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[Jmol-commits] CVS: Jmol/doc/source/guide scriptCommands.docbook.xml,NONE,1.1 scripts.docbook.xml,1.3,1.4
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From: Egon W. <eg...@us...> - 2004-11-05 14:25:39
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Update of /cvsroot/jmol/Jmol/doc/source/guide In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv32471/guide Modified Files: scripts.docbook.xml Added Files: scriptCommands.docbook.xml Log Message: Based new scripting documentation on Bob's website. It includes cmd name, cmd description and the examples. Defs and links will follow later --- NEW FILE: scriptCommands.docbook.xml --- <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> <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> <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> <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> <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> <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> <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> <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> <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> <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> <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> <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> <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. </para><variablelist><title>Examples</title></variablelist></section> <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> <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> <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> <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> <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> <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> <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> <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> <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> <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> <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> <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. </para><variablelist><title>Examples</title></variablelist></section> <section><title>refresh </title><para> Forces a screen repaint during script execution. (Unnecessary, and thus deprecated.) </para><variablelist><title>Examples</title></variablelist></section> <section><title>reset </title><para>Resets molecule to its original position: zoom 100; center; translate x 0; translate y 0; </para><variablelist><title>Examples</title></variablelist></section> <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> <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> <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> <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> <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> <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> <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> <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> <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> <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> <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><para>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. </para></listitem></varlistentry><varlistentry><term>set hetero on/off </term><listitem><para>Turns on and off display of non-hydrogen atoms. </para></listitem></varlistentry><varlistentry><term>set hydrogen on/off </term><listitem><para>Turns on and off display of hydrogen atoms. </para></listitem></varlistentry><varlistentry><term>set monitor [linewidth-pixels] </term><listitem><para>Sets the width of the monitor line in pixels. </para></listitem></varlistentry><varlistentry><term>set monitor on/off </term><listitem><para>Turns on and off the distance, angle, dihedral measurement monitor. </para></listitem></varlistentry><varlistentry><term>set solvent [probe-radius-Rasmol] </term><listitem><para></para></listitem></varlistentry><varlistentry><term>set solvent [probe-radius-in-angstroms]{default: 1.2} </term><listitem><para>Sets the radius of the solvent "ball" that would run around the structure defining its outline. </para></listitem></varlistentry><varlistentry><term>set solvent on/off </term><listitem><para>Turns on and off display of solvent atoms and solvent "probe" that can be displayed using dots. </para></listitem></varlistentry><varlistentry><term>set strands [strand-count]{default: 5} </term><listitem><para>Sets the number of strands to display. </para></listitem></varlistentry><varlistentry><term>set