, g, b], [xRRGGBB]
Examples:
select [CYS]32 ;label %a: %x %y %z;color labels white; set axes on;color axes green set axes on;color axes [xFF00FF];
Examples:
# color by polarity color background [xffa0a0] # pink #jx set perspectiveDepth on; #executed only in Jmol, not Chime or Rasmol zoom 125 #jc; # zoom to 125% in Chime and Rasmol but not in JmolSimilar comment controls exist in Chime. Commands prefixed with #! will be executed in Chime but not in RasMol. Commands containing ## will be ignored by Chime, but the portion preceding the ## will be executed in RasMol. Thus we have: # not read by Jmol, Chime, or Rasmol#jx [commands here] Jmol excecution only#! [commands here] Chime execution only[commands here] ## #jc Rasmol execution only[commands here] #jc Chime and Rasmol only [commands here] ## Jmol and Rasmol only
Defines the specified variable to the the atoms selected by the atom expression.
Syntax
Definitions
[variable-name]
is a (string)
[atom-expression]
is any expression that evaluates to a set of atoms -- (atom-expression)
Examples:
define mygroup within(5.0,[FS4]102) select mygroup color atoms white
Causes the screen to refresh and the script to stop executing for the specified number of seconds.
Syntax
Definitions
[time-delay]
is in seconds -- (integer|decimal, >=0)
Slab and Depth together control the percentage of the molecule to be displayed based on clipping planes. slab on turns slab/depth on. slab 50 shows the back 50% of the molecule. slab 25 show the back 25% of the molecule. Atoms appear solid; bonds appear hollow.
Syntax
Definitions
[slab-percent]
is an (integer, 0 to 100)
Examples:
slab 50; depth 0;slab on; # show the back half of the molecule slab 100;depth 50; slab on;# show the front half of the molecule slab 75; depth 25;slab on; # show middle 50% of the molecule slab 50;depth 50;slab on; # show a plane that is 1 pixel deep
Turns dotted surface on or off for Van der Waals radii or solvent probe (if in addition set solvent ON).
Syntax
Echos a string of text to the window at the location predefined by the "set echo" command as well as to the Java Console. "echo" by itself deletes the text at the selected position (top, middle, or bottom).
Syntax
Examples:
set echo top left font echo 30 serif bolditalic color echo green echo "I am green top left 30 serif bolditalic"
Stops execution of the script current script. In the case of a script that is running as a "child" (for example, from a "source" command, execution continues with the parent.
See also: animation or anim, delay, frame, loop, model, move, moveto, quit, script or source, ???, ???, ???, ???, ???,Sets font size and information in labels and other text-bearing elements.
Syntax
Definitions
[font-size]
is approximately the same as Rasmol -- (integer, 6 to 63)
[font-face]
is SERIF, SANSSERIF, or MONOSPACED
[font-style]
is PLAIN, BOLD, ITALIC, or BOLDITALIC
Sets the current animation frame (1 being the first). (Same as the model command.)
Syntax
Go to a specific frame.
Overlay all frames.
Go to next frame
Go to previous frame.
Examples:
model 1 model NEXT model -1 model 0;select *;wireframe 0.1;spacefill 0.2 anim on model 0;select *;wireframe off;spacefill off; select */1;wireframe 0.1;spacefill 0.2;color atoms red; select */35;wireframe 0.1;spacefill 0.2;color atoms blue
Hydrogen bonds can be turned on or off, colored, and given custom width in angstroms.
Syntax
Definitions
[width-in-angstroms]
is a (decimal, 2.0)
[width-by-Rasmol]
is in 1/250ths of an Angstrom (deprecated) -- (integer, 500)
Turns on and off pop-up labels that appear when the user "hovers" the mouse over the atom. If a string is given, it is used as the label. Special characters include: %a (atom name), %b (protein B-Factor), %c %s (protein chain and residue), %e (element symbol), %i (sequential number), %m (single letter amino acid code), %n (3-letter residue name), %r (PDB residue number), %U (same as %e %i). For a full list, see the example HTML page.
