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Command References
RasMol allows the execution of interactive commands. Each command must
be given on a separate line. Keywords are case insensitive and may be
entered in either upper or lower case letters. All white space characters
are ignored except to separate keywords and their arguments.
In RasTop, commands are either automatically generated by the menu or
manually entered in the dialog box opened by click the Edit>Command
menu item.
RasTop Specific:
Syntax: add <filename>
The RasTop 'add' command loads an RSM script file into
the world. Actual world parameters are used to position the molecule
instead of those indicated in the script. Other commands listed thereafter
are equally deactivated:
centre
set axes world
set slab
set shadow
set specular
set specpower
set shadepower
set ambient
set background
set light
set fontsize
set fontstroke
set stereo
set backfade
set depthcue
reset
zap
slab
depth
zoom
rotate world
rotate all
translate world
position world
scale
stereo
background
light
The 'add' command preserves the rendering and is used to in script saving.
Syntax: backbone {<boolean>}
backbone <value>
backbone dash
The RasMol 'backbone' command permits the representation of a polypeptide backbone as a series of bonds
connecting the adjacent alpha carbons of each amino acid in a chain. The
display of these backbone 'bonds' is turned on and off by the command
parameter in the same way as with the 'wireframe'
command. The command 'backbone off' turns off the selected
'bonds', and 'backbone on' or with a number turns them on.
The number can be used to specify the cylinder radius of the
representation in either Ångstrom or RasMol units. A parameter value of
500 (2.0 Ångstroms) or above results in a "Parameter value too
large" error. Backbone objects may be coloured using the RasMol 'colour
backbone' command.
The reserved word backbone is also used as a predefined set ("help
sets") and as a parameter to the 'set
hbond' and 'set
ssbond' commands. The RasMol command 'trace'
renders a smoothed backbone, in contrast to 'backbone'
which connects alpha carbons with straight lines.
The backbone may be displayed with dashed lines by use of the 'backbone
dash' command.
Syntax: background <colour>
The RasMol 'background' command 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 and 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 'background' command is synonymous with the RasMol
'set background'
command.
Syntax: bond <number> <number> +
bond <number> <number> pick
bond rotate {<boolean>}
RasTop Specific (self-explanatory):
Syntax: bond <number> <number> -
bond <number> <number> single
bond <number> <number> double
bond <number> <number> triple
bond <number> <number> unbound
The RasMol command 'bond <number> <number> +' adds the
designated bond to the drawing, increasing the bond order if the bond
already exists. The command 'bond <number> <number> pick'
selects the two atoms specified by the atom serial numbers as the two ends
of a bond around which the 'rotate bond <angle>' command will be
applied. If no bond exists, it is created (RasTop: The bond is not
created!).
Rotation around a previously picked bond may be specified by the 'rotate
bond <angle>' command, or may also be controlled with the mouse,
using the 'bond rotate on/off' or the equivalent 'rotate bond on/off'
commands.
Syntax: cartoon {<number>}
The RasMol 'cartoon' command does a display of a
molecule 'ribbons' as Richardson (MolScript)
style protein 'cartoons', implemented as thick (deep)
ribbons. The easiest way to obtain a cartoon representation of a protein
is to use the 'Cartoons' option on the 'Display'
menu. The 'cartoon' command represents the currently
selected residues as a deep ribbon with width specified by the command's
argument. Using the command without a parameter results in the ribbon's
width being taken from the protein's secondary structure, as described in
the 'ribbons' command. By default,
the C-termini of beta-sheets are displayed as arrow heads. This may be
enabled and disabled using the 'set
cartoons' 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.
Syntax: centre {all}
centre {<expression>} {translate|center}
centre [x,y,z]
RasTop Specific:
centre world
centre molecule
centre origin {translate|center}
The RasMol 'centre' command defines the point about
which the 'rotate' command and the
scroll bars rotate the current molecule. With 'all'
parameter or without a parameter the centre command resets the centre of
rotation to the centre of gravity of the molecule. If an atom
expression is specified, RasMol rotates the molecule about the centre of
gravity of the set of atoms specified by the expression. Hence, if a
single atom is specified by the expression, that atom will remain
'stationary' during rotations.
Type 'help expression' on the
command line for more information on RasMol atom expressions or consult
the document on atom expressions and the predefined
atom sets.
Alternatively the centering may be given as a comma separated triple of
[CenX, CenY, CenZ] offsets in RasMol units (1/250 of an Angstrom) from the
centre of gravity. The triple must be enclosed in square brackets.
The optional forms 'centre ... translate' and 'centre ... center' may be
used to specify use of a translated centre of rotation (not necessarily in
the centre of the canvas) or a centre of rotation which is placed at the
centre of the canvas. Starting with RasMol 2.7.2, the default is to center
the new axis on the canvas.
The RasTop 'centre world' command translates the entire
world and positions the world origin to the center of the canvas. A
translation along the z-axis is performed if necessary.
The RasTop 'centre molecule' command is a shortcut for
the command 'centre [0,0,0] translate', which switches the
center to the center of gravity of the molecule without translating the
molecule itself.
The RasTop 'centre origin' command transfers the
rotation center to the world origin. This special rotation center is
active only when the 'rotate all' command is 'on'
(or the 'rotate molecule' is 'off'). Applications
include cases where we need to rotate a single molecule from a center
outside the bounding box, and rotations of molecular assemblies that have
some degrees of symmetry.
The RasTop 'centre origin centre' command transfers the
world origin to the actual rotation center; molecules are not translated.
