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RasTop 2.0 Help
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dotnul.gif (43 bytes)
arrow1.gif (162 bytes)Using RasTop
arrow1.gif (162 bytes)RasTop World
arrow1.gif (162 bytes)Menu
arrow1.gif (162 bytes)Summary
arrow1.gif (162 bytes)Reference
arrow1.gif (162 bytes)Internal Parameters
arrow1.gif (162 bytes)Atom Expression
arrow1.gif (162 bytes)Colour Schemes
arrow1.gif (162 bytes)Atom Sets




Internal Parameters

RasMol has a number of internal parameters that may be modified using the 'set' command. These parameters control a number of program options such as rendering options and mouse button mappings.

Set Ambient

Syntax:  set ambient {<value>}

The RasMol 'ambient' parameter is used to control the amount of ambient (or surrounding) light in the scene. The 'ambient' value must be between 0 and 100. It controls the percentage intensity of the darkest shade of an object. For a solid object, this is the intensity of surfaces facing away from the light source or in shadow. For depth-cued objects this is the intensity of objects furthest from the viewer.

This parameter is commonly used to correct for monitors with different "gamma values" (brightness), to change how light or dark a hardcopy image appears when printed or to alter the feeling of depth for wireframe or ribbon representations.

up.gif (892 bytes) Set Axes

Syntax:  set axes <boolean>
	set axes world <boolean>

The RasMol 'axes' parameter controls the display of orthogonal coordinate axes on the current display. The coordinate axes are those used in the molecule data file, and the origin is the centre of the molecule's bounding box. The 'set axes' command is similar to the commands 'set boundbox' and 'set unitcell' that display the bounding box and the crystallographic unit cell, respectively.

RasTop Specific:

The command  'set axes world' controls the display of the world axes. The world axes are centered to the world origin where is the origin of the world coordinates.

up.gif (892 bytes) Set Backfade

Syntax:  set backfade <boolean>

The RasMol 'backfade' parameter is used to control backfade to the specified background colour, rather than black. This is controlled by the commands 'set backfade on' and 'set backfade off'. For example, this may be used to generate depth-cued images that fade to white, rather than black.

RasTop Specific: When depth queuing is on, backfading to the background colour often offers better rendering.

up.gif (892 bytes) Set Background

Syntax:  set background {<colour>}

The RasMol 'background' parameter is used to set the colour of the "canvas" background. The colour may be given as either a colour name or a comma separated triple of Red, Green, Blue (RGB) components enclosed in square brackets. Typing the command 'help colours' will give a list of the predefined colour names recognised by RasMol. When running under X Windows, RasMol also recognises colours in the X server's colour name database.

The command 'set background' is synonymous with the RasMol command 'background'.

up.gif (892 bytes) Set BondMode

Syntax:  set bondmode and
         set bondmode or
         set bondmode all
         set bondmode none
         set bondmode not bonded

The RasMol 'set bondmode' command controls the mechanism used to select individual bonds and modifies the display of bonded and non-bonded atoms by subsequent 'wireframe' commands.

When using the 'select' and 'restrict' commands, a given bond will be selected if i) the bondmode is 'or' and either of the connected atoms is selected, or ii) the bondmode is 'and' and both atoms connected by the bond are selected. Hence an individual bond may be uniquely identified by using the command 'set bondmode and' and then uniquely selecting the atoms at both ends.

