This may be enabled and disabled using the
set cartoons
Centre
Syntax: center {<expression>}
centre {<expression>}
The RasMol centre command defines the point about which the rotate command and the scroll bars rotate the current molecule. Without a parameter the centre command resets the centre of rotation to be 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 for more information on RasMol atom expressions.
Clipboard
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 transfering 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.
Colour
Syntax: colour {<object>} <colour>
color {<object>} <colour>
color {<object>} <[RGB triplet]>
Colour the atoms (or other objects) of the selected zone. 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. A typical RGB triplet is [255,255,255] which is the colour white. Typing the command help colours will give a list of all the predefined colour names recognised by RasMol.
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). This command is especially useful in script files.
Atom objects can also be coloured by cpk, amino, chain, group, shapely, structure, temperature, charge, and user. Hydrogen bonds can also be coloured by type and dot surfaces can also be coloured by electrostatic potential.
For more information see colours.
Connect
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 an extremely fast heuristic algorithmm that is suitable for determing 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 for 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 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.
Define
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.
Dots
Syntax: dots {<boolean>}
dots <value>
The RasMol dots command is used to generate a Van der Waal's 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 Waal's 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 it's closest atom at the time the surface is generated. The colour of the whole dot surface may be changed using the colour dots command.
Echo
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.
Exit
Syntax: exit
The RasMol exit command is used to terminate execution of a script (returning to the command line, or the calling script), or of inter-process communication, closing the link between programs.
The quit command, in contrast, terminates the execution of RasMol itself.
HBonds
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.
Help
Syntax: help {<topic> {<subtopic>}}
? {<topic> {<subtopic>}}
The RasMol help command provides on-line help on the given topic.
Label
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 of the displayed text may be changed using the set fontsize 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; three letter code
%r Residue Number
The syntax of RasMol atom expressions allows the selection
of individual molecule conformations if present in an NMR file.
The simplest form of the atom expression is the syntax
::25 to select model 25 from the molecule.
This is equivalent to the atom expression
model = 25
as the keyword model may now be used in comparison expressions. The most general form of atom expression is now CYS32:A:25.SG which denotes the gamma sulphur of residue cysteine-32 in chain A of model 25.
Individual chains may be specified by the syntax ":A" for chain A, or ":1" for chain 1 (i.e. the wildcard may be dropped from the expression "*:A"). This may also be extended to NMR models; ":A:4" denotes chain A of model 4, and even more terse means all atoms in all chains of NMR model 4.
Load
Syntax: load {<format>} <filename>
load {<format>} inline
Load a molecule co-ordinate file into RasMol2. Valid molecule file formats are pdb (Brookhaven Protein Databank), mdl (Molecular Design Limited's MOL file format), alchemy (Tripos' Alchemy file format), mol2 (Tripos' Sybyl Mol2 file format), mopac (mopac file format; either cartesian or z-matrix format), nmrpdb (nmr multi-pdb file format), charmm (CHARMm file format) or xyz (MSC's XMol XYZ file format). If no file format is specified, pdb is assumed by default. Only a single molecule may be loaded at a time. To delete a molecule prior to loading another use the RasMol zap command.
The load command selects all the atoms in the molecule, centres 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 less bonds than atoms, RasMol determines connectivity using the connect command.
The load inline command also allows Storing Atom Co-ordinates in Scripts to allow better integration with WWW browsers. A load command executed inside a script file may now specify the keyword inline instead of a conventional filename. This option specifies that the co-ordinates 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 co-ordinates in PDB file format. Because in Brookhaven PDB file format, any line not recognised by the parser should be ignored, only lines beginning ATOM, HETATM, TER, etc. are examined. Hence a file may be both a RasMol script and a PDB file simultaneously. This allows both co-ordinate and representation data to be transmitted as a single file. One possible use is a standard RasMol script prefix that may be concatenated with an appropriate PDB file on-the-fly.
Monitor
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.
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 it 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.
Pause
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 ushed 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 normal, 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: 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, allowing 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.
Techniques for high-resolution printing are discussed in the FAQ.
Quit
Syntax: quit
Exit from the RasMol program. The RasMol command exit has a different function.
Refresh
Syntax: refresh
The RasMol refresh command is used in script files to redraw the local image.
Renumber
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 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.
Reset
Syntax: reset
The RasMol reset command restores the original viewing transformation and centre of rotation. The scale is set to it 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.
This command should not be mistaken for the RasMol zap command which deletes the currently stored molecule, returning the program to its initial state.
Restrict
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 effect 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.
The restrict command now turns off the display of ribbons, strands, cartoons and backbones outside of the given atom expression.
Type "help expression" for more information on RasMol atom expressions.
Ribbons
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 Angstroms) for nucleic acids. The default width of protein alpha helices and beta sheets is 380 (1.52 Angstroms) and 100 (0.4 Angstroms) 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.