Inversely, the 'centre origin translate' command transfers
the rotation center to the world origin. One or more molecules are
translated, depending on the state on or off of the 'rotate
molecule' command. These two command are useful to align
molecules.
When the 'rotate all' command is 'on', selection
of other molecules does not change the rotation center. On the other hand,
the 'rotate molecule on' command brings
automatically the center in the bounding box of the active molecule, by
default at the gravity center and without translation.
Syntax: clipboard
The RasMol 'clipboard' command places a copy of the
currently displayed image on the local graphics 'clipboard'. Note: this
command is not yet supported on UNIX or VMS machines. It is intended to
make transferring images between applications easier under Microsoft
Windows or on an Apple Macintosh.
When using RasMol on a UNIX or VMS system this functionality may be
achieved by generating a raster image in a format that can be read by the
receiving program using the RasMol 'write'
command.
RasTop specific:
Syntax: clipboard selected
clipboard position
clipboard {image}
clipboard paste
The commands 'clipboard selected' and 'clipboard
position' generate scripts describing the current selection
and the current world position of the molecule. These scripts are
copied to the clipboard and are pasted from the clipboard using the
command 'clipboard paste' or more simply 'paste'. The
clipboard format used by RasTop is described in the document file
formats.
The command 'clipboard image' is equivalent to the RasMol command
'clipboard'. The keyword 'image' is optional.
Syntax: colour {<object>} <colour>
color {<object>} <colour>
Colour the atoms (or other objects) of the selected region. The colour
may be given as either a colour name or a comma separated triple of Red,
Green and Blue (RGB) components enclosed in square brackets. Typing the
command 'help colours' will give a
list of all the predefined colour names recognized by RasMol or consult
the document on colour schemes.
Allowed objects are 'atoms', 'bonds', 'backbone',
'ribbons', 'labels',
'dots', 'hbonds'
and 'ssbonds'. If no object is
specified, the default keyword 'atom' is assumed. Some colour
schemes are defined for certain object types. The colour scheme 'none'
can be applied to all objects except atoms and dots, stating that the
selected objects have no colour of their own, but use the colour of their
associated atoms (i.e. the atoms they connect). 'Atom'
objects can also be coloured by 'alt',
'amino', 'chain',
'charge', 'cpk',
'group', 'model',
'shapely', 'structure',
'temperature'
or 'user'. Hydrogen
bonds can also be coloured by 'type'
and dot surfaces can also be coloured by 'electrostatic
potential'. For more information type 'help
colour <colour>' or consult the document on colour
schemes.
RasTop Specific: The world axe colour is accessible by the
command 'colour world axes <colour>'; the
command 'colour dots none' is accepted.
RasTop specific command.
Syntax: copy selected
copy position
copy {image}
This command is synonymous to 'clipboard'.
Syntax: connect {<boolean>}
The RasMol 'connect' command is used to force RasMol to
(re)calculate the connectivity of the current molecule. If the original
input file contained connectivity information, this is discarded. The
command 'connect false' uses a fast heuristic algorithm
that is suitable for determining bonding in large bio-molecules such as
proteins and nucleic acids. The command "connect true"
uses a slower more accurate algorithm based upon covalent radii that is
more suitable to small molecules containing inorganic elements or strained
rings. If no parameters are given, RasMol determines which algorithm to
use based on the number of atoms in the input file. Greater than 255 atoms
causes RasMol to use the faster implementation. This is the method used to
determine bonding, if necessary, when a molecule is first read in using
the 'load' command.
Syntax: {wireframe} dash {<boolean>}
{wireframe} dash <value>
The RasMol 'dash' command represents each bond within
the selected region of the molecule as a dashed depth-cued vector.
Behavior of the 'dash' command follows the 'wireframe'
command.
Syntax: define <identifier> <expression>
The RasMol 'define' command allows the user to
associate an arbitrary set of atoms with a unique identifier. This allows
the definition of user-defined sets. These sets are declared statically, i.e.
once defined the contents of the set do not change, even if the expression
defining them depends on the current transformation and representation of
the molecule.
Type 'help expression' on the
command line for more information on RasMol atom expressions or consult
the document on atom expressions and the predefined
atom sets.
Syntax: depth {<boolean>}
depth <value>
The RasTop 'depth' command enables, disables or
positions the back-clipping plane of the molecule. The program only draws
those portions of the molecule that are closer than the clipping plane.
Integer values range from 0 at the very back of the molecule to 100 which
is completely in front of the molecule. Intermediate values determine the
percentage of the molecule to be drawn.
This command interacts with the 'slab <value>' command, which
clips to the front of a given z-clipping plane. Combinations of slabmode
and backclipping slice the molecule if the slab value if superior to the
depth value.
RasTop Specific:
Syntax: depth world origin
depth world <value>
The 'depth world origin' command sends the
back-clipping plane at the world origin. The 'depth world
<value>' command moves the plane of value Angstroms (if
value if a floating number) or value RasMol units (if value is an integer)
relatively to its current position. Future versions of RasMol may not
adopt this convention.
Syntax: dots {<boolean>}
dots <value>
The RasMol 'dots' command is used to generate a van der
Waals' dot surface around the currently selected atoms. Dot surfaces
display regularly spaced points on a sphere of van der Waals' radius about
each selected atom. Dots that would are 'buried' within the van der Waals'
radius of any other atom (selected or not) are not displayed. The command
'dots on' deletes any existing dot surface and generates a
dots surface around the currently selected atom set with a default dot
density of 100. The command 'dots off' deletes any
existing dot surface. The dot density may be specified by providing a
numeric parameter between 1 and 1000. This value approximately corresponds
to the number of dots on the surface of a medium sized atom.