The 'bondmode [all | none | not bonded]' commands add 'star 75' or 'spacefill 75' markers for the designated atoms to 'wireframe' displays. Stars are used when the specified wireframe radius is zero.

up.gif (892 bytes) Set Bonds

Syntax:  set bonds <boolean>

The RasMol 'bonds' parameter is used to control display of double and triple bonds as multiple lines or cylinders. Currently bond orders are only read from MDL Mol files, Sybyl Mol2 format files, Tripos Alchemy format files, CIF and mmCIF, and suitable PDB files. Double (and triple) bonds are specified in some PDB files by specifying a given bond twice (and three times) in CONECT records. The command 'set bonds on' enables the display of bond orders, and the command 'set bonds off' disables them.

up.gif (892 bytes) Set BoundBox

Syntax:  set boundbox <boolean>

The RasMol 'boundbox' parameter controls the display of the current molecule's bounding box on the display. The bounding box is orthogonal to the data file's original coordinate axes. The 'set boundbox' command is similar to the commands 'set axes' and 'set unitcell' that display orthogonal coordinate axes and the bounding box, respectively.

up.gif (892 bytes) Set Cartoon

Syntax:  set cartoon {<boolean>}
         set cartoon {<number>}

The RasMol 'cartoon' parameter is used to control display of the cartoon version of the 'ribbons' display. By default, the C-termini of beta-sheets are displayed as arrow heads. This may be enabled and disabled using the 'set cartoons <boolean>' command. The depth of the cartoon may be adjusted using the 'cartoons <number>' command. The 'set cartoons' command without any parameters returns these two options to their default values.

up.gif (892 bytes) Set CisAngle

Syntax:  set cisangle {<value>}

The RasMol 'cisangle' parameter controls the cutoff angle for identifying cis peptide bonds. If no value is given, the cutoff is set to 90 degrees.

up.gif (892 bytes) Set Coordinates

Syntax:  set coordinates molecule
         set coordinates world
	set coordinates screen
         set coordinates absolute

RasTop Specific:

The  'set picking coord' command uses 4 different systems for output, but only one is active at a time and is set by the  'set coordinates' command.

The molecular coordinate system is identical to the system used in previous versions of RasMol. Atom coordinates are those found in the original molecular file, in Angstrom, and slab and depth clipping plane positions are expressed in percents of the molecule that are drawn.

The world coordinate system expresses distances relatively to the world origin and the orthogonal world axes. Values are given in Angstroms, precision is no more than 1/250 Angstrom. After loading a molecular file and executing the  'rotate all' command, molecular and world coordinates are identical (more or less 1/250 Angstrom), even after rotation with the mouse on screen. As well, molecule axes and world axes are superimposed.

The screen coordinate origin is located at the center of the canvas with the orthogonal axes oriented to the right for the X-axis, down for the Y-axis, and in the back for the Z-axis. The absolute coordinate system is equivalent to the viewer coordinate system.

The absolute coordinate system is parallel to the screen system, but its origin is located at the world origin.

The Z-axis origin of both screen and absolute coordinate systems is located at the same depth than the world origin.

up.gif (892 bytes) Set DepthCue

Syntax:  set depthcue <boolean>
         set depthcue <1-4>

This command controls the depth queuing effect for spacefill, cylinder, and ribbon representations. When the slab plane is disabled, the maximum of light is in a plane located just in front of the closest molecule, otherwise the maximum of light is in the slab plane. The distance between the maximum of light and the plane where the light becomes extinct is controlled by the  'set worlddepth' command. There are four modes to control the depthcue rendering effect. In the mode 1, the light intensity varies linearly along the Z-axis, other modes bring more light to the front.

up.gif (892 bytes) Set Display

Syntax:  set display selected
         set display normal

This command controls the display mode within RasMol. By default, 'set display normal', RasMol displays the molecule in the representation specified by the user. The command 'set display selected' changes the display mode such that the molecule is temporarily drawn so as to indicate currently selected portion of the molecule. The user specified colour scheme and representation remains unchanged. In this representation all selected atoms are shown in yellow and all non selected atoms are shown in blue. The colour of the background is also changed to a dark grey to indicate the change of display mode. This command is typically only used by external Graphical User Interfaces (GUIs).

