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RasTop 1.3.1 Help
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Commands:
arrow1.gif (162 bytes)Using RasTop
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
Parameters:
Ambient
Axes
Background
BackFade
BondMode
Bonds
BoundBox
Cartoon
CisAngle
Display
Dot
FontSize
FontStroke
HBonds
Hetero
HourGlass
Hydrogen
Kinemage
Menus
Monitor
Mouse
Picking
Radius
ShadePower
Shadow
SlabMode
Solvent
Specular
SpecPower
Stereo
SSBonds
Strands
Transparent
UnitCell
VectPS
Write

 

 

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.


 Set Axes

Syntax:  set axes <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.


 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.


 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'.


 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.


 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.


 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.


 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.


 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.


 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).


 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.


 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.


 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.

 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.


 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'.


 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.


 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'.


 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.


 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.


 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'.


 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.


 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

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.

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.

Labelling 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.

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


 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.


 Set Shadepower

Syntax:  set shadepower <value>

RasTop specific command:

The shadepower variable controls the shade repartition. Rendering of volumes is obtained by creating a color shade on an object surface oriented along the direction of the light source. Shadepower does not change the maximum or the minimum values of these shades, as does 'set ambient', but modifies their gradient. A value of -20 concentrates the light on the top of spheres, giving a 'specular' rendering, a value of 20 saturates the light on the entire object. To a certain extend, shadepower is equivalent to contrast and ambient to brightness.


 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 appropiate viewpoint is selected, to provide a greater impression of depth.


 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".


 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).


 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.


 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.


 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.


 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.


 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.


 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.


 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.


 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'.


 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 Sunday, March 25, 2001