By default, the colour of each point on a dot surface is the colour of
its closest atom at the time the surface is generated. The colour of the
whole dot surface may be changed using the 'colour
dots' command.
Syntax: echo {<string>}
The RasMol 'echo' command is used to display a message
in the RasMol command/terminal window. The string parameter may optionally
be delimited in double quote characters. If no parameter is specified, the
'echo' command displays a blank line. This command is
particularly useful for displaying text from within a RasMol 'script'
file.
Syntax: hbonds {<boolean>}
hbonds <value>
The RasMol 'hbond' command is used to represent the
hydrogen bonding of the protein molecule's backbone. This information is
useful in assessing the protein's secondary structure. Hydrogen bonds are
represented as either dotted lines or cylinders between the donor and
acceptor residues. The first time the 'hbond' command is
used, the program searches the structure of the molecule to find hydrogen
bonded residues and reports the number of bonds to the user. The command 'hbonds
on' displays the selected 'bonds' as dotted lines, and the 'hbonds
off' turns off their display. The colour of hbond objects may be
changed by the 'colour hbond'
command. Initially, each hydrogen bond has the colours of its connected
atoms.
By default the dotted lines are drawn between the accepting oxygen and
the donating nitrogen. By using the 'set
hbonds' command the alpha carbon positions of the appropriate
residues may be used instead. This is especially useful when examining
proteins in backbone representation.
Syntax: help {<topic> {<subtopic>}}
? {<topic> {<subtopic>}}
The RasMol 'help' command provides on-line help on the
given topic.
RasTop Specific:
Syntax: help HTML {<filename | URL>}
The command 'help HTML' activates the default
browser and points its locator to an HTM-based help file. The 'help
HTML <filename>' command sets the address of the HTML-based
help file. This help could be an HTML document residing either locally on
the drive or externally on the world wide web. In this last case, the
address must be given as an URL (http://www.etc.).
Syntax: label {<string>}
label <boolean>
The RasMol 'label' command allows an arbitrary
formatted text string to be associated with each currently selected atom.
This string may contain embedded 'expansion specifiers' which display
properties of the atom being labelled. An expansion specifier consists of
a '%' character followed by a single alphabetic character specifying the
property to be displayed (similar to C's printf syntax). An actual '%'
character may be displayed by using the expansion specifier '%%'.
Atom labelling for the currently selected atoms may be turned off with
the command 'label off'. By default, if no string is given
as a parameter, RasMol uses labels appropriate for the current molecule.
RasMol uses the label '%n%r:%c.%a' if the molecule contains more than one
chain, '%e%i' if the molecule has only a single residue (a small molecule)
and '%n%r.%a' otherwise.
The colour of each label may be changed using the 'colour
label' command. By default, each label is drawn in the same
colour as the atom to which it is attached. The size and spacing of the
displayed text may be changed using the 'set
fontsize' command. The width of the strokes in the displayed
text may be changed using the 'set
fontstroke' command.
The following table lists the current expansion specifiers:
%a Atom Name
%b %t B-factor/Temperature
%c %s Chain Identifier
%e Element Atomic Symbol
%i Atom Serial Number
%m Single Letter Amino Acid Code
%n Residue Name
%r Residue Number
%M NMR Model Number (with leading "/")
%A Alternate Conformation Identifier
(with leading ";")
Syntax: load {<format>} <filename>
Load a molecule coordinate file into RasMol. Valid molecule file
formats are 'pdb' (Protein Data Bank format), 'mdl'
(Molecular Design Limited's MOL file format), 'alchemy' (Tripos'
Alchemy file format), 'mol2' (Tripos' Sybyl Mol2 file
format), 'charmm' (CHARMm file format), 'xyz'
(MSC's XMol XYZ file format), 'mopac' (J. P. Stewart's
MOPAC file format) or 'cif' (IUCr CIF or mmCIF file
format). If no file format is specified, 'PDB', 'CIF',
or 'mmCIF' is assumed by default.
Unlimited number of molecules may be loaded at a time. To select a
molecule for manipulation use the RasMol 'molecule
<n>' command. To delete specifically a molecule use the
RasMol 'zap molecule' command.
The 'load' command selects all the atoms in the
molecule, centers it on the screen and renders it as a CPK coloured
wireframe model. If the molecule contains no bonds (i.e. contains
only alpha carbons), it is drawn as an alpha carbon backbone. If the file
specifies fewer bonds than atoms, RasMol determines connectivity using the
'connect' command. If a default
script is available (see 'script default'
command), it will be ran automatically after loading.
The 'load inline' command also allows the storing of
atom coordinates in scripts to allow better integration with WWW browsers.
A load command executed inside a script file may specify the keyword 'inline'
instead of a conventional filename. This option specifies that the
coordinates of the molecule to load are stored in the same file as the
currently executing commands.
Typically this is used in the command 'load pdb inline',
which is followed by a number of RasMol commands terminated by the command
'exit'. The 'exit'
command terminates execution of the current script and returns control to
the command line (or the calling script). This means any lines following 'exit'
are never interpreted by RasMol. These may be used to store atomic
coordinates in PDB, CIF or mmCIF file format. One possible use is a
standard RasMol script prefix that may be concatenated with an appropriate
PDB file on-the-fly.
