


RASMOL(1)                 User Commands                 RASMOL(1)



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 representa-
     tions include depth-cued wireframes, 'Dreiding' sticks, spa-
     cefilling  (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 connect-
          ing 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



Sun Microsystems    Last change: October 1994                   1






RASMOL(1)                 User Commands                 RASMOL(1)



          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 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 data-
          base.

          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  com-
          mand  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 expres-
          sion.  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 `clip-
          board'. Note: this command is not yet supported on UNIX
          or  VMS  machines.  It  is intended to make transfering
          images between applications easier under Microsoft Win-
          dows or on an Apple Macintosh.

          When using RasMol on a UNIX or VMS  system  this  func-
          tionality  may be achieved by generating a raster image
          in a format that can be read by the  receiving  program
          using the RasMol write command.



Sun Microsystems    Last change: October 1994                   2






RASMOL(1)                 User Commands                 RASMOL(1)



     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 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 con-
          nect).  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 com-
          mand 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  expres-
          sion  defining  them depends on the current transforma-
          tion and representation of the molecule.




Sun Microsystems    Last change: October 1994                   3






RASMOL(1)                 User Commands                 RASMOL(1)



     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  exist-
          ing 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 sur-
          face 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 parame-
          ter may optionally be delimited in double quote charac-
          ters.  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.



Sun Microsystems    Last change: October 1994                   4






RASMOL(1)                 User Commands                 RASMOL(1)



     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 charac-
          ter 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.

          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 Data-
          bank), mdl (Molecular Design Limited's  MOL  file  for-
          mat), alchemy (Tripos' Alchemy file format), mol2 (Tri-
          pos' Sybyl Mol2 file format), charmm (CHARMm file  for-
          mat)  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



Sun Microsystems    Last change: October 1994                   5






RASMOL(1)                 User Commands                 RASMOL(1)



          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  func-
          tionality  may  be  achieved  by  either  generating  a
          PostScript file using the  RasMol  write  ps  or  write
          vectps  commands and printing that or generating a ras-
          ter 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 pro-
          teins, 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'  ter-
          minus.  All  chains  in the current database are renum-
          bered and gaps in the original  sequence  are  ignored.
          The starting value for numbering 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 parame-
          ter of a restrict command is a RasMol  atom  expression
          that  is  evaluated  for  every  atom  of  the  current



Sun Microsystems    Last change: October 1994                   6






RASMOL(1)                 User Commands                 RASMOL(1)



          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 "rib-
          bon" 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 com-
          mand is similar to the  RasMol  command  strands  which
          renders  the biomolecular ribbon as parallel 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 differ-
          ence is that without a format specifier the  save  com-
          mand  generates  a  PDB  file  and  the  write  command



Sun Microsystems    Last change: October 1994                   7






RASMOL(1)                 User Commands                 RASMOL(1)



          generates a GIF image.


     Script
          The RasMol script command reads a set  of  RasMol  com-
          mands  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  max-
          imum  "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 colour-
          ing 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.

          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



Sun Microsystems    Last change: October 1994                   8






RASMOL(1)                 User Commands                 RASMOL(1)



          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, spa-
          cefilll 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 Ras-
          ter 3D's COLOR record extension.

          The RasMol command cpk is synonymous with the spacefill
          command.


     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  cys-
          teines.  The  first  time  that  the ssbonds command is
          used, the program searches the structure of the protein



Sun Microsystems    Last change: October 1994                   9






RASMOL(1)                 User Commands                 RASMOL(1)



          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  sul-
          phur 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  rib-
          bon2  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 secon-
          dary 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



Sun Microsystems    Last change: October 1994                  10






RASMOL(1)                 User Commands                 RASMOL(1)



          The  RasMol  structure  command  calculates   secondary
          structure assignments for the currently loaded protein.
          If the original PDB file contained  structural  assign-
          ment  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 secon-
          dary 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 parame-
          ter 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"  displace-
          ment  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



Sun Microsystems    Last change: October 1994                  11






RASMOL(1)                 User Commands                 RASMOL(1)



          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' Mol-
          script program and the format kinemage the commands for
          David Richardson's program Mage.

          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  gen-
          erates 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 modi-
     fied  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  con-
          trols  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 sha-
          dow.  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 rib-
          bon 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



Sun Microsystems    Last change: October 1994                  12






RASMOL(1)                 User Commands                 RASMOL(1)



          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 respec-
          tively.


     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 tri-
          ple  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 data-
          base.

          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



Sun Microsystems    Last change: October 1994                  13






RASMOL(1)                 User Commands                 RASMOL(1)



          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  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  char-
          acter  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



Sun Microsystems    Last change: October 1994                  14






RASMOL(1)                 User Commands                 RASMOL(1)



          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.


     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 represen-
          tation in the generated output file.  The  command  set
          kinemage  true,  generates a more complex Kinemage that
          contains both the wireframe  and  backbone  representa-
          tions 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 typ-
          ically only used by graphical  user  interfaces  or  to
          create  as large as image as possible when using Micro-
          soft Windows.


