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[Jmol-commits] CVS: Jmol/doc/source/guide scriptCommands.docbook.xml,1.1,1.2 scripts.docbook.xml,1.4,1.5
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From: Egon W. <eg...@us...> - 2004-11-05 14:48:45
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Update of /cvsroot/jmol/Jmol/doc/source/guide In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv5755/guide Modified Files: scriptCommands.docbook.xml scripts.docbook.xml Log Message: Added definitions and added some more docbook markup so that the result is easier to read Index: scriptCommands.docbook.xml =================================================================== RCS file: /cvsroot/jmol/Jmol/doc/source/guide/scriptCommands.docbook.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- scriptCommands.docbook.xml 5 Nov 2004 14:25:29 -0000 1.1 +++ scriptCommands.docbook.xml 5 Nov 2004 14:48:35 -0000 1.2 @@ -5,109 +5,109 @@ <section><title>animation or anim </title><para>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). -</para><variablelist><title>Examples</title><varlistentry><term>animation direction +1 -</term><listitem><para>Sets the animation direction to be first frame to last frame. -</para></listitem></varlistentry><varlistentry><term>animation direction -1 -</term><listitem><para>Sets the animation direction to be from last frame to first frame. -</para></listitem></varlistentry><varlistentry><term>animation fps [frames-per-second] -</term><listitem><para>Sets the animation frames per second. -</para></listitem></varlistentry><varlistentry><term>animation frame [frame-option] -</term><listitem><para>Specifies which frame to go to. -</para></listitem></varlistentry><varlistentry><term>animation mode loop -</term><listitem><para>Sets the animation mode to restart the sequence automatically when the last frame has played. -</para></listitem></varlistentry><varlistentry><term>animation mode loop [time-delay1] [time-delay2] -</term><listitem><para>Allows for a time delay at the start and end of the loop. -</para></listitem></varlistentry><varlistentry><term>animation mode once -</term><listitem><para>Sets the animation to play once through and then stop (the default mode). -</para></listitem></varlistentry><varlistentry><term>animation mode palindrome -</term><listitem><para>Sets the animation to play forward and back endlessly. -</para></listitem></varlistentry><varlistentry><term>animation mode palindrome [time-delay1] [time-delay2] -</term><listitem><para>Allows for a time delay at the start and end of the palindrome. -</para></listitem></varlistentry><varlistentry><term>animation on/off -</term><listitem><para>Turns on or off animation. -</para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>animation direction +1 +</command></term><listitem><para>Sets the animation direction to be first frame to last frame. +</para></listitem></varlistentry><varlistentry><term><command>animation direction -1 +</command></term><listitem><para>Sets the animation direction to be from last frame to first frame. +</para></listitem></varlistentry><varlistentry><term><command>animation fps [frames-per-second] +</command></term><listitem><para>Sets the animation frames per second. +</para></listitem></varlistentry><varlistentry><term><command>animation frame [frame-option] +</command></term><listitem><para>Specifies which frame to go to. +</para></listitem></varlistentry><varlistentry><term><command>animation mode loop +</command></term><listitem><para>Sets the animation mode to restart the sequence automatically when the last frame has played. +</para></listitem></varlistentry><varlistentry><term><command>animation mode loop [time-delay1] [time-delay2] +</command></term><listitem><para>Allows for a time delay at the start and end of the loop. +</para></listitem></varlistentry><varlistentry><term><command>animation mode once +</command></term><listitem><para>Sets the animation to play once through and then stop (the default mode). +</para></listitem></varlistentry><varlistentry><term><command>animation mode palindrome +</command></term><listitem><para>Sets the animation to play forward and back endlessly. +</para></listitem></varlistentry><varlistentry><term><command>animation mode palindrome [time-delay1] [time-delay2] +</command></term><listitem><para>Allows for a time delay at the start and end of the palindrome. +</para></listitem></varlistentry><varlistentry><term><command>animation on/off +</command></term><listitem><para>Turns on or off animation. +</para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[frames-per-second]</option></term><listitem><para>is the animation rate -- (integer)</para></listitem></varlistentry><varlistentry><term><option>[frame-option]</option></term><listitem><para>is a frame option: -- (integer), "next", "nextwrap", "none", "play", "prev", "prevwrap", "revplay", "rewind"</para></listitem></varlistentry><varlistentry><term><option>[time-delay1]</option></term><listitem><para>is the time in seconds to pause on the first frame -- (integer|decimal)[>=0]</para></listitem></varlistentry><varlistentry><term><option>[time-delay2]</option></term><listitem><para>is the time in seconds to pause on the last frame -- (integer|decimal)[>=0]</para></listitem></varlistentry></variablelist></section> <section><title>backbone </title><para>Shows the backbone of a protein or nucleic acid macromolecule by connecting the alpha carbons. Backbone radius can be specified in angstroms using a decimal number (1.0, 2.0, etc.) -</para><variablelist><title>Examples</title><varlistentry><term>backbone [backbone-radius] -</term><listitem><para></para></listitem></varlistentry><varlistentry><term>backbone on/off{default: on} -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>backbone [backbone-radius] +</command></term><listitem><para></para></listitem></varlistentry><varlistentry><term><command>backbone on/off{default: on} +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[backbone-radius]</option></term><listitem><para>is