RasMol2 is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at teaching, display and generation of publication quality images. RasMol runs under Microsoft Windows and also UNIX and VMS systems with an 8bit or 24bit (32bit) colour X Windows display (X11R4 or later). The program reads in a molecule co-ordinate file and interactively displays the molecule on the screen in a variety of representations and colour schemes. Currently available molecule representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, biomolecular ribbon (either solid or strands) and dots. The RasMol help facility can be accessed by typing "help " or "help " from the command line. A complete list of RasMol commands may be displayed by typing "help commands". A single question mark may also be used to abbreviate the keyword "help". Copyright (c) 1992-1996 by Roger Sayle (rasmol@ggr.co.uk) ?commands ?keywords RasMol allows the execution of interactive commands typed at the "RasMol>" prompt in the terminal window. 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 whitespace characters are ignored except to separate keywords and their arguments. The commands/keywords currently recognised by RasMol are given below. Type "help " for more information on each RasMol function. backbone background centre colour dots define exit hbonds help load quit renumber reset restrict ribbons rotate save script select set show slab spacefill strands structure ssbonds translate wireframe write zap zoom ?backbone Backbone Syntax: backbone {} backbone 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 paramater the same as 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 determine the cylinder radius of the representation in 0.004 angstrom units. Backbone objects may be coloured using the RasMol `colour backbone' command. A parameter value of 500 (2 angstroms) or above results in an "Integer argument too large" error. The reserved work backbone is also used as a predefined set ("help sets") and as a parameter to the `set hbond' and `set ssbond' commands. ?background Background Syntax: background 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. ?center ?centre Centre Syntax: center {} centre {} 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. ?color ?colour Colour Syntax: colour {} color {} 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. Typing the command `help colours' will give a list of all the predefined colour names recognised by RasMol. Allowed objects are `atoms,' `bonds,' `backbone,' `dots,' `hbonds,' `ribbons' 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 all objects accept 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 `amino,' `cpk,' `chain,' `group,' `shapely,' `structure,' `temperature' and `user' and hydrogen bond objects can also be coloured by `type.' For more information type `help colour .' ?define Define Syntax: define 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 Dots Syntax: dots {} dots 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 Echo Syntax: echo {} 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. ?hbond ?hbonds HBonds Syntax: hbonds {} hbonds 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 Help Syntax: help { {}} ? { {} The RasMol `help' command provides on-line help on the given topic. ?load Load Syntax: load {} 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), `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. ?exit ?quit Quit Syntax: quit exit Exit from the RasMol program. ?renum ?renumber Renumber Syntax: renumber {{-} } 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 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 Restrict Syntax: restrict {} The RasMol `restrict' command both defines the currently active zone 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 zone. 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-active zone. Type "help expression" for more information on RasMol atom expressions. ?ribbon ?ribbons Ribbons Syntax: ribbons {} ribbons 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 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 `strands' which renders the biomolecular ribbon as parallel depth-cued curves. ?rotate Rotate Syntax: rotate {-} Rotate the molecule about the specified axis. Permited 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. ?save Save Syntax: save {pdb} save alchemy Save the currently selected set of atoms in either a Brookhaven Protein Database (PDB) or Alchemy(tm) format file. This command should not be confused with the RasMol `write' command which generates either image or script files. ?script Script Syntax: script The RasMol `script' command reads a set of commands sequentially from a text file and executes them. This allows sequences of commonly used commands to be stored and performed by a 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. ?select Select Syntax: select {} Define the currently active zone of the molecule. All subsequent RasMol commands that manipulate a molecule or modify its colour or representation, only effects the currently selected zone. The parameter of a `select' command is a RasMol expression that is evaluated for every atom of the current molecule. The currently selected (active) zone of the molecule are those atoms that cause the expression to evaluate true. To select the whole molecule use the RasMol command `select all.' Type "help expression" for more information on RasMol atom expressions. ?set Set Syntax: set {