Rastop Specific:

Under 'display selected' mode the currently active molecule is displayed as above; the other molecules are displayed in dark green. The rotation center is display as a small magenta cross. Hidden molecules are displayed with a similar colour scheme, but represented with dashed lines.

up.gif (892 bytes) Set Dot

Syntax:  set dot <value>

RasTop specific command:

This command controls dot size. Dots are represented as squares with sides of <value> pixels when <value> is superior to 1. When images are saved to large files, one-pixel dots may not be seen. This command allows to enlarge these dots and make them visible. For example, the command 'set dot 2' will transform one-pixel dots in 2x2 pixels squares.

up.gif (892 bytes) Set FontSize

Syntax:  set fontsize {<value>} { FS | PS }

The RasMol 'set fontsize' command is used to control the size of the characters that form atom labels. This value corresponds to the height of the displayed character in pixels. The maximum value of 'fontsize' is 48 pixels, and the default value is 8 pixels high. Fixed or proportional spacing may be selected by appending the "FS" or "PS" modifiers, respectively. The default is "FS". To display atom labels on the screen use the RasMol 'label' command and to change the colour of displayed labels, use the 'colour labels' command.

up.gif (892 bytes) Set FontStroke

Syntax:  set fontstroke {<value>}

The RasMol 'set fontstroke' command is used to control the size of the stroke width of the characters that form atom labels. This value is the radius in pixels of cylinders used to form the strokes. The special value of "0" is the default used for the normal single pixel stroke width, which allows for rapid drawing and rotation of the image. Non-zero values are provided to allow for more artistic atom labels for publication at the expense of extra time in rendering the image.

When wider strokes are used, a larger font size is recommend, e.g. by using the RasMol 'set fontsize 24 PS' command, followed by 'set fontstroke 2'

The character sets used by RasMol rendered with fixed spacing with single-pixel-width strokes and with proportional spacing with 2-pixel-radius cylinder strokes are shown in the following sample:

[font sample]


  To display atom labels on the screen use the RasMol 'label' command, and to change the colour of displayed labels use the 'colour labels' command.

up.gif (892 bytes) Set HBonds


Syntax:  set hbonds backbone
         set hbonds sidechain

The RasMol 'hbonds' parameter determines whether hydrogen bonds are drawn between the donor and acceptor atoms of the hydrogen bond, 'set hbonds sidechain' or between the alpha carbon atoms of the protein backbone and between the phosphorous atoms of the nucleic acid backbone, 'set hbonds backbone'. The actual display of hydrogen bonds is controlled by the 'hbonds' command. Drawing hydrogen bonds between protein alpha carbons or nucleic acid phosphorous atoms is useful when the rest of the molecule is shown in only a schematic representation such as 'backbone', 'ribbons' or 'strands'. This parameter is similar to the RasMol 'ssbonds' parameter.

up.gif (892 bytes) Set Headlight

Syntax:  set headlight default
	set headlight [x,y,z]

RasTop Specific:

The headlight is a light source located to infinity.  The intensity of the headlight is controlled by the 'ambient' parameter; its direction is given by the parameters x, y, and z, which determine the relative intensity to the X-, Y-, and Z-axis.  The actual values x, y, and z are corrected internally by the square root of (x2 + y2 + z2). The default headlight is obtained with the factors x = 2, y = 2, and z = -1, as originally given in early versions of RasMol. The commands 'set ligth'  and 'set lightsource' are synonymous.

up.gif (892 bytes) Set Hetero

Syntax:  set hetero <boolean>

The RasMol 'hetero' parameter is used to modify the 'default' behaviour of the RasMol 'select' command, i.e. the behaviour of 'select' without any parameters. When this value is 'false', the default 'select' region does not include any heterogeneous atoms (refer to the predefined set 'hetero' ). When this value is 'true', the default 'select' region may contain hetero atoms. This parameter is similar to the RasMol 'hydrogen' parameter which determines whether hydrogen atoms should be included in the default set. If both 'hetero' and 'hydrogen' are 'true', 'select' without any parameters is equivalent to 'select all'.

