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 RASMOL(1)                                                         RASMOL(1)
                                October 1994



 NAME
      rasmol - Molecular Graphics Visualisation Tool v2.5


 SYNOPSIS
      rasmol [-nodiplay] [[-format ] filename] [-script scriptfile]


 FORMATS
      -pdb        Brookhaven Protein Databank
      -mdl        MDL's MOL File Format
      -mol2       Tripos' Sybyl MOL2 Format
      -xyz        MSC's XYZ (XMol) Format
      -alchemy    Alchemy File Format
      -charmm     CHARMm File Format

 DESCRIPTION
      RasMol2 is a molecular graphics program intended for the visualisation
      of proteins, nucleic acids and small molecules. The program is aimed
      at display, teaching and generation of publication quality images.
      RasMol runs on Microsoft Windows, Apple Macintosh, UNIX and VMS
      systems. The UNIX and VMS systems require an 8, 24 or 32 bit 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 colour schemes and molecule representations. Currently
      available representations include depth-cued wireframes, 'Dreiding'
      sticks, spacefilling (CPK) spheres, ball and stick, solid and strand
      biomolecular ribbons, atom labels and dot surfaces.


 COMMANDS
      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.


      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 specify the cylinder radius of
           the representation in either angstrom or rasmol units. A
           parameter value of 500 (2.0 angstroms) or above results in a
           "Parameter value too large" error. Backbone objects may be



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 RASMOL(1)                                                         RASMOL(1)
                                October 1994



           coloured using the RasMol colour backbone command.


      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.

           The background command is synonymous with the RasMol set
           background command.


      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.


      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
           Colour the atoms (or other objects) of the selected region. The
           colour may be given as either a colour name or a comma separated
           triple of Red, Green and Blue (RGB) components enclosed in square
           brackets. Typing the command help colours will give a list of all
           the predefined colour names recognised by RasMol.

           Allowed objects are atoms, bonds, backbone, ribbons labels dots,
           hbonds, and ssbonds. If no object is specified, the default



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 RASMOL(1)                                                         RASMOL(1)
                                October 1994



           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 cpk, amino, chain, group, shapely, structure,
           temperature charge and user. Hydrogen bonds can also be type and
           dot surfaces can also be coloured by electrostatic potential. For
           more information type help colour <colour>.


      Connect
           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
           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 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



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 RASMOL(1)                                                         RASMOL(1)
                                October 1994



           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 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.


      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 The RasMol help command provides on-line help on the given topic.


      Label
           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.  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.




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 RASMOL(1)                                                         RASMOL(1)
                                October 1994



           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.


      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. If the
           file specifies less bonds than atoms, RasMol determines
           connectivity using the connect command.


      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.


      Quit Exit from the RasMol program. The RasMol commands exit and quit
           are synonymous.


      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



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 RASMOL(1)                                                         RASMOL(1)
                                October 1994



           may be negative.


      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
           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.

           Type "help expression" for more information on RasMol atom
           expressions.


      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 (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



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 RASMOL(1)                                                         RASMOL(1)
                                October 1994



           depth-cued curves.


      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 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
           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.

           The most common way to generate a RasMol script file is to use
           the write script or write rasmol commands to output the sequence
           of commands that are needed to regenerate the current view,
           representation and colouring of the currently displayed molecule.

           The RasMol command source is synonymous with the script command.


      Select
           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.



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 RASMOL(1)                                                         RASMOL(1)
                                October 1994



           Type "help expression" for more information on RasMol atom
           expressions.


      Set  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, ommiting the paramter option resets that parameter to
           its default value. A list of valid parameter names is given
           below.


      Show 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 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.


      Spacefill
           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.



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 RASMOL(1)                                                         RASMOL(1)
                                October 1994



      SSBonds
           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.


      Strands
           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.


      Structure
           The RasMol structure command calculates secondary structure



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 RASMOL(1)                                                         RASMOL(1)
                                October 1994



           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.


      Translate
           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
           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.


      Write
           Write the current image to a file in a standard raster format.
           Currently supported image file formats include gif (Compuserve
           GIF), ppm (Portable Pixmap), ras (Sun rasterfile), ps and epsf
           (Encapsulated PostScript), monops (Monochrome Encapsulated
           PostScript), 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 distinction between this command and the RasMol save command



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 RASMOL(1)                                                         RASMOL(1)
                                October 1994



           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.