     Set Mouse
          The RasMol set mouse command sets the rotation,  trans-
          lation, 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



Sun Microsystems    Last change: October 1994                  15






RASMOL(1)                 User Commands                 RASMOL(1)



          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 con-
          trols the clipping plane. The insight and  quanta  pro-
          vide  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 ray-
          tracing  of  the  currently  rendered image.  Currently
          only the spacefilling representation is shadowed or can
          cast  shadows.  Enabling  shadowing  will automatically
          disable the Z-clipping (slabbing) plane using the  com-
          mand 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



Sun Microsystems    Last change: October 1994                  16






RASMOL(1)                 User Commands                 RASMOL(1)



          the value of the solvent parameter,  the  dots  command
          either  generates a Van der Waal's or a solvent acessi-
          ble surface around the currently selected set of atoms.
          Changing  this parameter automatically resets the value
          of the RasMol radius parameter.  The command  set  sol-
          vent 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 indi-
          cates that a `Connolly' or `Richards' solvent  accessi-
          ble surface should be drawn and sets the radius parame-
          ter, 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 specu-
          lar highlight calculations. The specular highlights are
          enabled and disabled by the RasMol  set  specular  com-
          mand.  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
          The RasMol ssbonds parameter determines whether  disul-
          phide  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 back-
          bone, ribbons or strands. his parameter is  similar  to
          the RasMol hbonds parameter.




Sun Microsystems    Last change: October 1994                  17






RASMOL(1)                 User Commands                 RASMOL(1)



     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 com-
          mand.


     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  com-
          mands 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) combina-
     tions of the above expression types.

     The logical operators  allow  complex  queries  to  be  con-
     structed out of simpler ones using the standard boolean con-
     nectives and, or and not. These may be  abbreviated  by  the
     symbols  "&", "|" and "!"  respectively. Parentheses (brack-
     ets) may be used to alter the precedence of  the  operators.
     For  convenience,  a comma may also be used for boolean dis-
     junction.



Sun Microsystems    Last change: October 1994                  18






RASMOL(1)                 User Commands                 RASMOL(1)



     The atom expression is evaluated for each atom,  hence  pro-
     tein  and  backbone  selects  protein bacbone atoms, not the
     protein and [nucleic] acid backbone atoms!


     Primitive Expressions
          RasMol primitive expressions are the fundamental build-
          ing  blocks of atom expressions. There are two types of
          primitive expression.  The first type is used to  iden-
          tify  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  resi-
          dues)  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  tempera-
          ture 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.


     Within Expressions
          A RasMol within expression allows atoms to be  selected



Sun Microsystems    Last change: October 1994                  19






RASMOL(1)                 User Commands                 RASMOL(1)



          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 respec-
          tively). 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



Sun Microsystems    Last change: October 1994                  20






RASMOL(1)                 User Commands                 RASMOL(1)



          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 pro-
          tein 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  back-
          bone.   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



Sun Microsystems    Last change: October 1994                  21






RASMOL(1)                 User Commands                 RASMOL(1)



          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 con-
          tact with solvent molecules. This  set  refers  to  the
          amino acids preference and not the actual solvent aces-
          sibility 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 respec-
          tively). 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  neu-
          tral. This set is equivalent to the RasMol atom expres-
          sions 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



Sun Microsystems    Last change: October 1994                  22






RASMOL(1)                 User Commands                 RASMOL(1)



          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  deu-
          terium  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



Sun Microsystems    Last change: October 1994                  23






RASMOL(1)                 User Commands                 RASMOL(1)



          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)


     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



Sun Microsystems    Last change: October 1994                  24






RASMOL(1)                 User Commands                 RASMOL(1)



          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 key-
          word.


     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



Sun Microsystems    Last change: October 1994                  25






RASMOL(1)                 User Commands                 RASMOL(1)



          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 expres-
          sions 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 con-
          tact 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


     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 crystallog-
          raphy. 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 sup-
     ports  cpk,  amino,  chain,   group,   shapely,   structure,



Sun Microsystems    Last change: October 1994                  26






RASMOL(1)                 User Commands                 RASMOL(1)



     temperature,  charge  and  user  colour schemes for atoms, a
     hbond type colour scheme for hydrogen  bonds  and  electros-
     tatic   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 macromolec-
          ular  chain a unique colour. This colour scheme is par-
          ticularly useful for distinguishing the parts  of  mul-
          timeric  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  Kul-
          tun.  This  colour  scheme colour `atom' objects by the
          atom (element) type. This is the 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 pro-
          teins 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



Sun Microsystems    Last change: October 1994                  27






RASMOL(1)                 User Commands                 RASMOL(1)



          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 deter-
          mined  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



Sun Microsystems    Last change: October 1994                  28






RASMOL(1)                 User Commands                 RASMOL(1)



          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  (gen-
          erated 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.


SEE ALSO
     The RasMol User Manual!


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






Sun Microsystems    Last change: October 1994                  29