up.gif (892 bytes) Set HourGlass

Syntax:  set hourglass <boolean>

The RasMol 'hourglass' parameter allows the user to enable and disable the use of the 'hour glass' cursor used by RasMol to indicate that the program is currently busy drawing the next frame. The command 'set hourglass on' enables the indicator, whilst 'set hourglass off' prevents RasMol from changing the cursor. This is useful when spinning the molecule, running a sequence of commands from a script file or using interprocess communication to execute complex sequences of commands. In these cases a 'flashing' cursor may be distracting.

up.gif (892 bytes) Set Hydrogen

Syntax:  set hydrogen <boolean>

The RasMol 'hydrogen' parameter is used to modify the "default" behaviour of the RasMol 'select' command, i.e. the behaviour of 'select' without any parameters. When this value is 'false', the default 'select' region does not include any hydrogen, deuterium or tritium atoms (refer to the predefined set 'hydrogen' ). When this value is 'true', the default 'select' region may contain hydrogen atoms. This parameter is similar to the RasMol 'hetero' parameter which determines whether heterogeneous atoms should be included in the default set. If both 'hydrogen' and 'hetero' are 'true', 'select' without any parameters is equivalent to 'select all'.

up.gif (892 bytes) Set Kinemage

Syntax:  set kinemage <boolean>

The RasMol 'set kinemage' command controls the amount of detail stored in a Kinemage output file generated by the RasMol 'write kinemage' command. The output kinemage files are intended to be displayed by David Richardson's Mage program. 'set kinemage false', the default, only stores the currently displayed representation in the generated output file. The command 'set kinemage true', generates a more complex Kinemage that contains both the wireframe and backbone representations as well as the coordinate axes, bounding box and crystal unit cell.

up.gif (892 bytes) Set Menus

Syntax:  set menus <boolean>

The RasMol 'set menus' command enables the canvas window's menu buttons or menu bar. This command is typically only used by graphical user interfaces or to create as large an image as possible when using Microsoft Windows.

up.gif (892 bytes) Set Monitor

Syntax:  set monitor <boolean>

The RasMol 'set monitor' command enables 'monitors'. The distance monitor labels may be turned off with the command 'set monitor off', and re-enabled with the command 'set monitor on'.

up.gif (892 bytes) Set Mouse

Syntax:  set mouse rasmol
         set mouse insight
         set mouse quanta

The RasMol 'set mouse' command sets the rotation, translation, scaling and zooming mouse bindings. The default value is 'rasmol' which is suitable for two button mice (for three button mice the second and third buttons are synonymous); X-Y rotation is controlled by the first button, and X-Y translation by the second. Additional functions are controlled by holding a modifier key on the keyboard. [Shift] and the first button performs scaling, [shift] and the second button performs Z-rotation, and [control] and the first mouse button controls the clipping plane. The 'insight' and 'quanta' options provide the same mouse bindings as other packages for experienced users.

up.gif (892 bytes) Set Picking

Syntax:  set picking <boolean>
         set picking off
         set picking none
         set picking ident
         set picking distance
         set picking monitor
         set picking angle
         set picking torsion
         set picking label
         set picking centre
         set picking center
         set picking coord

	set picking atom
	set picking group
	set picking chain
	set picking molecule

RasTop Specific:
	set picking bond
	set picking rotate
	set picking headlight

The RasMol 'set picking' series of commands affects how a user may interact with a molecule displayed on the screen in RasMol.

Enabling/Disabling Atom Picking: Clicking on an atom with the mouse results in identification and the display of its residue name, residue number, atom name, atom serial number and chain in the command window. This behavior may be disabled with the command 'set picking none' and restored with the command 'set picking ident'. The command 'set picking coord' adds the atomic coordinates of the atom to the display; the orthogonal coordinate system used depends on the  'set coordinates' command.