      Zap  Deletes the contents of the current database and resets parameter
           variables to their initial default state.


      Zoom Change the magnification of the currently displayed image.
           Boolean parameters either magnify or reset the scale of current
           molecule. An integer parameter between 10 and 200 specifies the
           desired magnification as a percentage of the default scale.


 SET 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.


      Set Ambient
           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
           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.


      Set Background
           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



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 RASMOL(1)                                                         RASMOL(1)
                                October 1994



           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.


      Set BondMode
           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 BoundBox
           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 Display
           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
           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



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 RASMOL(1)                                                         RASMOL(1)
                                October 1994



           shown in only a schematic representation such as backbone,
           ribbons or strands. his parameter is similar to the RasMol
           ssbonds parameter.


      Set FontSize
           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
           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 an 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.


      Set HourGlass
           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
           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.



                                   - 13 -           Formatted:  June 5, 2020






 RASMOL(1)                                                         RASMOL(1)
                                October 1994



      Set Kinemage
           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
           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 Mouse
           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 Radius
           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
           The RasMol set shadow command enables and disables raytracing of
           the currently rendered image.  Currently only the spacefilling



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 RASMOL(1)                                                         RASMOL(1)
                                October 1994



           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
           The RasMol slabmode parameter controls the rendering method of
           objects cut by the slabbing (z-clipping) plane. Valid slabmode
           parameters are "reject", "half", "hollow", "solid" and "section".


      Set Solvent
           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
           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
           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.




                                   - 15 -           Formatted:  June 5, 2020






 RASMOL(1)                                                         RASMOL(1)
                                October 1994



      Set SSBonds
           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 Strands
           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 UnitCell
           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
           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


 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



                                   - 16 -           Formatted:  June 5, 2020






 RASMOL(1)                                                         RASMOL(1)
                                October 1994



      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!


      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.  The second part consists of a
           period character followed by an atom name.  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.



                                   - 17 -           Formatted:  June 5, 2020






 RASMOL(1)                                                         RASMOL(1)
                                October 1994



      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. A list of the
           currently predefined sets is given below.  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.


 Predefined Sets
      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



                                   - 18 -           Formatted:  June 5, 2020






 RASMOL(1)                                                         RASMOL(1)
                                October 1994



           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)





                                   - 19 -           Formatted:  June 5, 2020






 RASMOL(1)                                                         RASMOL(1)
                                October 1994



      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


      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



                                   - 20 -           Formatted:  June 5, 2020






 RASMOL(1)                                                         RASMOL(1)
                                October 1994



           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, 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



                                   - 21 -           Formatted:  June 5, 2020






 RASMOL(1)                                                         RASMOL(1)
                                October 1994



           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)


      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






                                   - 22 -           Formatted:  June 5, 2020






 RASMOL(1)                                                         RASMOL(1)
                                October 1994



      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)


      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




                                   - 23 -           Formatted:  June 5, 2020






 RASMOL(1)                                                         RASMOL(1)
                                October 1994



      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.


 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, a hbond type colour scheme for hydrogen bonds and electrostatic
      potential colour scheme for dot surfaces.  The currently predefined
      colour names are blue, black, cyan, green, greenblue, magenta, orange,
      purple, red, redorange, violet, white and yellow.


      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.


      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
           colour `atom' objects by the atom (element) type. This is the



                                   - 24 -           Formatted:  June 5, 2020






 RASMOL(1)                                                         RASMOL(1)
                                October 1994



           scheme conventionally used by chemists.


      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. Hence the N terminus of proteins and 5' terminus of nucleic
           acids are coloured red and the C terminus of proteins and 3'
           terminus of nucleic acids are drawn in blue. 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.


      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.





                                   - 25 -           Formatted:  June 5, 2020






 RASMOL(1)                                                         RASMOL(1)
                                October 1994



      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.


      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).


      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.





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 RASMOL(1)                                                         RASMOL(1)
                                October 1994



 SEE ALSO
      The RasMol User Manual!


 AUTHOR
      Copyright (C) 1992-94 by Roger Sayle. All rights reserved.
       (rasmol@ggr.co.uk)















































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