Syntax
Jmol can generate isosurfaces from scalar field data in files of the gaussian .cube format, which contains both atom positions and scalar data. The load command reads only the atom position data from the .cube file.A separate isosurface command is used to read the scalar field data and construct the isosurface. This surface represents the points in space where scalar values cross a specified "cutoff" value. Inside the surface, values are greater or equal to a specified positive cutoff or less than or equal to a specified negative cutoff. The default cutoff is 0.02. Note that positive and negative surfaces are created separately. You can give them distinct names and control their display properties independently. Parameters to the isosurface command control the cutoff value and the display characteristics of the surface. By reading the same .cube file more than once with different parameters, or by reading different .cube files, you can construct different isosurfaces with different shapes and sizes. By naming these individual surfaces with unique identifiers you can control display settings and color for each of the surfaces independently.The isosurface command is similar to the pmesh command in terms of options. The isosurface command takes the overall format:isosurface surfaceID cutoff [option] "filename.cube"(The filename must be in double quotes, but the extension '.cube' is not necessary.) The .cube file may be gzip-compressed. isosurfaceID is any name that you want to use later to refer to this particular surface.
Syntax
Selects a specific isosurface (or all isosurfaces) for subsequent color commands.
Turn on/off the specified isosurface.
Delete the specified isosurface.
Loads isosurface file "xyz.cub.gz", optionally assigned id isosurfaceID.
Controls whether or not dots are shown at the isosurface points.
Controls whether the isosurface appears solid (the default).
Controls whether lines between the isosurface points are drawn, given the appearance of a mesh.
Examples:
isosurface pos05 0.05 "examples/ethene-HOMO.cub.gz";isosurface neg05 -0.05 "examples/ethene-HOMO.cub.gz"; # now load some other surface further out;isosurface pos01 0.01 "examples/ethene-HOMO.cub.gz";isosurface neg01 -0.01 "examples/ethene-HOMO.cub.gz";color isosurface translucent; # make neg01 translucent isosurface pos01 nofill mesh; # make pos01 a mesh;color isosurface translucent; # make the pos01 mesh translucent, too isosurface neg01 dots; # make neg01 show dots, too isosurface neg01 nofill; # only dots isosurface nodots nomesh fill; #everybody is back to a solid ...;color isosurface opaque; # ... and opaque isosurface neg01; #select neg01;color isosurface green; isosurface pos01;color isosurface violet; slab on; slab 50; # slab in order to see the inside slab off; # all done!
Turns on and off atom labels based on a previous selection. If a string is given, it is used as the label. Special characters include: %a (atom name), %b (protein B-Factor), %c %s (protein chain and residue), %e (element symbol), %i (sequential number), %m (single letter amino acid code), %n (3-letter residue name), %r (PDB residue number), %U (same as %e %i). For a full list, see the example HTML page.
Syntax
Examples:
select nitrogen label %a: %x %y %z
Loads the specified file or URL.
Syntax
Jmol automatically determines file type based upon the contents of the file.
The format parameter is ignored. This form is allowed for backward compatibility with RasMol/Chime.
Definitions
[file name]
is a model filename or URL -- (string)
[param-ignored]
is for Rasmol/chime compatibility; ignored -- (string)
Causes the script to restart at the beginning, with an optional time delay.
Syntax
Definitions
[time-delay]
is in seconds -- (integer|decimal, >=0)
Examples:
color bonds red delay 3 color bonds green loop 1
Renders a measurement between the specified atoms. See also set measurement.
Syntax
Turns on and off the distance, angle, dihedral measurement labels while leaving the measurement line itself present.
Two atoms specify a distance measurement.
Three atoms specify an angle measurement.
Four atoms specify a dihedral angle measurement.
Definitions
[atom-number]
is the sequential number assigned to the atom -- (integer, >=1)
A mesh ribbon is similar to a strand, but is more the quality of a loosely woven fabric.
Syntax
Definitions
[mesh-ribbon-radius]
is the overall radius of the mesh ribbon -- (decimal, =4.0)
Sets the current model (1 being the first). (Same as the frame command.)
Syntax
Display a specific model.
Overlay all models.
Display the next model.
Display the previous model.
Examples:
model 1 model NEXT model -1 model 0;select *;wireframe 0.1;spacefill 0.2 anim on model 0;select *;wireframe off;spacefill off; select */1;wireframe 0.1;spacefill 0.2;color atoms red; select */35;wireframe 0.1;spacefill 0.2;color atoms blue
The move command provides powerful animation capabilities. It allows you to specify rotations, zooming, and translations to be performed in a specified period of time. xRot, yRot, and zRot are rotations about the cartesian axes in degrees. Zoom specifies a zoom factor (there is a good chance this is not currently implemented properly) xTrans, yTrans, and zTrans are translations in the range -100 to 100. If you do not know what slab is, just put in a zero. see the slab command for more information.
