Back to TABLE OF CONTENTS   Internal Parameters:  A-C   D-M   P-Z
Set Picking                                   Syntax:  
set picking on          set picking ident          set picking angle  
set picking off         set picking distance      set picking torsion
set picking none      set picking monitor       set picking label   set picking centre
   The 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.
   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.
Centering Rotation with the Mouse.
   A molecule may be centered on a specified atom position using the RasMol commands set picking center or set picking centre. 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 behavior 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 Waal's 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 Van der Waal's 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 Angstroms. The default value of this parameter is determined by the value of solvent; changing solvent resets radius to its new default value.
Set Shadow                                   Syntax:   set shadow <boolean>
   The RasMol set shadow command enables and disables raytracing 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. Raytracing typically takes about 10s for a moderately sized protein. It is recommended that shadowing be disabled normally while 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.
   Additional clarification from Eric Martz (2/28/98):
   There is no slab mode in RasMol which displays a true slab, namely, a section of constant nonzero thickness. Such a slab is defined by two 2 cutting planes, one 1 behind the other second 2nd. Everything behind the rearplane, or in front of the front plane, is hidden. (In contrast to RasMol, the slab mode in MAGE is a true slab; slab thickness is controlled by the "zslab" slider, and the center of the slab can be moved to the front or rear by the "ztran" slider.)
· reject: All atoms and bonds are rendered whole. Atoms or bonds cut by the z-clipping plane are entirely hidden. Cartoons, ribbons, and strands are cut at or near the z-clipping plane. This is the unconditional rendering for everything except spacefilled atoms
· half: Only the front halves of spacefilled atoms which are cut by the z-clipping plane are shown, and they are rendered as a hollow spherical surface with the portion in front of the z-clipping plane hidden. Therefore you can see through the holes in the fronts of these "ring" atoms to atoms behind.
· hollow: Spacefilled atoms which are cut by the z-clipping plane are rendered as a hollow spherical surface with the portion in front of the z-clipping planehidden. Therefore you can see inside these atoms to either the rear inside surface of the atom or to portions of other intersecting (bonded) atoms.
· solid: Spacefilled atoms cut by the z-clipping plane are rendered as a solid sphere with a flat cut surface (as though made of clay and cut with a knife). This is the default for spacefilled atoms.
· section: Only the cut surfaces of (solid) atoms cut by the z-clipping plane are rendered. All atoms behind or in front of the z-clipping plane are hidden. The image is a zero-thickness plane parallel to the viewing screen.

Set Solvent                                     Syntax: set solvent <boolean>
   The RasMol set solvent command is used to control the behavior of the RasMol dots command. Depending upon the value of the solvent parameter, the dots command either generates a Van der Waal's or a solvent acessible 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 Waal's 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 to the solvent radius, i.e.1.2 Å (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 coeffient 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 disulfide bridges are drawn between the sulfur -S-S- atoms in the sidechain (the default) or between the alpha carbon atoms of the cysteine residues in the backbone. The actual display of disulfide bridges is controlled by the ssbonds command. Drawing disulfide 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 on
                                                                               set stereo off
                                                                               set stereo <boolean>
   The RasMol set stereo parameter controls the separation between the left and right images. Turning stereo on and off doesn't reposition the center 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 relaxed viewing and negative values in crossed 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 on
                                                                                        set transparent off
   The RasMol write gif <filename> allows the generation of transparent GIFs. 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 data file. The RasMol command show symmetry displays 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 co-ordinate 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 to 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 by the command set vectps off
Set Write                                     Syntax:   set write <boolean>
   The RasMol set write command enables (and disables) the use of save and write in scripts, but 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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