Syntax: molecule <number>
Select one of up to n previously loaded molecules for active
manipulation. While all molecules may be rotated collectively (see the 'rotate
all' command), only one molecule at a time is active for manipulation
by the commands which control the details of rendering.
RasTop Specific:
Syntax: molecule hide
molecule show
The command 'molecule hide' toggles off the display of
a molecule. The molecule remains visible in 'display
selected mode' as a dashed wireframe. The command 'molecule
show' toggles back on the display of the molecule
Syntax: monitor <number> <number>
monitor {<boolean>}
The RasMol 'monitor' command allows the display of
distance monitors. A distance monitor is a dashed (dotted) line between an
arbitrary pair of atoms, optionally labelled by the distance between them.
The RasMol command 'monitor <number> <number>'
adds such a distance monitor between the two atoms specified by the atom
serial numbers given as parameters
Distance monitors are turned off with the command 'monitors off'.
By default, monitors display the distance between its two end points as a
label at the centre of the monitor. These distance labels may be turned
off with the command 'set
monitors off', and re-enabled with the command 'set
monitors on'. Like most other representations, the colour of
a monitor is taken from the colour of its end points unless specified by
the 'colour monitors' command.
Distance monitors may also be added to a molecule interactively with
the mouse, using the 'set picking
monitor' command. Clicking on an atom results in its being
identified on the rasmol command line. In addition every atom picked
increments a modulo counter such that, in monitor mode, every second atom
displays the distance between this atom and the previous one. The shift
key may be used to form distance monitors between a fixed atom and several
consecutive positions. A distance monitor may also be removed (toggled) by
selecting the appropriate pair of atom end points a second time.
Syntax: pause
wait
The RasMol 'pause' command is used in script files to
stop the script file for local manipulation by a mouse, until any key is
pushed to restart the script file. 'Wait' is synonymous
with 'pause'. This command may be executed in RasMol
script files to suspend the sequential execution of commands and allow the
user to examine the current image. When RasMol executes a 'pause'
command in a script file, it suspends execution of the rest of the file,
refreshes the image on the screen and allows the manipulation of the image
using the mouse and scroll bars, or resizing of the graphics window. Once
a key is pressed, control returns to the script file at the line following
the 'pause' command. While a script is suspended the
molecule may be rotated, translated, scaled, slabbed and picked as usual,
but all menu commands are disabled. The 'pause' can
probably be used most effectively with 'echo'
commands in education pre-scripted demonstrations, where a description of
the current image is presented to the user/student. Typically the command
before a 'pause' should be 'echo Press any key to
continue'.
Execution of a script can be cancelled by pressing Control-D or
Control-Z (on VAX/VMS, Control-C) while standing at a pause. The command 'set
picking none' disables picking, which avoids the display of
spurious messages whilst a script is suspended at a pause.
Syntax: position {x <number>} {y <number>} {z <number>}
position world {x <number>} {y <number>} {z <number>}
The command 'position' places molecules relatively to
the center of the screen and the world plane. The command 'position
world' places the world relatively to the center of the screen
and the world plane. Displacement values for more than one axis may be
indicated in the same command and are counted in RU for integer values or
angstrom for floating values.
Syntax: print
The RasMol 'print' command sends the currently
displayed image to the local default printer using the operating system's
native printer driver. Note: this command is not yet supported under UNIX
or VMS. It is intended to take advantage of Microsoft Windows and Apple
Macintosh printer drivers. For example, this allows images to be printed
directly on a dot matrix printer.
When using RasMol on a UNIX or VMS system this functionality may be
achieved by either generating a PostScript file using the RasMol 'write
ps' or 'write vectps'
commands and printing that or generating a raster image file and using a
utility to dump that to the local printer.
Syntax: quit
exit
Exit from the RasMol program. The RasMol commands 'exit'
and 'quit' are synonymous, except within nested scripts.
In that case, 'exit' terminates only the current level,
while 'quit' terminates all nested levels of scripts.
Syntax: refresh
The RasMol 'refresh' command redraws the current image.
This is useful in scripts to ensure application of a complex list of
parameter changes.
Syntax: renumber {{-} <value>}
The RasMol 'renumber' command sequentially numbers the
residues in a macromolecular chain. The optional parameter specifies the
value of the first residue in the sequence. By default, this value is one.
For proteins, each amino acid is numbered consecutively from the N
terminus to the C terminus. For nucleic acids, each base is numbered from
the 5' terminus to the 3' terminus. All chains in the current database are
renumbered and gaps in the original sequence are ignored. The starting
value for numbering may be negative.
RasTop Specific:
With the development of complex transformations such as bond
modifications and multiple molecules, the reset command needed more
precise specifications. The following is an attempt to explore various
reset possibilities. Their definition and action may change in future
versions of RasTop.
Syntax: reset
reset molecule
reset world
reset worlddepth
slab
depth
headlight
bonds
all
If only one molecule is loaded and the world is not active, the RasTop
'reset' and 'reset molecule' commands
restore the original viewing transformation and centre of rotation. The
scale is set to its default value, 'zoom 100',
the centre of rotation is set to the geometric centre of the currently
loaded molecule, 'centre all', this
centre is translated to the middle of the screen and the viewpoint set to
the default orientation. All world parameters are reset. This command
should not be mistaken for the RasMol 'zap'
command which deletes the currently stored molecule, returning the program
to its initial state.
If more than one molecule is loaded, the RasTop 'reset molecule'
command restores the original parameter of the molecule (rotation,
translation and centre).
The command 'reset world' restores the world
parameters (rotation, translation) and sets the scale to its default
value.