unitcell [line-width-or-type] </term><listitem><para>Turns on or off the unit cell for crystal structures, and determines its line style and line width (as a decimal number, in Angstroms). </para></listitem></varlistentry></variablelist></section> <section><title>show </title><para>"show" sends information about the model to the messageCallback function and to the Java Console </para><variablelist><title>Examples</title><varlistentry><term>show model </term><listitem><para>Delivers the total number of models in the set. </para></listitem></varlistentry><varlistentry><term>show orientation </term><listitem><para>Delivers the orientation of the model. Output consists of both a "moveTo" command and an alternative sequence of "reset; rotate z; rotate y; rotate z" commands that would result in the current orientation. Thus, this command allows reading and restoring specific user-specified orientations. </para></listitem></varlistentry><varlistentry><term>show pdbheader </term><listitem><para>Delivers the PDB file header. </para></listitem></varlistentry></variablelist></section> <section><title>slab </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. "slab 50" shows the back 50% of the molecule. "slab 25" show the back 25% of the molecule. </para><variablelist><title>Examples</title><varlistentry><term>slab [slab-percent] </term><listitem><para></para></listitem></varlistentry><varlistentry><term>slab on/off </term><listitem><para></para></listitem></varlistentry></variablelist></section> <section><title>spin </title><para>Starts and stops the molcule spinning. </para><variablelist><title>Examples</title></variablelist></section> <section><title>ssbonds </title><para>Cisteine disulfide bonds can be turned on or off, colored, and given customized widths in Angstroms. </para><variablelist><title>Examples</title><varlistentry><term>ssbonds [width-Rasmol] </term><listitem><para></para></listitem></varlistentry><varlistentry><term>ssbonds [width-angstroms] </term><listitem><para></para></listitem></varlistentry><varlistentry><term>ssbonds on/off{default: on} </term><listitem><para></para></listitem></varlistentry></variablelist></section> <section><title>strands </title><para>Strands offer a representation the protein backbone or nucleic acid helix using lines. For proteins, control points are chosen midway between adjacent alpha carbons (or phosphorus atoms in nucleic acids). The strands are arranged perpendicular to the peptide plane. A hermite cubic curve is used to smoothly connect the points. </para><variablelist><title>Examples</title><varlistentry><term>strands [strand-radius] </term><listitem><para>Normally, strands vary in width according to the amino acid atom positions. This command sets the radius of the set of strands to be a constant value (a decimal, in Angstroms). </para></listitem></varlistentry><varlistentry><term>strands on/off{default: on} </term><listitem><para></para></listitem></varlistentry></variablelist></section> <section><title>trace </title><para>A "trace" is a smooth curve through the center of the carbonyl carbon-alpha carbon bonds of a peptide or the ribose 1-O-P bond. </para><variablelist><title>Examples</title><varlistentry><term>trace [trace-radius] </term><listitem><para></para></listitem></varlistentry><varlistentry><term>trace on/off{default: on} </term><listitem><para></para></listitem></varlistentry></variablelist></section> <section><title>translate </title><para> Moves the molecule along the specified axes according to the amount specified by value. Value ranges from -100 to 100, and represents the percentage of the display window. Negative values move to the left (for the x axis) and down (for the y axis). A value of 100 will move the molecule completely out of the window. A value of 50 will move the center of the molecule to the edge of the window. </para><variablelist><title>Examples</title><varlistentry><term>translate [x or y or z] [percent-translation] </term><listitem><para></para></listitem></varlistentry></variablelist></section> <section><title>vector or vectors </title><para>Draws vectors arising from vibrational mode data. </para><variablelist><title>Examples</title><varlistentry><term>vector [diameter-pixels] </term><listitem><para></para></listitem></varlistentry><varlistentry><term>vector [radius-in-angstroms] </term><listitem><para></para></listitem></varlistentry><varlistentry><term>vector on/off </term><listitem><para></para></listitem></varlistentry><varlistentry><term>vector scale [vector-scale] </term><listitem><para>Adjusts the scale of the vector independently of the