Syntax
Definitions
[x-rotation]
is the degrees of rotation about x -- (integer)
[y-rotation]
is the degrees of rotation about y -- (integer)
[z-rotation]
is the degrees of rotation about z -- (integer)
[zoom-factor]
is a scaling factor -- (integer)
[x-translation]
is the distance offset along x -- (integer)
[y-translation]
is the distance offset along y -- (integer)
[z-translation]
is the distance offset along z -- (integer)
[slab-cutoff]
is the cutoff for the slab display -- (integer)
[seconds-total]
is the amount of time to wait -- (decimal)
[move-frames-per-second]
is the frames per second to move -- (integer)
[maximum-acceleration]
is the maximum acceleration -- (integer)
The moveto command rotates the molecule to a predefined orientation. The first parameter specifies the number of seconds during which the molecule should rotate smoothly from the current orientation to the new orientation. A 0 for this first parameter specifies an instantaneous reorientation. The next three parameters (x, y, and z) define the axis relative to the default orientation about which the molecule should be rotated. The fifth parameter defines the counterclockwise (right-hand) rotation in degrees about this axis. "moveto 0 0 0 0 0" rotates the model to the default orientation (equivalent to "reset"). If the fifth parameter is 0 but any one of x, y, or z is nonzero, then no reorientation occurs (because the axis has been specified, but the rotation is 0 degrees). In conjunction with "show orientation" this command allows reading and restoring specific user-specified orientations.
Syntax
Definitions
[time-in-seconds]
is in (seconds)
[coord-value]
is a (decimal)
[cw-rotation-deg]
is a (decimal)
Examples:
moveto 0 1 0 0 -90; #view from top moveto 0 0 1 0 90; #view from right moveto 0 0 1 0 -90; #view from left moveto 2 1 0 0 90; #view from bottom with smooth 2-second transition moveto 0 0 0 0 0; #default view with instantaneous transition
With the pmesh command you can add one or more surfaces to a model. The pmesh command is similar to the isosurface command in terms of options. The pmesh command takes the overall format:pmesh meshID [option] "filename.pmesh"(The filename must be in double quotes, but the extension '.pmesh' is not necessary.) The .pmesh file may be gzip-compressed. meshID is any name that you want to use later to refer to the mesh. The command also sets the 'current' mesh.Note: meshes are not currently model-specific and are limited to triangles and quadrilaterals.Format of the pmesh files required by Jmol:The format of a pmesh file is relatively simple (example file):
Syntax
Selects a specific pmesh (or all pmeshes) for subsequent color commands.
Turn on/off the specified mesh.
Delete the specified mesh.
Loads pmesh file "xyz.pmesh.gz", optionally assigned id pmeshID.
Controls whether or not dots are shown at the polygon vertices.
Controls whether the polygons are filled (the default).
Controls whether the edges of the polygons are drawn.
Examples:
pmesh myPlane "examples/10x10pmesh.txt" # load a pmesh with ID myPlane color pmesh translucent yellow # make it translucent yellow pmesh myWave "examples/wave.pmesh" # load another pmesh, with ID myWave pmesh dots # turn on dots on all loaded pmeshes pmesh myWave # select pmesh myWave color pmesh white # color it white pmesh myPlane mesh # only display the mesh for myPlane pmesh myPlane nodots # no dots for myPlane
Jmol supports polyhedral representation of molecular structures. Jmol will form tetrahedrons and octahedrons.Basis. Potential polyhedra centers are defined by the currently selected set of atoms. From this set of centers, polyhedra can be formed based upon bonds (polyhedra BONDS) or upon distance (polyhedra 2.0). If you construct them based on distance, then you may specify an optional set of atoms to be considered as vertices. This set of valid vertex atoms is in the form of a standard Jmol atom expression (such as hydrogen or atomno12 and not nitrogen) and must be specified in parentheses as shown in the examples given below.Valid Polyhedra. The following three rules govern the formation of polyhedra:
Syntax
Sets the current polyhedra to be "all" for subsequent use by the 'color polyhedra' command.
Show or hide polyhedra whose central atom is selected.