The command 'reset worlddepth' restores the
worlddepth parameters to its default value.
The result of the command 'reset' depends on the
active state of the world. If the world is active (see 'rotate
all'), this command is equivalent to 'reset
world', thus protecting the world assembly. If the world is not
active (see 'rotate molecule'),
this command is equivalent to 'reset molecule'.
The command 'reset headlight' restores the default
lighting (see 'set headlight
default' command).
The command 'reset slab' restores internal slab plane
parameters and inactivates slabmode if active. The command 'reset
depth' acts similarly.
The command 'reset bonds' restores all bond parameters
to their initial values, including bond creation, bond deletion, bond
rotation, and bond order.
The command 'reset all' includes the commands 'reset
world', 'reset slab', 'reset
depth', 'reset headlight', and 'reset
bonds'.
Syntax: restrict {<expression>}
The RasMol 'restrict' command both defines the
currently selected region of the molecule and disables the representation
of (most of) those parts of the molecule no longer selected. All
subsequent RasMol commands that modify a molecule's colour or
representation affect only the currently selected region. The parameter of
a 'restrict' command is a RasMol atom expression that is
evaluated for every atom of the current molecule. This command is very
similar to the RasMol 'select'
command, except 'restrict' disables the 'wireframe',
'spacefill' and 'backbone'
representations in the non-selected region.
Type 'help expression' on the
command line for more information on RasMol atom expressions or consult
the document on atom expressions and the predefined
atom sets.
Syntax: ribbons {<boolean>}
ribbons <value>
The RasMol 'ribbons' command displays the currently
loaded protein or nucleic acid as a smooth solid "ribbon"
surface passing along the backbone of the protein. The ribbon is drawn
between each amino acid whose alpha carbon is currently selected. The
colour of the ribbon is changed by the RasMol 'colour
ribbon' command. If the current ribbon colour is 'none'
(the default), the colour is taken from the alpha carbon at each position
along its length.
The width of the ribbon at each position is determined by the optional
parameter in the usual RasMol units. By default the width of the ribbon is
taken from the secondary structure of the protein or a constant value of
720 (2.88 Ångstroms) for nucleic acids. The default width of protein
alpha helices and beta sheets is 380 (1.52 Ångstroms) and 100 (0.4
Ångstroms) for turns and random coil. The secondary structure assignment
is either from the PDB file or calculated using the DSSP algorithm as used
by the 'structure' command. This
command is similar to the RasMol command 'strands'
which renders the biomolecular ribbon as parallel depth-cued curves.
Syntax: rotate <axis> {-} <value>
rotate bond {<boolean>}
rotate molecule {<boolean>}
rotate all {<boolean>}
Rotate the molecule about the specified axis. Permitted values for the
axis parameter are "x", "y"
and "z". The integer parameter states the angle
in degrees for the structure to be rotated. For the X and Y axes, positive
values move the closest point up and right, and negative values move it
down and left, respectively. For the Z axis, a positive rotation acts
clockwise and a negative angle anti-clockwise.
Alternatively, this command may be used to specify which rotations the
mouse or dials will control. If 'rotate bond true' is selected, the
horizontal scroll bar will control rotation around the axis selected by
the 'bond src dst pick' command. If 'rotate all true' is selected, and
multiple molecules have been loaded, then all molecules will rotate
together. In all other cases, the mouse and dials control the the rotation
of the molecule selected by the molecule n' command.
RasTop Specific:
Syntax: rotate <axis> {-} <value>
rotate world <axis> {-} <value>
rotate bond <value>
rotate molecule {<boolean>}
rotate all {<boolean>}
The 'rotate <axis>' command rotates the
active molecule. Only one molecule is moved at a time; other loaded
molecules and the world origin are not moved. The rotation center is
always located in the bounding box of the molecule and changed if
necessary. The command is independent of the 'rotate all'
and 'rotate molecule' state ('off' or 'on').
The 'rotate world <axis>' command rotates
the entire world, even when only one molecule is loaded. If not rotation
center is specified, the rotation occurs around the world origin.
The 'rotate bond' command rotates around the bond
axis selected by the 'bond src dst pick' command.
There is no distinction between the 'save'
and the 'write' command.
Syntax: save {world|molecule} {<filename>}
Syntax: save <format> <filename>
pdb <filename>
mdl <filename>
alchemy <filename>
xyz <filename>
iris
ppm
ras
ps
epsf
monops
pict
vectps
script
molscript
kinemage
povray
vrml
phipsi
rdf, ramachandrandatafile
rpp, ramachandranprinterplot
Saving <*.rsm>
scripts:
The 'save <filename>' command will just
do that. If the file has been modified, a simple 'save' command
without
specified filename will save the file automatically. By default, all
molecules are saved ( 'save world' option).
Note: Files are modified by virtually all RasMol commands; resizing a
screen is an exception.
Saving molecular files:
A format keyword and a filename are required. For example 'save pdb <filename>'
save the currently selected set of atoms in a Protein Data Bank (PDB) format
file. Only selected atoms of the currently selected molecule are saved. Accepted formats are:
PDB, MDL, Alchemy(tm) and XYZ format. Atom coordinates are saved in the current
coordinate system. The format Alchemy in molecular coordinates saves also the
current rotation. If
the world contains 2 (or more) molecules, two (or more) separate files must be
generated and joined manually to create a unique molecular file; make sure you
do not save the files in molecular coordinates.