vibration. </para></listitem></varlistentry></variablelist></section> <section><title>vibration </title><para>Adjusts the scale of the vibration independently of the vector. </para><variablelist><title>Examples</title><varlistentry><term>vibration scale [vibration-scale] </term><listitem><para></para></listitem></varlistentry></variablelist></section> <section><title>wireframe </title><para>Wireframe refers to the bonds drawn between the atoms. A boolean value of ON draws the selected bonds as lines. Alternatively, a numeric value may be used to specify the radius of the bonds. A decimal value such as 0.2 or 0.4 specifies Angstroms. </para><variablelist><title>Examples</title><varlistentry><term>wireframe [radius-Rasmol] </term><listitem><para></para></listitem></varlistentry><varlistentry><term>wireframe [radius-in-angstroms] </term><listitem><para></para></listitem></varlistentry><varlistentry><term>wireframe on/off{default: on} </term><listitem><para></para></listitem></varlistentry></variablelist></section> <section><title>zap </title><para> Clears the currently loaded molecule. RasMol forces you to zap prior to loading a new molecule. Jmol currently does not have this restriction and does not enforce it. </para><variablelist><title>Examples</title></variablelist></section> <section><title>zoom </title><para> Allows you to enlarge (or shrink) the molecule. "zoom off" disables zooming, while "zoom on" turns it back on to the current zoom setting. A percentage value specifies the zoom relative to 100, the default value. The default zoom in Jmol is calculated so that all molecules are completely visible on the screen through all rotations using the default vanderWaals rendering percentage. </para><variablelist><title>Examples</title><varlistentry><term>zoom [percent-zoom] </term><listitem><para></para></listitem></varlistentry><varlistentry><term>zoom on/off </term><listitem><para></para></listitem></varlistentry></variablelist></section> Index: scripts.docbook.xml =================================================================== RCS file: /cvsroot/jmol/Jmol/doc/source/guide/scripts.docbook.xml,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- scripts.docbook.xml 20 May 2003 14:04:50 -0000 1.3 +++ scripts.docbook.xml 5 Nov 2004 14:25:29 -0000 1.4 @@ -55,711 +55,11 @@ </para> <section> <title>RasMol/Chime commands</title> - <section> - <title>animate play|revplay|rewind|next|prev|nextwrap|prevwrap|frame - </title> - <para> - This is a Jmol specific command that is not available in - RasMol/Chime. - </para> - <para> - The animate command provides basic control over files which - contain multiple chemical frames. This mechanism can be used - to play short movies of reactions, vibrations, etc. - </para> - <para> - The <command>play</command> and <command>revplay</command> commands - will play all frames in the file, either in forward or reverse. The - frame rate is currently limited by a) the rendering speed of the - system, and b) with a maximum of 10 frames per second. - </para> - <para> - The <command>next</command>, <command>prev</command>, <command> - nextwrap</command>, <command>prevwrap</command> and <command> - rewind</command> commands allow one to step through a file frame - by frame. <command>nextwrap</command>/<command>prevwrap</command> - will wrap around to the first/last frame. - </para> - <para> - The <command>frame</command> command takes an integer argument - which specifies the frame number to show. - </para> - <para> - Additional work will be done on this command for the next - release of Jmol, allowing additional control over display frame - rate, interpolated frames, etc. - </para> - </section> - <section> - <title>background <color></title> - <para> - Sets color of the background. See Color Specification. - </para> - </section> - <section> - <title>center {<expression>}</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> - </section> - <section> - <title>color {<object>} <color></title> - <para> - Colors the object with the specified color. If no object is given - then atom is assumed. Currently supported objects are - <varname>atoms</varname>, <varname>bonds</varname>, - <varname>labels</varname> and <varname>axes</varname>. - </para> - </section> - <section> - <title>cpk <boolean> | cpk <value></title> - <para> - Renders selected atoms as shaded spheres. - </para> - <para> - A boolean value renders the spheres with the vanderWaals radius. - The current jmol implementation does a poor job of rendering - these because the renderer does nothandle intersecting objects. - </para> - <para> - A decimal value specifies sphere radius in