Rotate
Syntax: rotate <axis> {-} <value>
Rotate the molecule about the specified axis. Permited values for the axis parameter are "<tt><b>x</b></tt>", "<tt><b>y</b></tt>" and "<tt><b>z</b></tt>". 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.
Save
Syntax: save {pdb} <filename>
save alchemy <filename>
save mdl <filename>
Save the currently selected set of atoms in either a Brookhaven Protein Database (PDB) or Alchemy(tm) format file. The distinction between this command and the RasMol write command has been dropped. The only difference is that without a format specifier the save command generates a PDB file and the write command generates a GIF image.
Script
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 compilicated 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.
A RasMol script file can be generated with 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. Such automatically-generated scripts generate only a single image.
RasMol script files can also be created manually with a text editor. Such scripts, through use of the pause and refresh commands, can generate "movies". Detailed guides to script creation are available.
The RasMol command source is synonymous with the script command.
Select
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 effects 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" for more information on RasMol atom expressions.
There is a separate introduction to Select commands in Chime and RasMol.
Set
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, omiting the parameter option resets that parameter to its default value. A list of valid parameter names is given below.
Show
Syntax: show information
show sequence
show symmetry
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 sequence lists the residues that compose each chain of the molecule.
Slab
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. 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.
Rotation rotates the molecule through a fixed slab plane. Therefore, stereo does not produce a valid stereo image when slab is on.
See also set slabmode.
Spacefill
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, spacefilll 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 Angstrom) or a value containing a decimal point. A value of 500 (2.0 Angstroms) or greater results in a "Parameter value too large" error.
The temperature option sets the radius of each sphere to the value stored in its temperature field. Zero or negative values causes have no effect and values greater than 2.0 are truncated to 2. The user option allows the radius of each spheres to be specified by additional lines in the molecule's PDB file using Raster 3D's COLOR record extension.
The RasMol command cpk is synonymous with the spacefill command.
SSBonds
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 angstroms 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.
Stereo
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.
As of RasMol version 2.6-beta-2, the stereo command is only partially implemented. When stereo is turned on, the image is not properly recentered. (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. When slab is on together with stereo, the image which results is not a stereoscopic view.
Strands
Syntax: strands {<boolean>}
strands <value>
strands dashes
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 colour of 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 Angstroms wide). The default width of protein alpha helices and beta sheets is 380 (1.52 Angstroms) and 100 (0.4 Angstroms) 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.
Wireframe, backbone and strands representations may be displayed with dashed (dotted) lines. This is enabled by allowing the dash or dashes parameters to the wireframe, backbone and strands commands.
Structure
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 and SHEET) these are discarded. Initially, the hydrogen bonds of the current molecule are found, if this hasn't been done already. The secondary structure is the determined using Kabsch and Sander's DSSP algorithm. Once finished the program reports the number of helices, strands and turns found.
Trace
Syntax: trace {<boolean>}
trace <value>
trace temperature
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 each residue may be displayed as either a ribbon, strands, cartoon or trace, and enabling one of these representation disables the others. However, a residue may be displayed simultaneously as backbone and one of the above representations [though 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.
Translate
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. Permited 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 centres the molecule on the screen.
Wireframe
Syntax: wireframe {<boolean>}
wireframe <value>
wireframe dashes
The RasMol wireframe command represents each bond within the selected region of the molecule as either a cylinder, a line or 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 Angstroms. A parameter value of 500 (2.0 angstroms) or above results in an "Parameter value too large" error. Bonds may be coloured using the colour bonds command.
Wireframe, backbone and strands representations may be displayed with dashed (dotted) lines. This is enabled by allowing the dash or dashes parameters to the wireframe, backbone and strands commands.
Write
Syntax: write {<format>} <filename>
Write the current image to a file in a standard raster format. Currently supported image file formats include "gif" (Compuserve GIF), "iris" (IRIS RBG format), "ppm" (Portable Pixmap), "ras" (Sun rasterfile), "ps" and "epsf" (Encapsulated PostScript), "monops" (Monochrome Encapsulated PostScript), "vectps" (Vector PostScript, see below), "bmp" (Microsoft bitmap) and "pict" (Apple PICT). The write command may also be used to generate command scripts for other graphics programs. 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 RasMol command write vectps <filename> creates a postscript file at printer resolution, which can then be sent to your printer. (This command is not on RasMol's Export menu nor is it documented in the on-line help. The command write ps filename writes raster postscript at screen resolution.) The disadvantage of vector postscript is that at present it does not support ribbons, cartoons, strands, or traces. Note that the set vectps on command adds outlines to cylinder bonds or spheres. However, it presently does not work for spheres intersecting more than one other sphere. Thus, it works well for stick or ball-and-stick images but not for most spacefilling images.