Saving image files:
A format keyword is required. The following formats are supported:
'bmp' (Microsoft
bitmap),
'gif' (Compuserve GIF),
'iris'
(IRIS RGB),
'ppm' (Portable Pixmap),
'ras'
(Sun rasterfile),
'ps' and 'epsf'
(Encapsulated PostScript),
'monops' (Monochrome
Encapsulated PostScript),
'pict' (Apple PICT),
'vectps'
(Vector Postscript).
As of RasTop 2.1, only the 'bmp' and 'pict' formats are working properly in
32-bits. To save 'gif' file, please use the 8-bits version.
Saving script files:
See above for <*.rsm>
scripts; The format 'script'
writes out a file containing the RasMol 'script'
commands to reproduce the current image. The format 'molscript'
writes out the commands required to render the current view of the
molecule as ribbons in Per Kraulis' Molscript program and the format 'kinemage'
the commands for David Richardson's program Mage. The following formats
are useful for further processing: 'povray' (POVRay, version
3.5 ), 'vrml' (VRML file).
Note: As of RasTop 2.1, only the formats 'script'
and 'povray' are working properly (although not every
details of the scenery are saved in povray). If the molecular
coordinates system is used to export POVRay scripts, only the active molecule is
saved (in molecular coordinates), otherwise all objects are saved.
Saving data file:
Finally, several formats are provided to provide phi-psi data for listing
or for 'phipsi' (phi-psi data as an annotated list with
cis omegas), 'ramachan' and 'RDF' and 'RamachandranDataFile'
(phi-psi data as columns of numbers for gnuplot), 'RPP'
and 'RamachandranPrinterPlot' (phi-psi data as a printer
plot).
Syntax: scale <value>
The scale command changes the magnification of the currently displayed
image. The value determines the distance of the smallest size of the
window screen either in RU if it is an integer number or in angstrom if it
is a floating number. This command is an alternative to the 'zoom'
command that is independent of the worlddepth
parameter.
Syntax: script <filename>
The RasMol 'script' command reads a set of RasMol
commands sequentially from a text file and executes them. This allows
sequences of commonly used commands to be stored and performed by single
command. A RasMol script file may contain a further script command up to a
maximum "depth" of 10, allowing complicated sequences of actions
to be executed. RasMol ignores all characters after the first '#'
character on each line allowing the scripts to be annotated. Script files
are often also annotated using the RasMol 'echo'
command.
The most common way to generate a RasMol script file is to use the 'write
script' or 'write rasmol'
commands to output the sequence of commands that are needed to regenerate
the current view, representation and colouring of the currently displayed
molecule.
The RasMol command 'source' is synonymous with the 'script'
command.
Scripts may also be created with a text editor.
RasTop Specific:
Syntax: script default <filename>
This command allows a script to run automatically after any molecular
files loaded, thus replacing the standard RasMol initial representation.
The file name is saved for future sessions.
Syntax: select {<expression>}
Define the currently selected region of the molecule. All subsequent
RasMol commands that manipulate a molecule or modify its colour or
representation only affect the currently selected region. The parameter of
a 'select' command is a RasMol expression that is
evaluated for every atom of the current molecule. The currently selected
(active) region of the molecule are those atoms that cause the expression
to evaluate true. To select the whole molecule use the RasMol command 'select
all'. The behaviour of the 'select' command
without any parameters is determined by the RasMol 'hetero'
and 'hydrogen' parameters.
Type 'help expression' on the
command line for more information on RasMol atom expressions or consult
the document on atom expressions and the predefined
atom sets.
RasTop specific:
Syntax: select previous
Select the atoms that were selected before the last 'select'
command.
Syntax: select <</>> x1{-x2},...,xi{-xi+1},...<</>>
This INTERNAL command is used to describe atom sets in rsm
scripts generated by RasTop. The character '<'
or '>' immediately following the 'select'
keyword escapes the parser. Each block describes a subset of atoms
bearing consecutive numbers that is added to the current
selection. Wrong blocks are ignored as well undefined atom numbers.
The character '<' starts a new selection at
the beginning of a line and continues the selection at the end; the
character '>' continues the selection at the
beginning of the line and ends it at the end.
RasTop specific:
Syntax: select view
This command selects all atoms present in the current view. This
is a scripting alternative to atom selection using the lasso.
Syntax: set <parameter> {<option>}
The RasMol 'set' command allows the user to alter
various internal program parameters such as those controlling rendering
options. Each parameter has its own set or permissible parameter options.
Typically, omitting the parameter option resets that parameter to its
default value. A list of valid parameter names is given below.
Syntax: show information
show phipsi
show RamPrint
show selected { group | chain | atom }
show sequence
show symmetry
RasTop Specific:
show world
show worlddepth
The RasMol 'show' command display details of the status
of the currently loaded molecule. The command 'show information'
lists the molecule's name, classification, PDB code and the number of
atoms, chains, groups it contains. If hydrogen bonding, disulphide bridges
or secondary structure have been determined, the number of hbonds, ssbonds,
helices, ladders and turns are also displayed, respectively. The command 'show
phipsi' shows the phi and psi angles of the currently selected
residues and the omega angles of cis peptide bonds. The command 'show
RamPrint' (or 'show RPP' or 'show RamachandranPrinterPlot') shows
a simple Ramachandran printer plot in the style of Frances Bernstein's
fisipl program. The command 'show selected' (or 'show
selected group' or 'show selected chain' or 'show selected atom' ) shows
the groups (default), chains or atoms of the current selection. The
command 'show sequence' lists the residues that comprise
each chain of the molecule. The command 'show symmetry'
shows the space group and unit cell of the molecule.