the radius of the backbone -- (decimal)[<=40]</para></listitem></varlistentry></variablelist></section> <section><title>background </title><para>Sets color of the background. See Color Specification. -</para><variablelist><title>Examples</title><varlistentry><term>background HOVER [RGB-color] -</term><listitem><para>Sets the background for the pop-up label box that appears when the mouse "hovers" over an atom. -</para></listitem></varlistentry><varlistentry><term>background LABELS [RGB-color] -</term><listitem><para>Sets the background of the atom labels that appear with the "label" command -</para></listitem></varlistentry><varlistentry><term>background [RGB-color] -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>background HOVER [RGB-color] +</command></term><listitem><para>Sets the background for the pop-up label box that appears when the mouse "hovers" over an atom. +</para></listitem></varlistentry><varlistentry><term><command>background LABELS [RGB-color] +</command></term><listitem><para>Sets the background of the atom labels that appear with the "label" command +</para></listitem></varlistentry><varlistentry><term><command>background [RGB-color] +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[RGB-color]</option></term><listitem><para>is a name of a color or a color triple, eg [255,0,255] -- (color)</para></listitem></varlistentry></variablelist></section> <section><title>cartoon or cartoons </title><para>"Cartoons" are the classic shapes the are used to depict alpha helices and beta-pleated sheets. -</para><variablelist><title>Examples</title><varlistentry><term>cartoon [cartoon-radius] -</term><listitem><para></para></listitem></varlistentry><varlistentry><term>cartoon on/off{default: on} -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>cartoon [cartoon-radius] +</command></term><listitem><para></para></listitem></varlistentry><varlistentry><term><command>cartoon on/off{default: on} +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[cartoon-radius]</option></term><listitem><para>is the radius of the cartoon elements -- (decimal)[<=40]</para></listitem></varlistentry></variablelist></section> <section><title>center or centre </title><para>Sets the center of rotation to be the center of the set of atoms defined by the 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). -</para><variablelist><title>Examples</title><varlistentry><term>center [atom-expression] -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>center [atom-expression] +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[atom-expression]</option></term><listitem><para>is any expression that evaluates to a set of atoms -- (atom-expression)</para></listitem></varlistentry></variablelist></section> <section><title>color or colour </title><para>Colors the object with the specified color. If no object is given then atom is assumed, and the currently selected atoms are colored. -</para><variablelist><title>Examples</title><varlistentry><term>color [Rasmol-structure] [color-scheme] -</term><listitem><para>Sets the color of the specified Rasmol object based on a color scheme. -</para></listitem></varlistentry><varlistentry><term>color [atom-associated-object] [color-scheme] -</term><listitem><para>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 (NONE). -</para></listitem></varlistentry><varlistentry><term>color [atom-associated-object] [temperature-mode] -</term><listitem><para>Color atoms based on a crystallographic B-factor or "temperature" scale. Colors range from blue (least positional variability within the crystal) through white to red (most positional variability). Using a fixed scale (parameter "fixedTemperature") allows direct comparison between two structures. Using a relative scale (parameter "temperture" or "relativeTemperature") sets the blue-red range to match the range of varibility in the model itself. -</para></listitem></varlistentry><varlistentry><term>color [object-with-text] [RGB-color] -</term><listitem><para>Sets the color of various objects. -</para></listitem></varlistentry><varlistentry><term>color atoms CPK -</term><listitem><para>Sets selected atom colors to the standard Jmol "cpk" color scheme. -</para></listitem></varlistentry><varlistentry><term>color dots [RGB-color] -</term><listitem><para>Sets the color of the molecular surface dots. -</para></listitem></varlistentry><varlistentry><term>color hbonds TYPE -</term><listitem><para>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:ColorOffsetgreen-4cyan-3white+2magenta+3 (turns)red+4 (alpha-helix)orange+5yellowother (e.g. beta-pleated sheet) -</para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>color [Rasmol-structure] [color-scheme] +</command></term><listitem><para>Sets the color of the specified Rasmol object based on a color scheme. +</para></listitem></varlistentry><varlistentry><term><command>color [atom-associated-object] [color-scheme] +</command></term><listitem><para>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 (NONE). +</para></listitem></varlistentry><varlistentry><term><command>color [atom-associated-object] [temperature-mode] +</command></term><listitem><para>Color atoms based on a crystallographic B-factor or "temperature" scale. Colors range from blue (least positional variability within the crystal) through white to red (most positional variability). Using a fixed scale (parameter "fixedTemperature") allows direct comparison between two structures. Using a relative scale (parameter "temperture" or "relativeTemperature") sets the blue-red range to match the range of varibility in the model itself. +</para></listitem></varlistentry><varlistentry><term><command>color [object-with-text] [RGB-color] +</command></term><listitem><para>Sets the color of various objects. +</para></listitem></varlistentry><varlistentry><term><command>color atoms CPK +</command></term><listitem><para>Sets selected atom colors to the standard Jmol "cpk" color