Angstroms. - </para> - <para> - A positive integer specifies sphere radius in RasMol units, - 1/250th of an Angstrom. - </para> - <para> - Jmol extension: - A negative integer specifies sphere radius as a percentage of - the vanderWaals radius. Thus, a value of -25 specifies that the - selected atoms should be rendered with a sphere radius of 25% - of the vanderWaals radius for that element. - </para> - <para> - cpk is synonymous with spacefill. - </para> - </section> - <section> - <title>define <variable> <expression></title> - <para> - defines the specified variable to the the atoms selected by - the expression; - </para> - </section> - <section> - <title>delay {<delaytime>}</title> - <para> - Chime extended command. - </para> - <para> - Causes the screen to refresh and the script to stop executing - for 'delaytime' seconds. Decimal values can be used to - represent fractions of seconds. If 'delaytime' is not specified - the default delay is 1 second. - </para> - </section> - <section> - <title>echo <string></title> - <para> - Prints the specified string to the console. (We need to find a - better place to send the output. Status line?) - </para> - </section> - <section> - <title>exit</title> - <para> - Stops execution of the current script. In the case of a script - which is being run as a child script, execution continues with - the parent. - </para> - <para> - For programmers, this is a 'return' statement. - </para> - </section> - <section> - <title>label <boolean> | label <string></title> - <para> - Allows you to specify a label to be shown with the selected atoms. - %a Atom Name - %b %t Protein B-Factor/Temperature - %c %s Protein chain - %e Element atomic symbol - %i Atom serial number - %m single letter amino acid code - %n 3 letter residue name - %r PDB residue number - </para> - </section> - <section> - <title>load {<format>} <filename | url></title> - <para> - Loads the specified file or URL. - </para> - <para> - 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> - </section> - <section> - <title>loop {<delaytime>}</title> - <para> - Chime extended command. - </para> - <para> - Causes the current script file to re-execute from the top after - 'delaytime' seconds. Default value for 'delaytime' is 1 second. - </para> - </section> - <section> - <title>monitor <number> <number> {<number>} {<number>}</title> - <para> - Renders a measurement between the specified atoms. - </para> - <para> - Two atoms specify a distance measurement. - </para> - <para> - Jmol extension: Three atoms specify an angle measurement. - </para> - <para> - Jmol extension: Four atoms specify a dihedral angle measurement. - </para> - </section> - <section> - <title>move <xRot> <yRot> <zRot> <zoom> - <xTrans> <yTrans> <zTrans> <slab> - <time> {<FPS>} {<MaxAccel>} - </title> - <para> - Chime extended command. - </para> - <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. - </para> - <para> - xRot, yRot, and zRot are rotations about the cartesian axes - in degrees. - </para> - <para> - Zoom specifies a zoom factor (there is a good chance this - is not currently implemented properly) - </para> - <para> - xTrans, yTrans, and zTrans are translations in the range - -100 to 100. - </para> - <para> - If you don't know what slab is, just put in a zero. see the - 'slab' command for more information. - </para> - <para> - 'time' is the total time in seconds for the movement. - </para> - <para> - FPS and MaxAccel control the animation rate. The default - values work fine, non-default values may not work at all. - If you need and/or want these to work, send us an email - and we will get it working. - </para> - </section> - <section> - <title>quit</title> - <para> - In the current release of Jmol, quit is synonymous with exit. - </para> - <para> - This is inconsistent with RasMol, where quit means to exit - the program. - </para> - </section> - <section> - <title>refresh</title> - <para> - Forces screen repaint during script execution. - (Frankly, I am not sure under what circumstances this would be - necessary?) - </para> - </section> - <section> - <title>reset</title> - <para> - Resets molecule to its original position: zoom 100; center; - translate x 0; translate y 0; - </para> - </section> - <section> - <title>restrict <expression></title> - <para> - Selects the atoms identified by expression and hides all atoms - and bonds which are outside the selection set. - </para> - </section> - <section> - <title>rotate <axis> <value></title> - <para> - Rotates the model the specified angle about the specified axis. - Integer values specify degrees. Decimal values specify