The command 'show world' lists information regarding
world center and world axes position and all loaded molecules with
position in world and absolute coordinates. The command 'show
worlddepth' lists the actual and the default worlddepth.
Syntax: slab {<boolean>}
slab <value>
The RasMol 'slab' command enables, disables or
positions the z-clipping plane of the molecule. The program only draws
those portions of the molecule that are further from the viewer than the
slabbing plane. Integer values range from zero at the very back of the
molecule to 100 which is completely in front of the molecule. Intermediate
values determine the percentage of the molecule to be drawn.
This command interacts with the 'depth'
command, which clips to the rear of a given z-clipping plane.
RasTop Specific:
Syntax: slab world origin
slab world <value>
The 'slab world origin' command sends the clipping
plane at the world origin. The 'slab world <value>'
command moves the plane of value Angstroms (if value if a floating number)
or value RasMol units (if value is an integer) relatively to its current
position. Future versions of RasMol may not adopt this convention.
Syntax: spacefill {<boolean>}
spacefill temperature
spacefill user
spacefill {-}<value>
The RasMol 'spacefill' command is used to represent all
of the currently selected atoms as solid spheres. This command is used to
produce both union-of-spheres and ball-and-stick models of a molecule. The
command, 'spacefill true', the default, represents each
atom as a sphere of van der Waals radius. The command 'spacefill
off' turns off the representation of the selected atom as
spheres. A sphere radius may be specified as an integer in RasMol units
(1/250th Ångstrom) or a value containing a decimal point. A value of 500
(2.0 Ångstroms) or greater results in a "Parameter value too
large" error. A negative value indicates a percentage of van des
Waals radius.
The 'temperature' option sets the radius of each sphere
to the value stored in its temperature field. Zero or negative values have
no effect and values greater than 2.0 are truncated to 2.0. The 'user'
option allows the radius of each sphere to be specified by additional
lines in the molecule's PDB file using Raster 3D's COLOUR record
extension.
The RasMol command 'cpk' is synonymous with the 'spacefill'
command.
Syntax: ssbonds {<boolean>}
ssbonds <value>
The RasMol 'ssbonds' command is used to represent the
disulphide bridges of the protein molecule as either dotted lines or
cylinders between the connected cysteines. The first time that the 'ssbonds'
command is used, the program searches the structure of the protein to find
half-cysteine pairs (cysteines whose sulphurs are within 3 Ångstroms of
each other) and reports the number of bridges to the user. The command 'ssbonds
on' displays the selected "bonds" as dotted lines, and
the command 'ssbonds off' disables the display of ssbonds
in the currently selected area. Selection of disulphide bridges is
identical to normal bonds, and may be adjusted using the RasMol 'set
bondmode' command. The colour of disulphide bonds may be
changed using the 'colour ssbonds'
command. By default, each disulphide bond has the colours of its connected
atoms.
By default disulphide bonds are drawn between the sulphur atoms within
the cysteine groups. By using the 'set
ssbonds' command the position of the cysteine's alpha carbons
may be used instead.
Syntax: star {<boolean>}
star temperature
star user
star <value>
The RasMol 'star' command is used to represent all of
the currently selected atoms as stars (six strokes, one each in the x, -x,
y, -y, z and -z directions). The commands 'select not bonded'
followed by 'star 75' are useful to mark unbonded atoms in
a 'wireframe' display with less
overhead than provided by 'spacefill 75'.
This can be done automatically for all subsequent wireframe displays with
the command 'set bondmode not
bonded'.
The command 'star true', the default, represents each
atom as a star with strokes length equal to van der Waals radius. The
command 'star off' turns off the representation of the
selected atom as stars. A star stroke length may be specified as an
integer in RasMol units (1/250th Ångstrom) or a value containing a
decimal point. A value of 500 (2.0 Ångstroms) or greater results in a
"Parameter value too large" error.
The 'temperature' option sets the stroke length of each
star to the value stored in its temperature field. Zero or negative values
have no effect and values greater than 2.0 are truncated to 2.0. The 'user'
option allows the stroke length of each star to be specified by additional
lines in the molecule's PDB file using Raster 3D's COLOUR record
extension.
The RasMol 'spacefill' command
can be used for more artistic rendering of atoms as spheres.
RasTop specific:
Spheres and stars are mutually exclusive, i.e. only one of the two
representations is used at a time for a given atom.
Syntax: stereo on
stereo [-]<number>
stereo off
The RasMol 'stereo' command provides side-by-side
stereo display of images. 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.
The inclusion of '[-] <number>' in the 'stereo'
command, as for example in 'stereo 3' or 'stereo -5',
also controls angle and direction.
The stereo command is only partially implemented. When stereo is turned
on, the image is not properly recentred. (This can be done with a 'translate
x -<number>' command.) It is not supported in vector
PostScript output files, is not saved by the 'write script'
command, and in general is not yet properly interfaced with several other
features of the program.
Syntax: strands {<boolean>}
strands <value>
strands dash
The RasMol 'strands' command displays the currently
loaded protein or nucleic acid as a smooth "ribbon" of
depth-cued curves passing along the backbone of the protein. The ribbon is
composed of a number of strands that run parallel to one another along the
peptide plane of each residue. The ribbon is drawn between each amino acid
whose alpha carbon is currently selected. The colour of the ribbon is
changed by the RasMol 'colour ribbon'
command. If the current ribbon colour is 'none' (the
default), the colour is taken from the alpha carbon at each position along
its length. The central and outermost strands may be coloured
independently using the 'colour ribbon1'
and 'colour ribbon2' commands,
respectively. The number of strands in the ribbon may be altered using the
RasMol 'set strands'
command.