Disabling picking, by using 'set picking off' is useful when executing the 'pause' command in RasMol scripts as it prevents the display of spurious message on the command line while the script is suspended.

Measuring Distances, Angles and Torsions: Interactive measurement of distances, angles and torsions is achieved using the commands: 'set picking distance', 'set picking monitor', 'set picking angle' and 'set picking torsion', respectively. In these modes, clicking on an atom results in it being identified on the rasmol command line. In addition every atom picked increments a modulo counter such that in distance mode, every second atom displays the distance (or distance monitor) between this atom and the previous one. In angle mode, every third atom displays the angle between the previous three atoms and in torsion mode every fourth atom displays the torsion between the last four atoms. By holding down the shift key while picking an atom, this modulo counter is not incremented and allows, for example, the distances of consecutive atoms from a fixed atom to be displayed. See the 'monitor' command for how to control the display of distance monitor lines and labels.

Labeling Atoms with the Mouse: The mouse may also be used to toggle the display of an atom label on a given atom. The RasMol command 'set picking label' removes a label from a picked atom if it already has one or displays a concise label at that atom position otherwise.

Centering Rotation with the Mouse: A molecule may be centered on a specified atom position using the RasMol commands 'set picking centre' or 'set picking center'. In this mode, picking an atom causes all further rotations to be about that point.

Enabling Atom/Group/Chain/Molecule Selection: Atoms, groups, chains, and molecules may be selected (as if with the 'select' command), with the 'set picking atom', 'set picking group', 'set picking chain', 'set picking molecule' commands. For each of these commands, the shift key may be used to have a new selection added to the old, and the control key may be used to have a new selection deleted from the old. When the 'set picking atom' command is given, the mouse can be used to pick or to drag a box around the atoms for which selection is desired. When the 'set picking group' command is given, picking any an atom will cause selection of all atoms which agree in residue number with the picked atom, even if in different chains. When the 'set picking chain' command is given, picking any atom will cause selection of all atoms which agree in chain identifier with the picked atom. When the 'set picking molecule' command is given, picking any molecule will activate this molecule for rendering. This last command is only active when multiple molecules are loaded in the same world.

Adding, removing, and selecting bonds with the Mouse: Picking a Bond as a Rotation Axis: Any bond may be picked as an axis of rotation for the portion of the molecule beyond the second atom selected. Adding a bond: This operation is done by selecting a bond while pressing the 'shift' key. If no bond exists, a bond is added; a single bond is transformed into a double bond; a double bond is transformed into a triple. Removing a bond: Like for adding a bond, but while pressing the 'Ctrl' key.

Rotating bonds with the Mouse: 'set picking rotate' This feature should be used with caution, since it changes the conformation of the molecule. Rotation is available with the mouse only if a bond has been selected prior to the operation. During the rotation, the bounding box is adjusted accordingly to the novel size of the molecule. Disulphide bridges and hydrogen bonds are removed and must be recalculated for display.

Changing light source orientation with the Mouse:  The 'set picking headlight' command allows rotation of the headlight along the X- and the Y-axis with the mouse on screen.

up.gif (892 bytes) Set Radius

Syntax:  set radius {<value>}

The RasMol 'set radius' command is used to alter the behaviour of the RasMol 'dots' command depending upon the value of the 'solvent' parameter. When 'solvent' is 'true', the 'radius' parameter controls whether a true van der Waals' surface is generated by the 'dots' command. If the value of 'radius' is anything other than zero, that value is used as the radius of each atom instead of its true vdW value. When the value of 'solvent' is 'true', this parameter determines the 'probe sphere' (solvent) radius. The parameter may be given as an integer in rasmol units or containing a decimal point in Ångstroms. The default value of this parameter is determined by the value of 'solvent' and changing 'solvent' resets 'radius' to its new default value.

up.gif (892 bytes) Set Shadepower

Syntax:  set shadepower <value>

The shadepower parameter controls the shade repartition (the contrast) used in rendering solid objects. This value between 0 and 100 adjusts shading on an object surface oriented along the direction to the light source. Changing the shadepower parameter does not change the maximum or the minimum values of this shading, as does changing the 'ambient' parameter. A value of 100 concentrates the light on the top of spheres, giving a highly specular, glassy rendering (see the 'specpower' parameter). A value of 0 distributes the light on the entire object.