scheme. +</para></listitem></varlistentry><varlistentry><term><command>color dots [RGB-color] +</command></term><listitem><para>Sets the color of the molecular surface dots. +</para></listitem></varlistentry><varlistentry><term><command>color hbonds TYPE +</command></term><listitem><para>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:ColorOffsetgreen-4cyan-3white+2magenta+3 (turns)red+4 (alpha-helix)orange+5yellowother (e.g. beta-pleated sheet) +</para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[atom-associated-object]</option></term><listitem><para>is an object related to an atom -- atom, bond, label, hbonds, monitor, ssbonds, vectors</para></listitem></varlistentry><varlistentry><term><option>[color-scheme]</option></term><listitem><para>is to color based on a scheme -- (color), amino, chain, formalCharge, partialCharge, shapely, structure, NONE</para></listitem></varlistentry><varlistentry><term><option>[Rasmol-structure]</option></term><listitem><para>is atom, backbone, cartoon, mesh, ribbon, rocket, strands, trace</para></listitem></varlistentry><varlistentry><term><option>[RGB-color]</option></term><listitem><para>is a name of a color or a color triple, eg [255,0,255] -- (color)</para></listitem></varlistentry><varlistentry><term><option>[object-with-text]</option></term><listitem><para>is axes, echo, hover, label, monitor, unitcell</para></listitem></varlistentry><varlistentry><term><option>[temperature-mode]</option></term><listitem><para>is "fixedTemperature" or "relativeTemperature"</para></listitem></varlistentry></variablelist></section> <section><title>cpk or spacefill </title><para>Renders selected atoms as shaded spheres. A boolean value renders the spheres with the vanderWaals radius. A decimal value specifies the sphere radius in Angstroms. An integer followed by "%" specifies sphere radius as a percentage of the Van der Waals radius. -</para><variablelist><title>Examples</title><varlistentry><term>cpk IONIC -</term><listitem><para>Generates a sphere for each atom according to an approximation of its ionic radius. -</para></listitem></varlistentry><varlistentry><term>cpk TEMPERATURE -</term><listitem><para>Generates a sphere for eah atom according to its crystallographic B-factor -</para></listitem></varlistentry><varlistentry><term>cpk [radius-Rasmol] -</term><listitem><para></para></listitem></varlistentry><varlistentry><term>cpk [radius-in-angstroms] -</term><listitem><para></para></listitem></varlistentry><varlistentry><term>cpk [radius-percent-vdw] -</term><listitem><para></para></listitem></varlistentry><varlistentry><term>cpk on/off{default: on} -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>cpk IONIC +</command></term><listitem><para>Generates a sphere for each atom according to an approximation of its ionic radius. +</para></listitem></varlistentry><varlistentry><term><command>cpk TEMPERATURE +</command></term><listitem><para>Generates a sphere for eah atom according to its crystallographic B-factor +</para></listitem></varlistentry><varlistentry><term><command>cpk [radius-Rasmol] +</command></term><listitem><para></para></listitem></varlistentry><varlistentry><term><command>cpk [radius-in-angstroms] +</command></term><listitem><para></para></listitem></varlistentry><varlistentry><term><command>cpk [radius-percent-vdw] +</command></term><listitem><para></para></listitem></varlistentry><varlistentry><term><command>cpk on/off{default: on} +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[radius-in-angstroms]</option></term><listitem><para>is a (decimal)[<=3]</para></listitem></varlistentry><varlistentry><term><option>[radius-percent-vdw]</option></term><listitem><para>is as a percent of the Van der Waals radius -- (integer)[-100 to -1]</para></listitem></varlistentry><varlistentry><term><option>[radius-Rasmol]</option></term><listitem><para>is in 1/250ths of an Angstrom (deprecated) -- (integer)[1 to 749]</para></listitem></varlistentry></variablelist></section> <section><title>define </title><para>Defines the specified variable to the the atoms selected by the expression/ -</para><variablelist><title>Examples</title><varlistentry><term>define [variable-name] [atom-expression] -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>define [variable-name] [atom-expression] +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[variable-name]</option></term><listitem><para>is a (string)</para></listitem></varlistentry><varlistentry><term><option>[atom-expression]</option></term><listitem><para>is any expression that evaluates to a set of atoms -- (atom-expression)</para></listitem></varlistentry></variablelist></section> <section><title>delay </title><para>Causes the screen to refresh and the script to stop executing for the specified number of seconds. -</para><variablelist><title>Examples</title><varlistentry><term>delay [time-delay] -</term><listitem><para></para></listitem></varlistentry><varlistentry><term>delay on -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>delay [time-delay] +</command></term><listitem><para></para></listitem></varlistentry><varlistentry><term><command>delay on +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[time-delay]</option></term><listitem><para>is in seconds -- (integer|decimal)[>=0]</para></listitem></varlistentry></variablelist></section> <section><title>depth </title><para> Slab and Depth together control the percentage of the molecule to be displayed based on clipping planes. "slab on" turns slab/depth on. "depth 50" shows the front 50% of the molecule. "depth 25" show the front 25% of the molecule. -</para><variablelist><title>Examples</title><varlistentry><term>depth [slab-percent] -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>depth [slab-percent] +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[slab-percent]</option></term><listitem><para>is an (integer)[0 to 100]</para></listitem></varlistentry></variablelist></section> <section><title>dots </title><para>Turns Van der Waals radii dotted surface