The width of the ribbon at each position is determined by the optional
parameter in the usual RasMol units. By default the width of the ribbon is
taken from the secondary structure of the protein or a constant value of
720 for nucleic acids (which produces a ribbon 2.88 Ångstroms wide). The
default width of protein alpha helices and beta sheets is 380 (1.52
Ångstroms) and 100 (0.4 Ångstroms) for turns and random coil. The
secondary structure assignment is either from the PDB file or calculated
using the DSSP algorithm as used by the 'structure'
command. This command is similar to the RasMol command 'ribbons'
which renders the biomolecular ribbon as a smooth shaded surface.
Syntax: structure
The RasMol 'structure' command calculates secondary
structure assignments for the currently loaded protein. If the original
PDB file contained structural assignment records (HELIX, SHEET and TURN)
these are discarded. Initially, the hydrogen bonds of the current molecule
are found, if this hasn't been done already. The secondary structure is
then determined using Kabsch and Sander's DSSP algorithm. Once finished
the program reports the number of helices, strands and turns found.
Syntax: trace {<boolean>}
trace
trace temperature
trace dots <value>
The RasMol 'trace' command displays a smooth spline
between consecutive alpha carbon positions. This spline does not pass
exactly through the alpha carbon position of each residue, but follows the
same path as 'ribbons', 'strands'
and 'cartoons'. Note that residues may
be displayed as 'ribbons', 'strands',
'cartoons' or as a 'trace'.
Enabling one of these representations disables the others. However, a
residue may be displayed simultaneously as backbone and as one of the
above representations. This may change in future versions of RasMol. Prior
to version 2.6, 'trace' was synonymous with 'backbone'.
'Trace temperature' displays the backbone as a wider
cylinder at high temperature factors and thinner at lower. This
representation is useful to X-ray crystallographers and NMR
spectroscopists.
'Trace dots' displays the backbone as a
series of dots. This commands is useful to link parts of the
molecule represented with a full cylinder. The subcommand '<value>'
is RasTop specific and fixe the radius of the dots.
Syntax: translate <axis> {-} <value>
The RasMol 'translate' command moves the position of
the centre of the molecule on the screen. The axis parameter specifies
along which axis the molecule is to be moved and the integer parameter
specifies the absolute position of the molecule centre from the middle of
the screen. Permitted values for the axis parameter are "x",
"y" and "z".
Displacement values must be between -100 and 100 which correspond to
moving the current molecule just off the screen. A positive "x"
displacement moves the molecule to the right, and a positive "y"
displacement moves the molecule down the screen. The pair of commands 'translate
x 0' and 'translate y 0' centers the molecule on
the screen.
RasTop Specific:
The displacement values in the classical RasMol command are expressed
in percent of either the screen width or the screen height; displacement
values along the Z-axis are ineffective. In RasTop, the 3 axis are active.
Displacements values are expressed in percent of the smallest screen side,
either width or height. Translation displacements are limited in RasMol to
values between -100 and 100. In RasTop, displacement are unlimited. See
also the command 'position' ,
which places molecules independently of the zoom value.
Syntax: translate world <axis> {-} <value>
The 'translate world' command translates the
origin of the world and all molecules along the X- and the Y-axis.
Displacement values along the Z-axis are made relatively to the world
plane.
Syntax: unbond <number> <number>
The RasMol command 'unbond <number> <number>' removes the
designated bond from the drawing.
The command 'unbond' without arguments removes a bond previously picked by
the 'bond <number> <number> pick' command.
Syntax: wireframe {<boolean>}
wireframe <value>
wireframe dash
The RasMol 'wireframe' command represents each bond within the
selected region of the molecule as a cylinder, a line, a dashed line, or a
depth-cued vector. The display of bonds as depth-cued vectors (drawn
darker the further away from the viewer) is turned on by the command 'wireframe'
or 'wireframe on'. The selected bonds are displayed as cylinders by
specifying a radius either as an integer in RasMol units or containing a
decimal point as a value in Ångstroms. A parameter value of 500 (2.0
Ångstroms) or above results in an "Parameter value too large"
error. Bonds may be coloured using the 'colour bonds'
command.
Non-bonded atoms, which could become invisible in an ordinary 'wireframe'
display can be marked by a preceding 'set
bondmode not bonded' command. If nearly co-linear bonds to
atoms cause them to be difficult to see in a wireframe display, the 'set
bondmode all' command will add markers for 'all'
atoms in subsequent 'wireframe' command executions.
The distinction between this command and the RasMol 'save'
command has been dropped; See RasMol 'save'
command.
Syntax: zap {all | world }
zap selected
zap molecule
RasTop Specific:
Deletes the contents of all current databases and resets parameter
variables to their initial default state. The command 'zap
selected' or 'zap molecule' deletes only the
active molecule.
Syntax: zoom {<boolean>}
zoom <value>
Change the magnification of the currently displayed image. Boolean
parameters either magnify or reset the scale of current molecule. An
integer parameter specifies the desired magnification as a percentage of
the default scale. The minimum parameter value is 10; the maximum
parameter value is dependent upon the size of the molecule being
displayed. For medium sized proteins this is about 500.
RasTop specific:
Syntax: zoom world <value>
Change the magnification of the currently displayed image from the
center of the screen, independently of the actual center position, giving
a zoom-translation effect.
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