radians. - </para> - </section> - <section> - <title>script <filename | url></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> - <para> - The command <function>source</function> is a synonym for - <function>script</function>. - </para> - </section> - <section> - <title>select {<expression>}</title> - <para> - Selects the atoms identified by the expression. - </para> - <para> - If no expression is given then all atoms are selected. - </para> - <tip> - <title>Displaying Selections</title> - <para> - RasMol does not hilite selections. To see selected atoms use - the command <function>set display selected</function> - </para> - </tip> - <note> - <title>Feedback Wanted</title> - <para> - The handling of selection hilites is a problem for Jmol. We are - torn between providing RasMol compatibility and useful visual - feedback to the user. - </para> - <para> - If you have suggestions on how this can be improved please let us know. - </para> - </note> - </section> - <section> - <title>set <parameter> {<value>}</title> - <para> - See separate section for set parameters. - </para> - </section> - <section> - <title>slab <boolean> | <percentage></title> - <para> - Slab mode provides a z-clipping plane that allows you to specify - the percentage of the molecule to be displayed. - </para> - <para> - A boolean parameter turns slabbing on or off. - </para> - <para> - A percentage from 0 to 100 controls the amount of the molecult - to be shown. A value of 0 shows nothing. A value of 100 shows - everything. A value of 50 shows the back 50% of the molecule. A - value of 25 shows the back quarte of the molecule. - </para> - <para> - (I have never seen the term slab used in this way before. As far - as I know, the term is only used in RasMol.) - </para> - </section> - <section> - <title>spacefill {<boolean>} | <value></title> - <para> - see cpk - </para> - </section> - <section> - <title>translate <axis> <value></title> - <para> - Moves the molecule along the specified axes according to the amount - specified by value. Value ranges from -100 to 100, and represents - the percentage of the display window. - Negative values move to the left (for the x axis) and down - (for the y axis). A value of 100 will move the - molecule completely out of the window. A value of 50 will move the - center of the molecule to the edge of the window. - </para> - <para> - (A translation along the z axis is defined in the RasMol - documentation. As far as I can tell, it does nothing. If anybody - knows anything different, please let us know.) - </para> - </section> - <section> - <title>wireframe {<boolean>} | <value></title> - <para> - In RasMol terminology, wireframe refers to the bonds drawn between - the atoms. A boolean value of 'on' draws the selected bonds as - lines. Alternatively, a numeric value may be used to specify - the radius of the bonds. A decimal value specifies Angstroms. - An integer value specifies RasMol units (1/250th Angstrom). - </para> - </section> - <section> - <title>zap</title> - <para> - Clears the currently loaded molecule. - </para> - <para> - RasMol forces you to 'zap' prior to loading a new molecule. Jmol - currently does not have this restriction and does not enforce it. - </para> - </section> - <section> - <title>zoom {<boolean>} | <percentage></title> - <para> - Allows you to enlarge (or shrink) the molecule. - </para> - <para> - A boolean value turns zooming on or off. - </para> - <para> - A percentage value specifies the zoom percentage. 100 is the default - value. The smallest acceptable value is 10. The largest acceptable - value is 500. (Note that these are arbitrary restrictions that - were put in for RasMol compatiblity. If someone wants to lift - these restrictions please let us know.) - </para> - <para> - The default size in Jmol is calculated so that all molecules are - completely visible on the screen through all rotations using the - default vanderWaals rendering percentage as defined in - Edit->Preferences... - </para> - </section> -</section> -<section> - <title>Set Parameters</title> - <section> - <title>set axes on | off</title> - <para> - Controls the display of cartesians axes with origin at the - center of the bounding box. - </para> - </section> - <section> - <title>set background <color></title> - <para> - Synonymous with the background command. - </para> - </section> - <section> - <title>set bondmode and | or</title> - <para> - Atom expressions are used to select atoms. The selection of bonds - is controled by the bondmode setting. When set to 'and', the - default, a bond is selected only if both atoms are selected. When - set to 'or' a bond is selected if either atom is selected. - </para> - <para> - You may want to select bonds in order to control their color - (color bonds <color>) or their size (wireframe 32). - </para> - </section> - <section> - <title>set bonds on | off</title> - <para> - Controls the display of double and triple bonds. When the setting - is off then all bonds are shown as single bonds. - </para> - <para> - Note that there are several factors which control rendering of - multiple bonds. 