Techniques for high-resolution printing are discussed in the FAQ.
The distinction between this command and the RasMol save command has been dropped. The only difference is that without a format specifier the save command generates a PDB file and the write command generates a GIF image.
The set write command enables and disables the use of "save" and "write" in scripts.
The "write gif <filename>" command allows generation of transparent GIFs. This may be controlled by the "set transparent on" and "set transparent off" commands.
Zap
Syntax: zap
Deletes the contents of the current database and resets parameter variables to their initial default state.
Zoom
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.
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 under the set command.
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 that 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 co-ordinate axes on
the current display. The co-ordinate 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 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 postive direction of the cartesian axes.
Set Backfade
Syntax: set backfade on
set backfade off
Shading to an arbitrary background colour, 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 {<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.
The RasMol set bondmode command controls the mechanism used to select individual bonds. When using the
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 commands "set bonds off" and "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 molecules 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-terminus of beta-sheets are displayed as arrow heads.
This may be enabled and disabled using the set cartoons
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 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. his parameter is similar to the RasMol ssbonds parameter.
Set FontSize
Syntax: set fontsize {<value>}
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 32 pixels, and the default value is 8 pixels high. 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 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 heterogenous 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. See also the group colour scheme, which is affected by the value of the hetero parameter. The Hetero Atoms item on RasMol's Options menu can also be used to toggle the value of the hetero parameter.
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 enable 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 or deuterium 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 heterogenous 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 co-ordinate 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 as image as possible when using Microsoft Windows.
Set Monitor
Syntax: set monitor on
set monitor off
The distance monitor labels may be turned off with the command set monitors off, and re-enabled with the command set monitors 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 provide the same mouse bindings as other packages for experienced users.
Set Picking
Syntax: set picking on
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
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 it residue name, residue number, atom name,
atom serial number and chain in the command window.
This behaviour 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 whist 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 isn't 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 command
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 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 it 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 Angstroms. The default value of this parameter is determined by the value of solvent and 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 is 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 spacefilled atoms cut by the slabbing (z-clipping) plane. The rendering of bonds, cartoons, ribbons, and strands is a reject mode (see below), and is not affected by the slab mode. Valid slabmode parameters are reject (the default for bonds and cartoons), half, hollow, solid (the default for spacefilled atoms), and section.
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 cutting planes, one behind the other. Everything behind the rear plane, 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 plane hidden. 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 behaviour 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, the solvent radius, to 1.2 Angstroms (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 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. his parameter is similar to the RasMol hbonds parameter.
Set Stereo
command.
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.
The command stereo on . 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 display details of the crystal's space group and unit cell axes. The set unitcell command is similar the 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 by 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 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 such as Mosaic or NetScape). However, animators may start up RasMol interactively, type set write on and then execute a script to generate each frame using the source command.
Atom Expressions
RasMol atom expressions uniquely identify an arbitrary group of atoms within a molecule. Atom expressions are composed of either primitive expressions, predefined sets, comparison operators, within expressions, or logical (boolean) combinations of the above expression types.The logical operators allow complex queries to be constructed out of simpler ones using the standard boolean connectives and, or and not. These may be abbreviated by the symbols "&", "|", and "!", respectively. Parentheses (brackets) may be used to alter the precedence of the operators. For convenience, a comma may also be used for boolean disjunction.
The atom expression is evaluated for each atom, hence protein and backbone selects protein bacbone atoms, not the protein and [nucleic] acid backbone atoms!
Examples: backbone and not helix
within( 8.0, ser70 )
not (hydrogen or hetero)
not *.FE and hetero
8, 12, 16, 20-28
arg, his, lys
Example Expressions
The following table gives some useful examples of RasMol atom expressions.
Expression Interpretation
* All atoms
cys Atoms in cysteines
hoh Atoms in heterogenous water molecules
as? Atoms in either asparagine or aspartic acid
*120 Atoms at residue 120 of all chains
*p Atoms in chain P
*.n? Nitrogen atoms
cys.sg Sulphur atoms in cysteine residues
ser70.c? Carbon atoms in serine-70
hem*p.fe Iron atoms in the Heme groups of chain P
Primitive Expressions
RasMol primitive expressions are the fundamental building blocks of atom expressions. There are two types of primitive expression. The first type is used to identify a given residue number or range of residue numbers. A single residue is identified by its number (position in the sequence), and a range is specified by lower and upper bounds separated by a hyphen character. For example select 5,6,7,8 is also select 5-8. Note that this selects the given residue numbers in all macromolecule chains.
The second type of primitive expression specifies a sequence of fields that must match for a given atom. The first part specifies a residue (or group of residues) and an optional second part specifies the atoms within those residues. The first part consists of a residue name, optionally followed by a residue number and/or chain identifier.
