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.
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.
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.
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'.
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.
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'.
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.
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.
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'.
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.
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.
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.
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 2.7.2.1. RSM files from previous version may display wrong values
of shadepower.
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.
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".
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).
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.
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.
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.
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.
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.
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.
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.
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'.
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' .
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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