on/off. -</para><variablelist><title>Examples</title><varlistentry><term>dots on/off -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>dots on/off +</command></term><listitem><para></para></listitem></varlistentry></variablelist></section> <section><title>echo </title><para>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). -</para><variablelist><title>Examples</title><varlistentry><term>echo (string) -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>echo (string) +</command></term><listitem><para></para></listitem></varlistentry></variablelist></section> <section><title>exit </title><para> 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. @@ -115,70 +115,70 @@ <section><title>font </title><para>Sets font size and information in labels and other text-bearing elements. -</para><variablelist><title>Examples</title><varlistentry><term>font [object-with-text] [font size] [font face]{default: SansSerif} [font style]{default: Plain} -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>font [object-with-text] [font size] [font face]{default: SansSerif} [font style]{default: Plain} +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[object-with-text]</option></term><listitem><para>is axes, echo, hover, label, monitor, unitcell</para></listitem></varlistentry><varlistentry><term><option>[font size]</option></term><listitem><para>is approximately the same as Rasmol -- (integer)[6 to 63]</para></listitem></varlistentry><varlistentry><term><option>[font face]</option></term><listitem><para>is SERIF, SANSSERIF, or MONOSPACED </para></listitem></varlistentry><varlistentry><term><option>[font style]</option></term><listitem><para>is PLAIN, BOLD, ITALIC, or BOLDITALIC</para></listitem></varlistentry></variablelist></section> <section><title>frame or model </title><para>Sets the current animation frame. -</para><variablelist><title>Examples</title><varlistentry><term>frame [frame-option] -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>frame [frame-option] +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[frame-option]</option></term><listitem><para>is a frame option: -- (integer), "next", "nextwrap", "none", "play", "prev", "prevwrap", "revplay", "rewind"</para></listitem></varlistentry></variablelist></section> <section><title>hbonds </title><para>Hydrogen bonds can be turned on or off, colored, and given custom width in angstroms. -</para><variablelist><title>Examples</title><varlistentry><term>hbonds -</term><listitem><para></para></listitem></varlistentry><varlistentry><term>hbonds [width-by-Rasmol] -</term><listitem><para></para></listitem></varlistentry><varlistentry><term>hbonds [width-in-angstroms] -</term><listitem><para></para></listitem></varlistentry><varlistentry><term>hbonds on/off -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>hbonds +</command></term><listitem><para></para></listitem></varlistentry><varlistentry><term><command>hbonds [width-by-Rasmol] +</command></term><listitem><para></para></listitem></varlistentry><varlistentry><term><command>hbonds [width-in-angstroms] +</command></term><listitem><para></para></listitem></varlistentry><varlistentry><term><command>hbonds on/off +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[width-in-angstroms]</option></term><listitem><para>is a (decimal)[<2]</para></listitem></varlistentry><varlistentry><term><option>[width-by-Rasmol]</option></term><listitem><para>is in 1/250ths of an Angstrom (deprecated) -- (integer)[<500]</para></listitem></varlistentry></variablelist></section> <section><title>hover </title><para>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. -</para><variablelist><title>Examples</title><varlistentry><term>hover [on/off or a string ] -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>hover [on/off or a string ] +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[on/off or a string ]</option></term><listitem><para>is on, off, or a string -- on, off, (string)</para></listitem></varlistentry></variablelist></section> <section><title>label or labels </title><para>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. -</para><variablelist><title>Examples</title><varlistentry><term>label [on/off or a string ] -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>label [on/off or a string ] +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[on/off or a string ]</option></term><listitem><para>is on, off, or a string -- on, off, (string)</para></listitem></varlistentry></variablelist></section> <section><title>load </title><para> Loads the specified file or URL. Jmol automatically determines file type based upon the contents of the file. Therefore, the format parameter is ignored. It is allowed for backward compatibility with RasMol/Chime. -</para><variablelist><title>Examples</title><varlistentry><term>load [file name] -</term><listitem><para></para></listitem></varlistentry><varlistentry><term>load [param-ignored] [file name] -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>load [file name] +</command></term><listitem><para></para></listitem></varlistentry><varlistentry><term><command>load [param-ignored] [file name] +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[file name]</option></term><listitem><para>is a model filename or URL -- (string)</para></listitem></varlistentry><varlistentry><term><option>[param-ignored]</option></term><listitem><para>is for Rasmol/chime compatibility; ignored -- (string)</para></listitem></varlistentry></variablelist></section> <section><title>loop </title><para>Causes the script to restart at the beginning, with an optional time delay. -</para><variablelist><title>Examples</title><varlistentry><term>loop [time-delay] -</term><listitem><para></para></listitem></varlistentry><varlistentry><term>loop on -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>loop [time-delay] +</command></term><listitem><para></para></listitem></varlistentry><varlistentry><term><command>loop on +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[time-delay]</option></term><listitem><para>is