A residue name typically consists of up to three alphabetic characters, which are case insensitive. Hence the primitive expressions SER and ser are equivalent, identifying all serine residues. Residue names that contain non-alphabetic characters, such as sulphate groups, may be delimited using square brackets, i.e. [SO4]
The residue number is the residue's position in the macromolecule sequence. Negative sequence numbers are permited. For example, SER70 Care must be taken when specifying both residue name and number, it the group at the specified position isn't the specified residue no atoms are selected.
The chain identifier is typically a single case-insensitive alphabetic or numeric character. Numeric chain identifiers must be distinguished or separated from residue numbers by a colon character. For example, SER70A or SER70:1
The second part consists of a period character followed by an atom name. An atom name may be up to four alphabetic or numeric characters.
An asterisk may be used as a wild card for a whole field and a question mark as a single character wildcard.
Comparison Operators
Parts of a molecule may also be distinguished using equality, inequality and ordering operators on their properties. The format of such comparison expression is a property name, followed by a comparison operator and then an integer value.
The atom properties that may be used in RasMol are atomno for the atom serial number, elemno for the atom's atomic number (element), resno for the residue number, radius for the spacefill radius in RasMol units (or zero if not represented as a sphere) and temperature for the PDB anisotropic temperature value.
The equality operator is denoted either = or ==. The inequality operator as either <>, !=, or /=. The ordering operators are < for less than, <= for less than or equal to, > for greater than, and >= for greater than or equal to.
Examples: resno < 23
temperature >= 900
atomno == 487
Within Expressions
A RasMol within expression allows atoms to be selected on their proximity to another set of atoms. A within expression takes two parameters separated by a comma and surrounded by parenthesis. The first argument is an integer value called the "cut-off" distance of the within expression and the second argument is any valid atom expression. The cut-off distance is expressed in either integer RasMol units or Angstroms containing a decimal point. An atom is selected if it is within the cut-off distance of any of the atoms defined by the second argument. This allows complex expressions to be constructed containing nested within expressions.
For example, the command select within(3.2,backbone) selects any atom within a 3.2 Angstrom radius of any atom in a protein or nucleic acid backbone. Within expressions are particularly useful for selecting the atoms around an active site.
Predefined Sets
RasMol atom expressions may contain predefined sets. These sets are single keywords that represent portions of a molecule of interest. Predefined sets are often abbreviations primitive atom expressions, and in some cases of selecting areas of a molecule that could not otherwise be distinguished. The Venn diagram below, kindly contributed by Kurt Giles, summarizes most of the predefined terms. A hyperlinked list of the currently predefined sets is tabulated below the diagram. In addition to the sets listed here, RasMol also treats element names (and their plurals) as predefined sets containing all atoms of that element type, i.e. the command select oxygen is equivalent to the command select elemno=8.
AT Set
This set contains the atoms in the complementary nucleotides adenosine and thymidine (A and T respectively). All nucleotides are classified as either the set at or the set cg This set is equivalent to the RasMol atom expressions "a,t" and "nucleic and not cg"
Acidic Set
The set of acidic amino acids. These are the residue types Asp and Glu. All amino acids are classified as either acidic, basic or neutral. This set is equivalent to the RasMol atom expressions "asp, glu" and "amino and not (basic or neutral)"
Acyclic Set
The set of atoms in amino acids not containing a cycle or ring. All amino acids are classified as either cyclic or acyclic. This set is equivalent to the RasMol atom expression "amino and not cyclic"
Aliphatic Set
This set contains the aliphatic amino acids. These are the amino acids Ala, Gly, Ile, Leu and Val. This set is equiavlent to the RasMol atom expression "ala, gly, ile, leu, val"
Alpha Set
The set of alpha carbons in the protein molecule. This set is approximately equivalent to the RasMol atom expression "*.CA" This command should not be confused with the predefined set helix which contains the atoms in the amino acids of the protein's alpha helices.
Amino Set
This set contains all the atoms contained in amino acid residues. This is useful for distinguishing the protein from the nucleic acid and heterogenous atoms in the current molecule database.
Aromatic Set
The set of atoms in amino acids containing aromatic rings. These are the amino acids His, Phe, Trp and Tyr. Because they contain aromatic rings all members of this set are member of the predefined set cyclic. This set is equivalent to the RasMol atom expressions "his, phe, trp, tyr" and "cyclic and not pro"
Backbone Set
This set contains the four atoms of each amino acid that form the polypeptide N-C-C-O backbone of proteins, and the atoms the sugar phosphate backbone of nucleic acids. Use the RasMol predefined sets protein and nucleic to distinguish between the two forms of backbone. Atoms in nucleic acids and proteins are either backbone or sidechain. This set is equivalent to the RasMol expression "(protein or nucleic) and not sidechain"
The predefined set mainchain is synonymous with the set backbone.