Delete the polyhedra associated with central atoms that are selected.
Constructs polyhedra based upon bonding information. Selected atoms are search for centers that have exactly 4 or 6 bonds with the vertex atoms in a conforming orientation.
Constructs polyhedra based upon distance. Centers must contain exactly 4 or 6 atoms within the specified radius, in Angstroms (a decimal number).
Constructs polyhedra based upon distance with control over which atoms are considered as vertices. Centers must contain exactly 4 or 6 atoms within the specified atom expression that are also within the specified radius in angstroms. Note that the atom expression must be specified in parentheses.
Highlight the edges of the polyhedra whose central atom is in the currently selected set.
Highlight only the front edges of the polyhedra whose central atom is in the currently selected set.(Useful when color is translucent.)
Turn off edge highlighting.
Definitions
[atom-expression]
is any expression that evaluates to a set of atoms -- (atom-expression)
Examples:
select *;polyhedra bonds; color polyhedra grey select atomno=19; polyhedra 3.0 (hydrogen);color polyhedra yellow select *;polyhedra 2.0 #all three select *;polyhedra 2.0 (not within (1.1225, carbon)) #note how this disallows one of the three select *;color polyhedra translucent; # now we can see the carbons inside select *; polyhedra edges; # hilite the edges color polyhedra translucent orange; select *;polyhedra off
In the current release of Jmol, quit is synonymous with exit. This is inconsistent with RasMol, where quit means to exit the program.
See also: animation or anim, delay, exit, frame, loop, model, move, moveto, script or source, ???, ???, ???, ???, ???,Forces a screen repaint during script execution. (Unnecessary, and thus deprecated.)
See also: reset, rotate,Resets molecule to its original position: zoom 100; center; translate x 0; translate y 0;
See also: refresh, rotate,Selects the atoms identified by the atom expression and hides all atoms and bonds which are outside the selection set. NOTE: This command cannot be reversed without reloading the model!
Syntax
Restricts to all atoms;possibly not H atoms.
Restricts atoms based on an atom expression.
Definitions
[atom-expression]
is any expression that evaluates to a set of atoms -- (atom-expression)
Examples:
restrict protein restrict solvent restrict within(3.0,[FS4]102)
Ribbons offer a representation the protein backbone or nucleic acid helix using a flat band that smoothly traces the midpoints of adjacent alpha carbon atoms (or phosphorus atoms in nucleotide chains). The ribbon is perpendicular to the peptide plane.
Syntax
Normally, ribbons vary in width according to the amino acid atom positions. This command sets the width of the ribbon to be a connstant value (a decimal, in Angstroms).
Definitions
[ribbon-radius]
is half of the overall width of the ribbon -- (decimal, =4.0)
Creates a "rocket" cartoon.
Syntax
Definitions
[rocket-radius]
is half of the overall width of the rocket barrel -- (decimal, =4.0)
Rotates the model the specified angle about the specified axis. Integer values specify degrees.
Syntax
Definitions
[number-of-degrees]
is the number of degrees -- (integer)
Loads and executes the specified script file/url. The hash/pound/sharp character (#) character marks a comment to the end of the line. The semicolon character (;) separates multiple statements on the same line. A script file may load another script file, up to 10 deep.
Syntax
Definitions
[file-name]
is any valid filename or URL -- (string)
Selects the atoms identified by the expression. If no expression is given then all atoms are selected.
Syntax
Selects all atoms (possibly not H atoms).
Selects atoms based on an atom expression. To select atoms specific to a specific model when more than one model is present, use "/n" where "n" is the model number. For example, to select all atoms of model 3, use select */3.
Definitions
[atom-expression]
is any expression that evaluates to a set of atoms -- (atom-expression)
Examples:
select carbon;color white select protein;ribbons on select *:D;color blue select [HIS]:D;spacefill 300 select [HIS]92:D.N;spacefill 600 select [HIS]92:D.C?;color orange select [HIS]92.N;color [255,196,196] select elemno7;spacefill 200 select within(group, within(10.0, :a));color green;select :a;color red select within(chain, [HIS]92);color white; select within(chain, within(3.0,[HIS]92:D));color purple; select within(chain,within(5.0,[HIS]92));color white # this last a bug?
This group of commands sets the appearance of various optional bond effects for the model.