in seconds -- (integer|decimal)[>=0]</para></listitem></varlistentry></variablelist></section> <section><title>mesh </title><para>A mesh is similar to a strand, but is more the quality of a loosely woven fabric. -</para><variablelist><title>Examples</title><varlistentry><term>mesh [mesh-radius] -</term><listitem><para></para></listitem></varlistentry><varlistentry><term>mesh on/off{default: on} -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>mesh [mesh-radius] +</command></term><listitem><para></para></listitem></varlistentry><varlistentry><term><command>mesh on/off{default: on} +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[mesh-radius]</option></term><listitem><para>is the overall radius of the mesh -- (decimal)[<=40]</para></listitem></varlistentry></variablelist></section> <section><title>monitor or measure </title><para> Renders a measurement between the specified atoms. -</para><variablelist><title>Examples</title><varlistentry><term>monitor [atom-number] [atom-number] -</term><listitem><para>Two atoms specify a distance measurement. -</para></listitem></varlistentry><varlistentry><term>monitor [atom-number] [atom-number] [atom-number] -</term><listitem><para>Three atoms specify an angle measurement. -</para></listitem></varlistentry><varlistentry><term>monitor [atom-number] [atom-number] [atom-number] [atom-number] -</term><listitem><para>Four atoms specify a dihedral angle measurement. -</para></listitem></varlistentry><varlistentry><term>monitor on/off{default: on} -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>monitor [atom-number] [atom-number] +</command></term><listitem><para>Two atoms specify a distance measurement. +</para></listitem></varlistentry><varlistentry><term><command>monitor [atom-number] [atom-number] [atom-number] +</command></term><listitem><para>Three atoms specify an angle measurement. +</para></listitem></varlistentry><varlistentry><term><command>monitor [atom-number] [atom-number] [atom-number] [atom-number] +</command></term><listitem><para>Four atoms specify a dihedral angle measurement. +</para></listitem></varlistentry><varlistentry><term><command>monitor on/off{default: on} +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[atom-number]</option></term><listitem><para>is the sequential number assigned to the atom -- (integer)</para></listitem></varlistentry></variablelist></section> <section><title>moveto </title><para>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. -</para><variablelist><title>Examples</title><varlistentry><term>moveto [time-in-seconds] [coord-value] [coord-value] [coord-value] [cw-rotation-deg] -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>moveto [time-in-seconds] [coord-value] [coord-value] [coord-value] [cw-rotation-deg] +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[time-in-seconds]</option></term><listitem><para>is in (seconds)</para></listitem></varlistentry><varlistentry><term><option>[coord-value]</option></term><listitem><para>is a (decimal)</para></listitem></varlistentry><varlistentry><term><option>[cw-rotation-deg]</option></term><listitem><para>is a (decimal)</para></listitem></varlistentry></variablelist></section> <section><title>move </title><para>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. -</para><variablelist><title>Examples</title><varlistentry><term>move [x-rotation] [y-rotation] [z-rotation] [zoom-factor] [x-translation] [y-translation] [z-translation] [slab-cutoff] [seconds-total] [move-frames-per-second]{default: 30} [maximum-acceleration]{default: 5} -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>move [x-rotation] [y-rotation] [z-rotation] [zoom-factor] [x-translation] [y-translation] [z-translation] [slab-cutoff] [seconds-total] [move-frames-per-second]{default: 30} [maximum-acceleration]{default: 5} +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[x-rotation]</option></term><listitem><para>is the degrees of rotation about x -- (integer)</para></listitem></varlistentry><varlistentry><term><option>[y-rotation]</option></term><listitem><para>is the degrees of rotation about y -- (integer)</para></listitem></varlistentry><varlistentry><term><option>[z-rotation]</option></term><listitem><para>is the degrees of rotation about z -- (integer)</para></listitem></varlistentry><varlistentry><term><option>[zoom-factor]</option></term><listitem><para>is a scaling factor -- (integer)</para></listitem></varlistentry><varlistentry><term><option>[x-translation]</option></term><listitem><para>is the distance offset along x -- (integer)</para></listitem></varlistentry><varlistentry><term><option>[y-translation]</option></term><listitem><para>is the distance offset along y -- (integer)</para></listitem></varlistentry><varlistentry><term><option>[z-translation]</option></term><listitem><para>is the distance offset along z -- (integer)</para></listitem></varlistentry><varlistentry><term><option>[slab-cutoff]</option></term><listitem><para>is the cutoff for the slab display -- (integer)</para></listitem></varlistentry><varlistentry><term><option>[seconds-total]</option></term><listitem><para>is the amount of time to wait -- (decimal)</para></listitem></varlistentry><varlistentry><term><option>[move-frames-per-second]</option></term><listitem><para>is the frames per second to move -- (integer)</para></listitem></varlistentry><varlistentry><term><option>[maximum-acceleration]</option></term><listitem><para>is the maximum acceleration -- (integer)</para></listitem></varlistentry></variablelist></section> <section><title>quit </title><para> In the current release of Jmol, quit is synonymous with exit. This is inconsistent with RasMol, where quit means to exit the program. @@ -194,143 +194,143 @@ <section><title>restrict </title><para> Selects the atoms identified by expression and hides all atoms and bonds which are outside the selection set. -</para><variablelist><title>Examples</title><varlistentry><term>restrict [atom-expression] -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>restrict [atom-expression] +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[atom-expression]</option></term><listitem><para>is any expression that evaluates to a set of atoms -- (atom-expression)</para></listitem></varlistentry></variablelist></section> <section><title>ribbon or ribbons </title><para> 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. -</para><variablelist><title>Examples</title><varlistentry><term>ribbon [ribbon-radius] -</term><listitem><para>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). -</para></listitem></varlistentry><varlistentry><term>ribbon on/off{default: on} -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>ribbon [ribbon-radius] +</command></term><listitem><para>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). +</para></listitem></varlistentry><varlistentry><term><command>ribbon on/off{default: on} +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[ribbon-radius]</option></term><listitem><para>is half of the overall width of the ribbon -- (decimal)[<=40]</para></listitem></varlistentry></variablelist></section> <section><title>rocket or rockets </title><para>Creates a "rocket" cartoon. -</para><variablelist><title>Examples</title><varlistentry><term>rocket _rocket_radius -</term><listitem><para></para></listitem></varlistentry><varlistentry><term>rocket on/off{default: on} -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>rocket _rocket_radius +</command></term><listitem><para></para></listitem></varlistentry><varlistentry><term><command>rocket on/off{default: on} +</command></term><listitem><para></para></listitem></varlistentry></variablelist></section> <section><title>rotate </title><para>Rotates the model the specified angle about the specified axis. Integer values specify degrees. -</para><variablelist><title>Examples</title><varlistentry><term>rotate [x or y or z] [number-of-degrees] -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>rotate [x or y or z] [number-of-degrees] +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[x or y or z]</option></term><listitem><para>is x, y, z</para></listitem></varlistentry><varlistentry><term><option>[number-of-degrees]</option></term><listitem><para>is the number of degrees -- (integer)</para></listitem></varlistentry></variablelist></section> <section><title>script or source </title><para> 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. -</para><variablelist><title>Examples</title><varlistentry><term>script [file-name] -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>script [file-name] +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[file-name]</option></term><listitem><para>is any valid filename or URL -- (string)</para></listitem></varlistentry></variablelist></section> <section><title>select </title><para> Selects the atoms identified by the expression. If no expression is given then all atoms are selected. -</para><variablelist><title>Examples</title><varlistentry><term>select [atom-expression] -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>select [atom-expression] +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[atom-expression]</option></term><listitem><para>is any expression that evaluates to a set of atoms -- (atom-expression)</para></listitem></varlistentry></variablelist></section> <section><title>set (bond styles) </title><para>This group of commands sets the appearance of various optional bond effects for the model. -</para><variablelist><title>Examples</title><varlistentry><term>set bondmode AND -</term><listitem><para>When script commands affect a set of atoms, BOTH atoms must be in the set for the bonds between them to also be affected. -</para></listitem></varlistentry><varlistentry><term>set bondmode OR -</term><listitem><para>When script commands affect a set of atoms, EITHER atom may be in the set for the bonds also to be affected. -</para></listitem></varlistentry><varlistentry><term>set bonds on/off -</term><listitem><para>In some file formats (.mol files, for example) the connection data may indicate the bond type--single, double, triple, or quadruple. The bonds flag determines whether or not multiple bonds are displayed. Set this flag off if you want all bonds to appear as single bonds. -</para></listitem></varlistentry><varlistentry><term>set hbonds -</term><listitem><para>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. -</para></listitem></varlistentry><varlistentry><term>set hbonds BACKBONE -</term><listitem><para></para></listitem></varlistentry><varlistentry><term>set hbonds SIDECHAIN -</term><listitem><para></para></listitem></varlistentry><varlistentry><term>set ssbonds -</term><listitem><para>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. -</para></listitem></varlistentry><varlistentry><term>set ssbonds BACKBONE -</term><listitem><para></para></listitem></varlistentry><varlistentry><term>set ssbonds SIDECHAIN -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>set bondmode AND +</command></term><listitem><para>When script commands affect a set of atoms, BOTH atoms must be in the set for the bonds between them to also be affected. +</para></listitem></varlistentry><varlistentry><term><command>set bondmode OR +</command></term><listitem><para>When script commands affect a set of atoms, EITHER atom may be in the set for the bonds also to be affected. +</para></listitem></varlistentry><varlistentry><term><command>set bonds on/off +</command></term><listitem><para>In some file formats (.mol files, for example) the connection data may indicate the bond type--single, double, triple, or quadruple. The bonds flag determines whether or not multiple bonds are displayed. Set this flag off if you want all bonds to appear as single bonds. +</para></listitem></varlistentry><varlistentry><term><command>set hbonds +</command></term><listitem><para>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. +</para></listitem></varlistentry><varlistentry><term><command>set hbonds BACKBONE +</command></term><listitem><para></para></listitem></varlistentry><varlistentry><term><command>set hbonds SIDECHAIN +</command></term><listitem><para></para></listitem></varlistentry><varlistentry><term><command>set ssbonds +</command></term><listitem><para>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. +</para></listitem></varlistentry><varlistentry><term><command>set ssbonds BACKBONE +</command></term><listitem><para></para></listitem></varlistentry><varlistentry><term><command>set ssbonds SIDECHAIN +</command></term><listitem><para></para></listitem></varlistentry></variablelist></section> <section><title>set (colors) </title><para>The set color command sets the scheme by which atoms are colored. -</para><variablelist><title>Examples</title><varlistentry><term>set color JMOL -</term><listitem><para></para></listitem></varlistentry><varlistentry><term>set color RASMOL -</term><listitem><para></para></listitem></varlistentry><varlistentry><term>set color [RGB-color] -</term><listitem><para></para></listitem></varlistentry><varlistentry><term>set color [color-scheme] -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>set color JMOL +</command></term><listitem><para></para></listitem></varlistentry><varlistentry><term><command>set color RASMOL +</command></term><listitem><para></para></listitem></varlistentry><varlistentry><term><command>set color [RGB-color] +</command></term><listitem><para></para></listitem></varlistentry><varlistentry><term><command>set color [color-scheme] +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[RGB-color]</option></term><listitem><para>is a name of a color or a color triple, eg [255,0,255] -- (color)</para></listitem></varlistentry><varlistentry><term><option>[color-scheme]</option></term><listitem><para>is to color based on a scheme -- (color), amino, chain, formalCharge, partialCharge, shapely, structure, NONE</para></listitem></varlistentry></variablelist></section> <section><title>set (highlights) </title><para>This command group allows for annotation and highlighting of atoms in terms of labels and "halos." -</para><variablelist><title>Examples</title><varlistentry><term>set debugscript on/off -</term><listitem><para>Turns on and off debugging (going to a JavaScript message callback). -</para></listitem></varlistentry><varlistentry><term>set display NORMAL -</term><listitem><para>Turns off selection halos -</para></listitem></varlistentry><varlistentry><term>set display SELECTED -</term><listitem><para>Sets the option ON to dispay a "halo" around atoms when they are or become selected as a way of highlighting specific atoms. -</para></listitem></varlistentry><varlistentry><term>set echo OFF -</term><listitem><para>Turns off all three echo texts. -</para></listitem></varlistentry><varlistentry><term>set echo [vertical-position] [horizontal-position]{default: center for top and middle; left for bottom} -</term><listitem><para>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. -</para></listitem></varlistentry><varlistentry><term>set fontsize [font size]{default: 8} -</term><listitem><para>Sets the font size (for what?) -</para></listitem></varlistentry><varlistentry><term>set frank on/off -</term><listitem><para>Determines whether or not "Jmol" is indicated in the bottom right corner of the window. -</para></listitem></varlistentry><varlistentry><term>set labeloffset [x-offset] [y-offset] -</term><listitem><para>Sets the label offset relative to the atom being labeled. -</para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>set debugscript on/off +</command></term><listitem><para>Turns on and off debugging (going to a JavaScript message callback). +</para></listitem></varlistentry><varlistentry><term><command>set display NORMAL +</command></term><listitem><para>Turns off selection halos +</para></listitem></varlistentry><varlistentry><term><command>set display SELECTED +</command></term><listitem><para>Sets the option ON to dispay a "halo" around atoms when they are or become selected as a way of highlighting specific atoms. +</para></listitem></varlistentry><varlistentry><term><command>set echo OFF +</command></term><listitem><para>Turns off all three echo texts. +</para></listitem></varlistentry><varlistentry><term><command>set echo [vertical-position] [horizontal-position]{default: center for top and middle; left for bottom} +</command></term><listitem><para>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. +</para></listitem></varlistentry><varlistentry><term><command>set fontsize [font size]{default: 8} +</command></term><listitem><para>Sets the font size (for what?) +</para></listitem></varlistentry><varlistentry><term><command>set frank on/off +</command></term><listitem><para>Determines whether or not "Jmol" is indicated in the bottom right corner of the window. +</para></listitem></varlistentry><varlistentry><term><command>set labeloffset [x-offset] [y-offset] +</command></term><listitem><para>Sets the label offset relative to the atom being labeled. +</para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[font size]</option></term><listitem><para>is approximately the same as Rasmol -- (integer)[6 to 63]</para></listitem></varlistentry><varlistentry><term><option>[x-offset]</option></term><listitem><para>is the x-offset -- (integer)</para></listitem></varlistentry><varlistentry><term><option>[y-offset]</option></term><listitem><para>is the y-offset -- (integer)</para></listitem></varlistentry><varlistentry><term><option>[vertical-position]</option></term><listitem><para>is one of the following: -- "top", "middle", "bottom"</para></listitem></varlistentry><varlistentry><term><option>[horizontal-position]</option></term><listitem><para>is one of the following: -- "left", "center", "middle"</para></listitem></varlistentry></variablelist></section> <section><title>set (lighting and perspective) </title><para>This commands in this group determine the overall lighting effects, size, and rotation for the model. -</para><variablelist><title>Examples</title><varlistentry><term>set