1) Whether or not the file contains bond - connection information. 2) whether or not Jmol calculates multiple - bonds 3) whether or not the bond setting is on or off (this setting) - 4) the size of the bonds. - </para> - <para> - Item 4 needs a little more explanation. RasMol only shows multiple - bonds if the radius of the bonds is <= 32 RasMol units - (32/250 = 0.128 Angstroms). Presumably this is done because - multiple bonds would look ugly if they were larger. - Jmol currently respects this for backward compatibility with - existing scripts. - </para> - </section> - <section> - <title>set boundbox on | off </title> - <para> - Controls rending of the bounding box which completely encloses the - molecule. The bounding box is defined by the minimum and maximum - coordinate values of the centers of the atoms along each of the - x, y and z axes. - </para> - </section> - <section> - <title>set display normal | selected</title> - <para> - RasMol does not hilite or change colors on selected atoms. - You can 'set display selected' to go to some wild color scheme. - Jmol implements this by using 'halos' around the selected atoms. - 'set display normal' turns off the halos. - </para> - <para> - This is a problem area for us and we would like feedback from - experienced users on how this should behave. We want to maintain - compatibility with existing RasMol/Chime scripts, - but we think that the visual - feedback of selection halos is good during script development. - We also think that new/inexperienced users would benefit from - using the halos. Any suggestions/ideas/feedback would be appreciated. - </para> - </section> - <section> - <title>set fontsize <value></title> - <para> - Sets the fontsize used for atom and monitor labels. - </para> - <para> - Jmol extension: A value of 0 specifies the Jmol default size. - The Jmol default size is calculated as a function of the atom - size. So small atoms use a small font and large atoms use a - large font. - </para> - <para> - This is another area where we would like user feedback on how - we can extend the functionality while maintaining backward - compatibility with existing RasMol/Chime scripts. - </para> - </section> - <section> - <title>set hetero on | off</title> - <para> - Controls the default selection behavior of heterogenous atoms - in protein molecules in .PDB files. When turned 'on' the command - 'select all' will include heterogenous atoms that are included - in the .PDB file. - </para> - <para> - See also: the predefined set 'hetero' and the - 'set hydrogen on | off' command. - </para> - </section> - <section> - <title>set hydrogen on | off</title> - <para> - Controls the default selection behavior of hydrogen atoms - in protein molecules in .PDB files. When turned 'on' the command - 'select all' will include hydrogen atoms that are included - in the .PDB file. - </para> - <para> - See also: 'set hetero on | off' command. - </para> - <para> - (But .PDB files do not usually include hydrogen atoms?) - </para> - </section> - <section> - <title>set monitor on | off</title> - <para> - In RasMol terminology, a 'monitor' is a distance measurement. - These are called 'measurements' in the Jmol menus. - This command controls the display of the numeric labels (for - distance, angle, or dihedral angle). That is, with - 'set monitor off' the lines will still be drawn, but the - measurement values will not be shown. - </para> - <para> - See also: monitor command - </para> - </section> -</section> -<section> - <title>Atom Expressions</title> <para> - Atom expressions are queries which specify selection criteria - for sets of atoms. They are used as parameters to several commands, - particularly 'select', 'restrict' and 'define'. + This documentation is autogenerated form the content on this website: + <ulink href="http://www.stolaf.edu/people/hansonr/jmol/docs/"/>. </para> - <para> - Most of the selection criteria are protein and .PDB file related. - If you have used RasMol then you know what these things are. And - all RasMol atom expressions should work. - </para> - <para> - The following are some examples using the select command: - select all - select * - select elemno=1 // selects hydrogens - select elemno=1 or elemno=6 or elemno=8 // H, C, O - </para> - <para> - The following are some more complicated protein-specific expressions: - select cys // cystines - select cys.CA // alpha carbons in cystines - select cys*A.CA // alpha carbons in cystines in chain A - select 1 // all atoms in residue 1 - select 1A.C? // all carbons in residue 1 of chain a - </para> - <section> - <title>boolean operators</title> - <para> - Boolean operators 'and', 'or' and 'not' can be used to combine - sets of selected atoms. These operators can be abbreviated as - '&', '|' and '!', respectively. - </para> - </section> - <section> - <title>comparison operators</title> - <para> - Comparisons can be made based upon a few selected atom attributes. - Comparisons are always of the form - <attribute> <comparator> <value> - </para> - <para> - Acceptable attributes are: - elemno (element number) - atomno (atom number) - radius (current spacefill radius in RasMol units) - temperature (protein .PDB anisotropic temperature value) - resno (protein .PDB residue number) - </para> - <para> - Comparators are: - = or == - <> or != or /= - <, <=, >=, > - </para> - </section> - <section> - <title>within(<distance>, <set>)</title> - <para> - The within function can be used to select all atoms that - are within a specified distance from any atoms in the - given set. Of course the he resulting set can be combined - using boolean operators to build more complex specifications. - </para> - <para> - If the distance contains a decimal point (dot) then the - number is interpreted as angstroms. If the distance is an - integer then the units are RasMol units. - </para> - <para> - // all atoms within 2 angstroms of a chlorine atom - select within(2.0, chlorine) - // all nitrogens more than 3 angstroms away from any carbon - select nitrogen & !within(3.0, carbon) - </para> - </section> -</section> -<section> - <title>Predefined Sets</title> - <para> - Predefined sets consist of 'all', 'none', 'selected', the element - names, and a number of protein .PDB specific sets. - </para> - <para> - 'all' and 'none' should be self-explanatory. 'selected' allows you - to use the currently selected set of atoms in a subsequent - atom expression. - </para> - <para> - Element names can be used instead of 'elemno=#'. Both singular - and plural forms of the element names may be used. The following - are all equivalent: - 'select hydrogen', 'select hydrogens', 'select elemno=1', - 'select elemno==1' - </para> - <para> - When working with protein molecules in .PDB files you can use - a number of predefined sets to select the atoms in amino acids - or selected groups of amino acids. - </para> - <para> - All three letter amino abbreviations work. There are also single - letter abbreviations which work. All are compatible with RasMol. - ala(a), arg(r), asn(n), asp(d), cys(c), glu(e), gln(q), gly(g), - his(h), ile(i), leu(l), lys(k), met(m), phe(f), pro(p), ser(s), - thr(t), trp(w), tyr(y), val(v) - </para> - <para> - The following sets are defined as in RasMol: at, acidic, acyclic, - aliphatic, alpha, amino, aromatic, backbone, basic, bonded, - buried, cg, charged, cyclic, cystine, helix, hetero, hydrogen, - hydrophobic, ions, large, ligand, medium, neutral, nucleic, - polar, protein, purine, pyrimidine, sheet, sidechain, small, - solvent, surface, turn, water. - </para> -</section> -<section> - <title>Rendering Commands</title> - <section> - <title>set shadows</title> - <para> - <cmdsynopsis> - <command>set shadows</command> - <group> - <arg>true</arg> - <arg>false</arg> - </group> - </cmdsynopsis> - </para> - <para> - Turns on shading when rendering. - </para> - </section> -</section> -<section> - <title>Export Commands</title> - <para> </para> -</section> -<section> - <title>Misc. Commands</title> - <para> </para> -</section> -<section> - <title>Colour Schemes</title> - <para> </para> -</section> -<section> - <title>Parameters</title> - <section> - <title>shadows</title> - <para> - <cmdsynopsis> - <command>set shadows</command> - <group> - <arg>true</arg> - <arg>false</arg> - </group> - </cmdsynopsis> - </para> - <para> - Turns on shading when rendering. - </para> - </section> - <section> - <title>autorefresh</title> - <para> - <cmdsynopsis> - <command>set refresh</command> - <group> - <arg>true</arg> - <arg>false</arg> - </group> - </cmdsynopsis> - </para> - <para> - Does a scripted refresh after every command. Slows - down the process a bit, but can be handy when entering - commands manually. - </para> - </section> + &guideScriptCommands; </section> </chapter> |