Syntax
In some file formats (.mol files, for example) the connection data may indicate the bond type--single, double, triple, or quadruple. The set bonds command determines whether or not multiple bonds are displayed. Use set bonds OFF when you want all bonds to appear as single bonds.
When script commands affect a set of atoms, BOTH atoms must be in the set for the bonds between them to also be affected.
When script commands affect a set of atoms, EITHER atom may be in the set for the bonds also to be affected.
Hydrogen bonds between protein amino acid residues or nucleic acid base pairs are displayed as lines. These lines can be displayed whether or not the H atoms are present in the file, and can be drawn either between the two non-hydrogen atoms involved in the bond (O or N, typically, the default) or, alternatively, between the two backbone alpha-carbon atoms, depending upon the desired effect.
Sulfur-sulfur bonds in cysteine bridges of proteins are displayed as lines. These lines can either be between the two sidechain sulfur atoms (the default) or between the two backbone alpha-carbon atoms, depending upon the desired effect.
Sets the default color scheme to be the traditional Rasmol/Chime scheme or the newer, more subtle, Jmol scheme. This command does not actually change the display for an object unless that object is currently being displayed using the default color scheme. See the Jmol Colors page for default color scheme details.
Syntax
This command group allows for annotation and highlighting of atoms in terms of labels and "halos."
Syntax
Sets the option ON to dispay a "halo" around atoms when they are or become selected as a way of highlighting specific atoms.
Turns off selection halos
Selects which of the three possible echo positions (top, middle, or bottom) will be written to by the next "echo" command and, optionally, sets the horizontal position of that text to left, center, or right.
Turns off all three echo texts.
Sets the font size for atom labels.
Determines whether or not "Jmol" is indicated in the bottom right corner of the window.
Sets the label offset relative to the atom being labeled.
Definitions
[vertical-position]
is one of the following: -- TOP, MIDDLE, BOTTOM
[horizontal-position]
is one of the following: -- LEFT, CENTER, RIGHT
[font-size]
is approximately the same as Rasmol -- (integer, 6 to 63)
[x-offset]
is the x-offset -- (integer)
[y-offset]
is the y-offset -- (integer)
This commands in this group determine the overall lighting effects, size, and rotation for the model.
Syntax
Sets the amount of "ambient" light filling the shadows created by the apparent light source. An ambient value of 0 creates an effect of a spotlight on a stage; a value of 100 removes the shadow entirely, creating a flat, nonrealistic effect.
Sets the amount of "diffuse" light apparently emanating from the spotlight, but not hitting and reflecting off the model directly. Setting the diffuse value to 0 turns this effect off; giving the effect of the model in a black-walled room where no light reflection is possible, effectively turning off all shadows.
Sets perspective depth on or off. OFF is required for proper function of absolute scale (set scale3d x).
Sets the absolute scale of the model by setting the viewing distance from the user to the model in arbitrary units. The actual scale will depend upon the sizes of both the applet window and the screen.
Sets the density of dots in the specular reflection.
Sets the size of the apparent reflection from a light source. set specular 0 turns off this effect.
Definitions
[ambient-percent]
is an (integer, 0 to 100)
[diffuse-percent]
is an (integer, 0 to 100)
[viewing-distance]
is the apparent distance from the model to the user in arbitrary units -- (integer), (decimal)
[specular-power]
is an (integer)
[specular-percent]
is an (integer, 0 to 100)
This command group turns on or off specific sets of atoms and axes/cell-related options.
Syntax
Turns on or off displayed axes, and determines their line style and line width (as a decimal number, in Angstroms).
Turns on or off a wire-frame box that contains the model, and determines the line style and line width (as a decimal number, in Angstroms) of that box.
Disables (set disablePopupMenu ON) or enables (set disablePopupMenu OFF) the pop-up menu.
Sets the radius of the solvent "ball" that would run around the structure defining its outline. After set radius, you must (re)issue dots ON for it to take effect, and the solvent probe option for dots must be set on using set solvent ON (below).
Turns on and off display of hydrogen atoms.
Turns on and off display of solvent "probe" that can be displayed using dots. After set solvent ON, a subsequent dots ON
Definitions
[line-width-or-type]
is a line width or type for a drawing object -- ON, OFF, DOTTED, (integer, 1 to 19), (decimal, 2.0)
[probe-radius-in-angstroms]
is a (decimal)
[strand-count]
is the number of strands -- (integer, 0 to 20)