Basic Set
The set of basic amino acids. These are the residue types Arg, His and Lys. All amino acids are classified as either acidic, basic or neutral. This set is equivalent to the RasMol atom expressions "arg, his, lys" and "amino and not (acidic or neutral)"
Bonded Set
This set contain all the atoms in the current molecule database that are bonded to atleast one other atom.
Buried Set
This set contains the atoms in those amino acids that tend (prefer) to buried inside protein, away from contact with solvent molecules. This set refers to the amino acids preference and not the actual solvent acessibility for the current protein. All amino acids are classified as either surface or buried. This set is equivalent to the RasMol atom expression "amino and not surface", or "ala, leu, val, ile, phe, cys, met, trp", or "(hydrophobic and not pro) or cys".
CG Set
This set contains the atoms in the complementary nucleotides cytidine and guanoine (C and G respectively). All nucleotides are classified as either the set at or the set cg This set is equivalent to the RasMol atom expressions "c,g" and "nucleic and not at"
Charged Set
This set contains the charged amino acids. These are the amino acids that are either acidic or basic. Amino acids are classified as being either charged or neutral. This set is equivalent to the RasMol atom expressions "acidic or basic" and "amino and not neutral"
Cyclic Set
The set of atoms in amino acids containing a cycle or rings. All amino acids are classified as either cyclic or acyclic. This set consists of the amino acids His, Phe, Pro, Trp and Tyr. The members of the predefined set aromatic are members of this set. The only cyclic but non-aromatic amino acid is proline. This set is equivalent to the RasMol atom expressions "his, phe, pro, trp, tyr" and "aromatic or pro" and "amino and not acyclic"
Cystine Set
This set contains the atoms of cysteine residues that form part of a disulphide bridge, i.e. half cystines. RasMol automatically determines disulphide bridges, if neither the predefined set cystine nor the RasMol ssbonds command have been used since the molecule was loaded. The set of free cysteines may be determined using the RasMol atom expression "cys and not cystine"
Helix Set
This set contains all atoms that form part of a protein alpha helix as determined by either the PDB file author or Kabsch and Sander's DSSP algorithm. By default, RasMol uses the secondary structure determination given in the PDB file if it exists. Otherwise, it uses the DSSP algorithm as used by the RasMol structure command.
This predefined set should not be confused with the predefined set alpha which contains the alpha carbon atoms of a protein.
Hetero Set
This set contains all the heterogenous atoms in the molecule. These are the atoms described by HETATM entries in the PDB file. These typically contain water, cofactors and other solvents and ligands. All hetero atoms are classified as either ligand or solvent atoms. These heterogenous solvent atoms are further classified as either water or ions.
Hydrogen Set
This predefined set contains all the hydrogen and deuterium atoms of the current molecule. This predefined set is equivalent to the RasMol atom expression "elemno=1"
Hydrophobic Set
This set contains all the hydrophobic amino acids. These are the amino acids Ala, Leu, Val, Ile, Pro, Phe, Met and Trp. All amino acids are classified as either hydrophobic or polar. This set is equivalent to the RasMol atom expressions "ala, leu, val, ile, pro, phe, met, trp" and "amino and not polar"
Ions Set
This set contains all the heterogenous phosphate and sulphate ions in the current molecule data file. A large number of these ions are sometimes associated with protein and nucleic acid structures determined by X-ray crystallography. These atoms tend to clutter an image. All hetero atoms are classified as either ligand or solvent atoms. All solvent atoms are classified as either water or ions.
Large Set
All amino acids are classified as either small, medium or large. This set is equivalent to the RasMol atom expression "amino and not (small or medium)"
Ligand Set
This set contains all the heterogenous cofactor and ligand moieties that are contained in the current molecule data file. At this set is defined to be all hetero atoms that are not solvent atoms. Hence this set is equivalent to the RasMol atom expression "hetero and not solvent"
Medium Set
All amino acids are classified as either small, medium or large. This set is equivalent to the RasMol atom expression "amino and not (large or small)", or "val, thr, asp, asn, pro, cys".
Neutral Set
The set of neutral amino acids. All amino acids are classified as either acidic, basic or neutral. This set is equivalent to the RasMol atom expression "amino and not (acidic or basic)"
Nucleic Set
The set of all atoms in nucleic acids, which consists of the four nucleotide bases adenosine, cytidine, guanosine and thymidine (A, C, G and T respectively). All neucleotides are classified as either purine or pyrimidine. This set is equivalent to the RasMol atom expressions "a,c,g,t" and "purine or pyrimidine"
Polar Set
This set contains the polar amino acids. All amino acids are classified as either hydrophobic or polar. This set is equivalent to the RasMol atom expression "amino and not hydrophobic"
Protein Set
The set of all atoms in proteins. This consists of the RasMol predefined set amino and common post-translation modifications.