RasTop Users:

Implementation in version 2.0 follows the choice of range (0 to 100) in RasMol RSM files from previous version may display wrong values of shadepower.

up.gif (892 bytes) Set Shadow

Syntax:  set shadow <boolean>

The RasMol 'set shadow' command enables and disables ray-tracing of the currently rendered image. Currently only the spacefilling representation is shadowed or can cast shadows. Enabling shadowing will automatically disable the Z-clipping (slabbing) plane using the command 'slab off'. Ray-tracing typically takes about several seconds for a moderately sized protein. It is recommended that shadowing be normally disabled whilst the molecule is being transformed or manipulated, and only enabled once an appropriate viewpoint is selected, to provide a greater impression of depth.

up.gif (892 bytes) Set SlabMode

Syntax:  set slabmode <slabmode>

The RasMol 'slabmode' parameter controls the rendering method of objects cut by the slabbing (z-clipping) plane. Valid slabmode parameters are "reject", "half", "hollow", "solid" and "section".

up.gif (892 bytes) Set Solvent

Syntax:  set solvent <boolean>

The RasMol 'set solvent' command is used to control the behaviour of the RasMol 'dots' command. Depending upon the value of the 'solvent' parameter, the 'dots' command either generates a van der Waals' or a solvent accessible surface around the currently selected set of atoms. Changing this parameter automatically resets the value of the RasMol 'radius' parameter. The command 'set solvent false', the default value, indicates that a van der Waals' surface should be generated and resets the value of 'radius' to zero. The command 'set solvent true' indicates that a 'Connolly' or 'Richards' solvent accessible surface should be drawn and sets the 'radius' parameter, the solvent radius, to 1.2 Ångstroms (or 300 RasMol units).

up.gif (892 bytes) Set Specular

Syntax:  set specular <boolean>

The RasMol 'set specular' command enables and disables the display of specular highlights on solid objects drawn by RasMol. Specular highlights appear as white reflections of the light source on the surface of the object. The current RasMol implementation uses an approximation function to generate this highlight.

The specular highlights on the surfaces of solid objects may be altered by using the specular reflection coefficient, which is altered using the RasMol 'set specpower' command.

up.gif (892 bytes) Set SpecPower

Syntax:  set specpower {<value>}

The 'specpower' parameter determines the shininess of solid objects rendered by RasMol. This value between 0 and 100 adjusts the reflection coefficient used in specular highlight calculations. The specular highlights are enabled and disabled by the RasMol 'set specular' command. Values around 20 or 30 produce plastic looking surfaces. High values represent more shiny surfaces such as metals, while lower values produce more diffuse/dull surfaces.

up.gif (892 bytes) Set SSBonds

Syntax:  set ssbonds backbone
         set ssbonds sidechain

The RasMol 'ssbonds' parameter determines whether disulphide bridges are drawn between the sulphur atoms in the sidechain (the default) or between the alpha carbon atoms in the backbone of the cysteines residues. The actual display of disulphide bridges is controlled by the 'ssbonds' command. Drawing disulphide bridges between alpha carbons is useful when the rest of the protein is shown in only a schematic representation such as 'backbone', 'ribbons' or 'strands'. This parameter is similar to the RasMol 'hbonds' parameter.

up.gif (892 bytes) Set Stereo

Syntax:  set stereo <boolean>
         set stereo [-] <number>

The RasMol 'set stereo' parameter controls the separation between the left and right images. Turning stereo on and off doesn't reposition the centre of the molecule.

