Internal Parameters A-C

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Internal Parameters: A-C D-M P-Z

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.

A complete list of internal parameter names is given below.

Ambient Axes Backfade Background BondMode Bonds BoundBox Cartoon Display FontSize HBonds Hetero HourGlass Hydrogen Kinemage Menus Monitor Mouse Picking Radius Shadow SlabMode Solvent Specular SpecPower SSBonds Stereo Viewing Strands Transparent GIF UnitCell VectPS Write

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; this 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>
         set axes on
         set axes off

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 center of the molecule's bounding box. The set axes command is similar the the commands set boundbox and set unitcell that display the bounding box and the crystallographic unit cell respectively.

With set axes on the characters X, Y and Z are displayed on the positive direction of the Cartesian axes.

Set Backfade

Syntax:  set backfade on
         set backfade off

Shading to an arbitrary background color, rather than just black, can be performed. This is controlled by the commands set backfade on and set backfade off. For example, this may be used to generate depth-cued wireframe images that fade to white, rather than black.

Set Background

Syntax:  set background {<color>}

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

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

Set BondMode

Syntax:  set bondmode and
         set bondmode or

The RasMol set bondmode command controls the mechanism used to select individual bonds. 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.

Set Bonds

Syntax:  set bonds <boolean>

The RasMol set bonds command controls 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 and suitable Brookhaven PDB files. Double (and triple) bonds are specified in PDB files by specifying a given bond twice (and three times) in CONECT records. The command set bonds on enables the display of bond order, and the command set bonds off disable them. See the FAQ for detailed examples.

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 co-ordinate axes. The set boundbox command is similar the the commands set axes and set unitcell that display orthogonal co-ordinate axes and the bounding box respectively.

Set Cartoon

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

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 set cartoons <number> command. The set cartoons command without any parameters returns these two options to their default values.

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Internal Parameters: A-C D-M P-Z