Purine Set
The set of purine nucleotides. These are the bases adenosine and guanosine (A and G respectively). All nucleotides are either purines or pyrimidines. This set is equivalent to the RasMol atom expressions "a,g" and "nucleic and not purine"
Pyrimidine Set
The set of pyrimidine nucleotides. These are the bases cytidine and thymidine (C and T respectively). All nucleotides are either purines or pyrimidines. This set is equivalent to the RasMol atom expressions "c,t" and "nucleic and not pyrimidine"
Selected Set
This set contains the set of atoms in the currently selected region. The currently selected region is defined by the preceding select or restrict command and not the atom expression containing the selected keyword.
Sheet Set
This set contains all atoms that form part of a protein beta sheet as determined by either the PDB file author or Kabsch and Sander's DSSP algorithm. By default, RasMol uses the secondary structure determination given in the PDB file if it exists. Otherwise, it uses the DSSP algorithm as used by the RasMol structure command.
Sidechain Set
This set contains the functional sidechains of any amino acids and the base of each nucleotide. These are the atoms not part of the polypeptide N-C-C-O backbone of proteins or the sugar phosphate backbone of nucleic acids. Use the RasMol predefined sets protein and nucleic to distinguish between the two forms of sidechain. Atoms in nucleic acids and proteins are either backbone or sidechain. This set is equivalent to the RasMol expression "(protein or nucleic) and not backbone"
Small Set
All amino acids are classified as either small, medium or large. This set is equivalent to the RasMol atom expression "amino and not (medium or large)", or "ala, gly, ser".
Solvent Set
This set contains the solvent atoms in the molecule co-ordinate file. These are the heterogenous water molecules, phosphate and sulphate ions. All hetero atoms are classified as either ligand or solvent atoms. All solvent atoms are classified as either water or ions. This set is equivalent to the RasMol atom expressions "hetero and not ligand" and "water or ions"
Surface Set
This set contains the atoms in those amino acids that tend (prefer) to be on the surface of proteins, in contact with solvent molecules. This set refers to the amino acids preference and not the actual solvent accessibility for the current protein. All amino acids are classified as either surface or buried. This set is equivalent to the RasMol atom expression "amino and not buried" or "gly, ser, thr, lys, asp, asn, glu, pro, arg, gln, tyr, his" or "(polar and not cys) or pro".
Turn Set
This set contains all atoms that form part of a protein turns as determined by either the PDB file author or Kabsch and Sander's DSSP algorithm. By default, RasMol uses the secondary structure determination given in the PDB file if it exists. Otherwise, it uses the DSSP algorithm as used by the RasMol structure command.
Water Set
This set contains all the heterogenous water molecules in the current database. A large number of water molecules are sometimes associated with protein and nucleic acid structures determined by X-ray crystallography. These atoms tend to clutter an image. All hetero atoms are classified as either ligand or solvent atoms. The solvent atoms are further classified as either water or ions.
Colours and Colour Schemes
The RasMol colour command allows different objects (such as atoms, bonds and ribbon segments) to be given a specified colour. Typically this colour is either a RasMol predefined colour name or an RGB triple. Additionally RasMol also supports:- cpk
- amino
- chain
- group
- shapely
- structure
- temperature
- charge and
- user colour schemes for atoms,
- hbond type for hydrogen bonds, and the
- electrostatic potential colour scheme for dot surfaces.
NAME RASMOL HTML *
black [0,0,0] 00 00 00
white [255,255,255] FF FF FF
blue [0,0,255] 00 00 FF
green [0,255,0] 00 FF 00
red [255,0,0] FF 00 00
yellow [255,255,0] FF FF 00
magenta [255,0,255] FF 00 FF
cyan [0,255,255] 00 FF FF
orange [255,165,0] FF A5 00
redorange [255,69,0] FF 45 00
violet [238,130,238] EE 82 EE
purple [160,32,240] A0 20 F0
greenblue [46,139,87] 2E 8B 57
* RGB = Red, Green, Blue. Decimal values are given
for assigning colors in RasMol with its 'color' command.
Hexadecimal is given to match text colors in HTML, e.g.
<font color="#8F8FFF">Nitrogen</font>,
which looks like this: Nitrogen.
Here is a CPK color key as an HTML table which could be used,
for example, next to a Chime display:
| C H O N S |
If you frequently wish to use a colour not predefined, you can write a one-line script. For example, if you make the file grey.spt containing the line
colour [180,180,180] #grey
then the command script grey.spt colours the currently selected atom set grey. (Or, you can color it gray. :-)
Amino Colours
The RasMol amino colour scheme colours amino acids according to traditional amino acid properties. The purpose of colouring is to identify amino acids in an unusual or surprising environment. The outer parts of a protein that are polar are visible (bright) colours and non-polar residues darker. Most colours are hallowed by tradition. This colour scheme is similar to the shapely scheme.