ambient [ambient-percent] -</term><listitem><para>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. -</para></listitem></varlistentry><varlistentry><term>set diffuse [diffuse-percent] -</term><listitem><para>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. -</para></listitem></varlistentry><varlistentry><term>set perspectivedepth on/off{default: on} -</term><listitem><para>Sets perspective depth on or off. OFF is required for proper function of absolute scale (set scale3d x). -</para></listitem></varlistentry><varlistentry><term>set scale3d [viewing-distance] -</term><listitem><para>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. -</para></listitem></varlistentry><varlistentry><term>set specpower [specular-power] -</term><listitem><para>Sets the density of dots in the specular reflection. -</para></listitem></varlistentry><varlistentry><term>set specular [specular-percent] -</term><listitem><para>Sets the size of the apparent reflection from a light source. set specular 0 turns off this effect. -</para></listitem></varlistentry><varlistentry><term>set spin -</term><listitem><para>Sets the spin axis and rate. Note that the axes referred to are the fixed axes of the window, not the cartesian axes of the molecular coordinates. Thus, regardless of how the molecule has been rotated by the user or using the move command, x is always the horizontal axis, y is always the vertical axis, and z is always the axis directed toward the user. The spin rate, in degrees per second, determines how fast the model rotates; the number of frames per second determines how smoothly the model rotates. No actual spinning occurs until the spin ON command is issued or the user turns spinning on using the mouse menu. -</para></listitem></varlistentry><varlistentry><term>set spin FPS [frames-per-second] -</term><listitem><para></para></listitem></varlistentry><varlistentry><term>set spin [x or y or z] [degrees-per-second] -</term><listitem><para></para></listitem></varlistentry></variablelist></section> +</para><variablelist><title>Examples</title><varlistentry><term><command>set ambient [ambient-percent] +</command></term><listitem><para>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. +</para></listitem></varlistentry><varlistentry><term><command>set diffuse [diffuse-percent] +</command></term><listitem><para>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. +</para></listitem></varlistentry><varlistentry><term><command>set perspectivedepth on/off{default: on} +</command></term><listitem><para>Sets perspective depth on or off. OFF is required for proper function of absolute scale (set scale3d x). +</para></listitem></varlistentry><varlistentry><term><command>set scale3d [viewing-distance] +</command></term><listitem><para>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. +</para></listitem></varlistentry><varlistentry><term><command>set specpower [specular-power] +</command></term><listitem><para>Sets the density of dots in the specular reflection. +</para></listitem></varlistentry><varlistentry><term><command>set specular [specular-percent] +</command></term><listitem><para>Sets the size of the apparent reflection from a light source. set specular 0 turns off this effect. +</para></listitem></varlistentry><varlistentry><term><command>set spin +</command></term><listitem><para>Sets the spin axis and rate. Note that the axes referred to are the fixed axes of the window, not the cartesian axes of the molecular coordinates. Thus, regardless of how the molecule has been rotated by the user or using the move command, x is always the horizontal axis, y is always the vertical axis, and z is always the axis directed toward the user. The spin rate, in degrees per second, determines how fast the model rotates; the number of frames per second determines how smoothly the model rotates. No actual spinning occurs until the spin ON command is issued or the user turns spinning on using the mouse menu. +</para></listitem></varlistentry><varlistentry><term><command>set spin FPS [frames-per-second] +</command></term><listitem><para></para></listitem></varlistentry><varlistentry><term><command>set spin [x or y or z] [degrees-per-second] +</command></term><listitem><para></para></listitem></varlistentry></variablelist><variablelist><title>Definitions</title><varlistentry><term><option>[specular-percent]</option></term><listitem><para>is an (integer)[0 to 100]</para></listitem></varlistentry><varlistentry><term><option>[specular-power]</option></term><listitem><para>is an (integer)</para></listitem></varlistentry><varlistentry><term><option>[ambient-percent]</option></term><listitem><para>is an (integer)[0 to 100]</para></listitem></varlistentry><varlistentry><term><option>[diffuse-percent]</option></term><listitem><para>is an (integer)[0 to 100]</para></listitem></varlistentry><varlistentry><term><option>[viewing-distance]</option></term><listitem><para>is the apparent distance from the model to the user in arbitrary units -- (integer), (decimal)</para></listitem></varlistentry><varlistentry><term><option>[x or y or z]</option></term><listitem><para>is x, y, z</para></listitem></varlistentry><varlistentry><term><option>[degrees-per-second]</option></term><listitem><para>is an (integer)</para></listitem></varlistentry><varlistentry><term><option>[frames-per-second]</option></term><listitem><para>is an (integer)</para></listitem></varlistentry></variablelist></section> <section><title>set (visibility) </title><para>This command group turns on or off specific sets of atoms and axes/cell-related options. -</para><variablelist><title>Examples</title><varlistentry><term>set axes [line-width-or-type] -</term><listitem><para>Turns on or off displayed axes, and determines their line style and line width (as a decimal number, in Angstroms). -</para></listitem></varlistentry><varlistentry><term>set boundbox [line-width-or-type] -</term><listitem><p... 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