Stereo viewing of a molecule may be turned on (and off) either by selecting 'Stereo' from the 'Options' menu, or by typing the commands 'stereo on' or 'stereo off'.

The separation angle between the two views may be adjusted with the 'set stereo [-] <number>' command, where positive values result in crossed eye viewing and negative values in relaxed (wall-eyed) viewing. Currently, stereo viewing is not supported in 'vector PostScript' output files.

up.gif (892 bytes) Set Strands

Syntax:  set strands {<value>}

The RasMol 'strands' parameter controls the number of parallel strands that are displayed in the ribbon representations of proteins. The permissible values for this parameter are 1, 2, 3, 4, 5 and 9. The default value is 5. The number of strands is constant for all ribbons being displayed. However, the ribbon width (the separation between strands) may be controlled on a residue by residue basis using the RasMol 'ribbons' command.

up.gif (892 bytes) Set Transparent

Syntax:  set transparent <boolean>

The RasMol 'transparent' parameter controls the writing of transparent GIFs by the 'write gif <filename>' command. This may be controlled by the 'set transparent on' and 'set transparent off' commands.

up.gif (892 bytes) Set UnitCell

Syntax:  set unitcell <boolean>

The RasMol 'unitcell' parameter controls the display of the crystallographic unit cell on the current display. The crystal cell is only enabled if the appropriate crystal symmetry information is contained in the PDB, CIF or mmCIF data file. The RasMol command 'show symmetry' display details of the crystal's space group and unit cell axes. The 'set unitcell' command is similar to the commands 'set axes' and 'set boundbox' that display orthogonal coordinate axes and the bounding box, respectively.

up.gif (892 bytes) Set VectPS

Syntax:  set vectps <boolean>

The RasMol 'vectps' parameter is use to control the way in which the RasMol 'write' command generates vector PostScript output files. The command 'set vectps on' enables the use of black outlines around spheres and cylinder bonds producing "cartoon-like" high resolution output. However, the current implementation of RasMol incorrectly cartoons spheres that are intersected by more than one other sphere. Hence "ball and stick" models are rendered correctly but not large spacefilling spheres models. Cartoon outlines can be disabled, the default, by the command 'set vectps off'.


up.gif (892 bytes) Set WorldDepth

RasTop Specific:
Syntax:  set worlddepth <value>

This is an 'advanced' scripting command.

The worlddepth is a distance that measures the longest side of the bounding box or the longest side of the largest bounding boxes when multiple molecule are loaded. Normally, the worlddepth is calculated internally and increased automatically when larger molecules are loaded. Since translation values are dependent of the zoom parameter and the zoom parameter is itself dependent of the worlddepth, calculating translation values could become very complicated in a multiple molecule environment. The  'set worlddepth' command is used at script start to specify the world size that will be used along a project. This ensures correctness of the RasMol 'translate' command at any point of the script. Actual and default internal values are obtained with the  'show world' or the 'show worlddepth' command. The <value> parameter is either an integer in RasMol Unit (1/250 Angstrom) or a floating number in Angstrom.

The worlddepth also regulates the depthcue effect. It measures the distance between the plane where the light intensity is maximal and the deeper plane where the light intensity becomes null. In classical RasMol, this value is equal to the longest side of the bounding box. If variable worlddepth must be used along a script, the commands  'position' and  'scale' are better to indicate molecule locations and zoom values. To reset the worlddepth to its internal default value, use the command 'reset worlddepth' .

up.gif (892 bytes) Set Write

Syntax:  set write <boolean>

The RasMol 'write' parameter controls the use of the 'save' and 'write' commands within scripts, but it may only be executed from the command line. By default, this value is 'false', prohibiting the generation of files in any scripts executed at start-up (such as those launched from a WWW browser). However, animators may start up RasMol interactively: type 'set write on' and then execute a script to generate each frame using the source command.


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Last updated on Saturday, December 29, 2001