ASP,GLU bright red [230,10,10] E6 0A 0A LYS,ARG blue [20,90,255] 14 5A FF PHE,TYR mid blue [50,50,170] 32 32 AA GLY light grey [235,235,235] EB EB EB ALA dark grey [200,200,200] C8 C8 C8 HIS pale blue [130,130,210] 82 82 D2 CYS,MET yellow [230,230,0] E6 E6 00 SER,THR orange [250,150,0] FA 96 00 ASN,GLN cyan [0,220,220] 00 DC DC LEU,VAL,ILE green [15,130,15] 0F 82 0F TRP pink [180,90,180] B4 5A B4 PRO flesh [220,150,130] DC 96 82
Chain Colours
The RasMol chain colour scheme assigns each macromolecular chain a unique colour. This colour scheme is particularly useful for distinguishing the parts of multimeric structure or the individual `strands' of a DNA chain.
CPK Colours
The RasMol
cpk
colour scheme is based upon the colours of the popular plastic
spacefilling models which were developed by Corey, Pauling and later
improved by Kultun. This colour scheme colours `atom' objects by the
atom (element) type. This is the scheme conventionally used by chemists.
The assignment of element type to colours is given below.
(Information below is based on RasMol's source code and as of
February 19, 1998, is believed to be complete and correct here
for the first time.)
ELEMENT COLOR NAME RGB DECIMAL RGB HEXADECIMAL
Carbon light grey [200,200,200] C8 C8 C8
Oxygen red [240,0,0] F0 00 00
Hydrogen white [255,255,255] FF FF FF
Nitrogen light blue [143,143,255] 8F 8F FF
Sulphur sulphur yellow [255,200,50] FF C8 32
Chlorine, Boron green [0,255,0] 00 FF 00
Phosphorus, Iron, Barium orange [255,165,0] FF A5 00
Sodium blue [0,0,255] 00 00 FF
Magnesium forest green [34,139,34] 22 8B 22
Zn, Cu, Ni, Br brown [165,42,42] A5 2A 2A
Ca, Mn, Al, Ti, Cr, Ag dark grey [128,128,144] 80 80 90
F, Si, Au goldenrod [218,165,32] DA A5 20
Iodine purple [160,32.240] A0 20 F0
Lithium firebrick [178,34,34] B2 22 22
Helium pink [255,192,203] FF C0 CB
Unknown deep pink [255,20,147] FF 14 93
Group Colours
The RasMol group colour scheme colour codes residues by their position in a macromolecular chain. Each chain is drawn as a smooth spectrum from blue through green, yellow and orange to red. The N termini of proteins are coloured blue (similar to the CPK colour for nitrogen) and the C termini, red (similar to the CPK colour for oxygen). The 5' termini of nucleic acids are coloured blue, and the 3' termini, red.
If a chain has a large number of heterogenous molecules associated with it, the macromolecule may not be drawn in the full range of the spectrum. When RasMol performs group colouring it decides the range of colours it uses from the residue numbering given in the PDB file. Hence the lowest residue number is displayed in blue and the highest residue number is displayed as red. Unfortunately, if a PDB file contains a large number of hetatoms, such as water molecules, that occupy the high residue numbers, the protein is displayed in the blue-green end of the spectrum and the waters in the yellow-red end of the spectrum. This is aggrevated by there typically being many more water molecules than amino acid residues. The solution to this problem is to use the command set hetero off before applying the group colour scheme. This can also be achieved by toggling Hetero atoms on the Options menu before selecting Group on the Colour menu. This command instructs RasMol to only use non-hetero residues in the group colour scaling.
Shapely Colours
The RasMol shapely colour scheme colour codes residues by amino acid property. This scheme is based upon Bob Fletterick's "Shapely Models". Each amino acid and nucleic acid residue is given a unique colour. The shapely colour scheme is used by David Bacon's Raster3D program. This colour scheme is similar to the amino colour scheme.
Structure Colours
The RasMol structure colour scheme colours the molecule by protein secondary structure. Alpha helices are coloured magenta, [240,0,128], beta sheets are coloured yellow, [255,255,0], turns are coloured pale blue, [96,128,255] and all other residues are coloured white. The secondary structure is either read from the PDB file (HELIX and SHEET records), if available, or determined using Kabsch and Sander's DSSP algorithm. The RasMol structure command may be used to force DSSP's structure assignment to be used.
Temperature Colours
The RasMol temperature colour scheme colour codes each atom according to the anisotropic temperature (beta) value stored in the PDB file. Typically this gives a measure of the mobility/uncertainty of a given atom's position. High values are coloured in warmer (red) colours and lower values in colder (blue) colours. This feature is often used to associate a "scale" value [such as amino acid variability in viral mutants] with each atom in a PDB file, and colour the molecule appropriately.
The difference between the temperature and charge colour schemes is that increasing temperature values proceed from blue to red, whereas increasing charge valuse go from red to blue.
Charge Colours
The RasMol charge colour scheme colour codes each atom according to the charge value stored in the input file (or beta factor field of PDB files). High values are coloured in blue (positive) and lower values coloured in red (negative). Rather than use a fixed scale this scheme determines the maximum and minimum values of the charge/temperature field and interpolates from red to blue appropriately. Hence, green cannot be assumed to be `no net charge' charge.
The difference between the charge and temperature colour schemes is that increasing temperature values proceed from blue to red, whereas increasing charge valuse go from red to blue.
If the charge/temperature field stores reasonable values it is possible to use the RasMol colour dots potential command to colour code a dot surface (generated by the dots command) by electrostatic potential.
User Colours
The RasMol user colour scheme allows RasMol to use the colour scheme stored in the PDB file. The colours for each atom are stored in COLO records placed in the PDB data file. This convention was introduced by David Bacon's Raster3D program.
If you wish to use a custom colouring scheme, it is typically much simpler to construct a short script to accomplish this than to insert values into the PDB file. The script also has the advantage that it can be invoked for any currently displayed molecule. An example of such a script is available.
HBond Type Colours
The RasMol type colour scheme applies only to hydrogen bonds, hence is used in the command "colour hbonds type" This scheme colour codes each hydrogen bond according to the distance along a protein chain between hydrogen bond donor and acceptor. This schematic representation was introduced by Belhadj-Mostefa and Milner-White. This representation gives a good insight into protein secondary structure (hbonds forming alpha helices appear red, those forming sheets appear yellow and those forming turns appear magenta).
Offset Colour Triple
+2 white [255,255,255]
+3 magenta [255,0,255]
+4 red [255,0,0]
+5 orange [255,165,0]
-3 cyan [0,255,255]
-4 green [0,255,0]
default yellow [255,255,0]
Potential Colours
The RasMol potential colour scheme applies only to dot surfaces, hence is used in the command "colour dots potential" This scheme colours each currently displayed dot by the electrostatic potential at that point in space. This potential is calculated using Coulomb's law taking the temperature/charge field of the input file to be the charge assocated with that atom. This is the same interpretation used by the colour charge command. Like the charge colour scheme low values are blue/white and high values are red. The table below shows the static assignment of colours using a dielectric constant value of 10.
25 < V red [255,0,0]
10 < V < 25 orange [255,165,0]
3 < V < 10 yellow [255,255,0]
0 < V < 3 green [0,255,0]
-3 < V < 0 cyan [0,255,255]
-10 < V < 3 blue [0,0,255]
-25 < V < -10 purple [160,32,240]
V < -25 white [255,255,255]
Revision History
- 98/08/10: Added Venn diagram of predefined terms contributed by Kurt Giles.
- 98/04/26: Added definitions of Medium, Small (whence Large), Buried, and Surface predefined terms obtained by examination of the source code. Prepared a separate introduction to select expressions, linked under the Select command.
- 98/03/23: Added paragraph at the very beginning with link to the original source of this manual, and reorganized the section before the table of contents.
- 98/02/28: Provided more detailed descriptions of the slab and set slabmode commands.
- 98/02/19: Added the vectps option to the write command. Provided link to discussion of high-resolution printing in the FAQ under the write and print commands. Completed the table of CPK color assignments used by RasMol, and added a colored GIF image illustrating them.
- 97/07/25: Added some missing RGB values in the CPK color scheme, and also a sample color key table in HTML.
- 97/07/04: Added hexadecimal RGB values for amino and predefined colors.
- 97/06/29: Added RGB values for the CPK Color Scheme in both decimal and hexidecimal.
- 97/03/16: Expanded the section on the group colour scheme, explaining the use of set hetero off to control the spectrum of colors. Also corrected the colours given for the ends of proteins, which were inadvertantly reversed in the manual.
- 96/09/02: Added new section on the trace command, and revised backbone accordingly. Added dashes option to backbone, strands, and wireframe commands. Added section for set bonds. Added more detail about use of pause including synonymy with wait. Added section on set bonds. Indexed the section on set write under set (it had inadvertantly been omitted). Fixed incorrectly formatted "disappearing" instances of "<filename>". Added new section on exit which is now distinct from quit.
- 96/08/14: Filename changed from rasman26.htm to rasman.htm so links will remain version-independent. Minor typos and formatting changes.
- 96/08/13: Updated Introduction and added General Operations sections, which were taken from the non-html manual bundled with version 2.5. These were revised to bring them into accord with version 2.6 beta-2 (see comments in html source).