0 FRODO
1 .ALL
      Defines the status of all the atoms in the  residue  of  the
  subsequently hit atoms.  .YES/.NO act as with .STAT., ie if .NO 
  is set they are all made dummy, if .YES is set (or not .NO) they
  are made real.

1 .ANGL
      Displays the angle defined by three subsequently hit  atoms. 
  (or point)  In the PS300 version the angle is not updated if one of
  the 3  atoms moves.  Like .DIST, it stays active until .NODA or .WAIT
  is set. 

1 .BADD
      Add the map bricks around the current point (see .POIN), within
  a cube of half-width set by the chat command WIDTH. An active point
  will be accepted before adding bricks (this is done by setting .YES,
  so any active FBRT, TOR, MOVE will be accepted as well).

1 .BOBR
      To break the bond between the next two hit atoms. This is
  useful for FBRT and RSR. If after breaking a bond,  an atom has 
  no bonds to it, it should appear as a cross. The
  distance between the two selected atoms also appears via .DIST. 

1 .BOND
      A bond is formed between the next two hit atoms.  The distance
  between the two selected atoms also appears via .DIST.

1 .BREL
      Release (ie don't display) the map bricks around the current point 
  (see .POIN), within a cube of half-width set by the chat command WIDTH.
  An active point will be accepted before releasing bricks (this is done 
  by setting .YES, so any active FBRT, TOR, MOVE will be accepted as well).

1 .CENT
      Move to new screen centre. This is not useful in ZONE mode. Any
  active manipulations (.FBRT, .TOR, MOVE) are accepted, the 
  coordinates are saved (see .SAVE), and the sphere centre is moved to 
  the next hit atom (or point). If maps are being displayed and the
  auto-cover flag is ON (see Chat AUTO), the new piece of map will be
  loaded. 

1 .CONT
      Now renamed .CENT

1 .DIST
      Display the distance between 2 subsequently hit atoms (or
  point). In the PS300 version the distance is not updated if one or
  both atoms move. The function stays active for subsequent pairs of
  atoms until switched off by .NODA or .WAIT. 

1 .FBRT
      This stands for foreground-  background  rotate-  translate,
  and  is  used  to move a group of connected atoms.  All the atoms
  connected to the next hit atom move as a rigid  group.   The  hit
  atom acts as the central pivot point.  Six A-D converters control
  the  X,   Y,   Z   rotations   and   translations.
      PS300: The shifts and  rotations  are along the screen axes.
  The dials are connected  to  .FBRT  by pressing '2' on the PS300
  keyboard or right keypad.  The  atoms and bonds in the FBRT object
  are no longer pickable. 
      Hitting .YES accepts the new position, .NO  or .WAIT 
  restores the  old  coordinates. As with .MOVE or .TOR, .SET resets
  the FBRT atoms to their original positions without deactivating
  .FBRT.
      As the atoms move, their coordinates DO NOT get updated 
  and the results of .DIST, ANGL, NAYB commands are meaningless.
  The current limit of atoms in the .FBRT object is 3000.
      The  user  must  isolate  or  define  the  fragment  to   be
  manipulated  with  .BOBR and .BOND before activating .FBRT.  ONCE
  THE FRAGMENT HAS BEEN DEFINED, CHANGING THE CONNECTIVITY WILL NOT
  CHANGE WHAT ATOMS ARE AFFECTED BY .FBRT. 
    Note that .FBRT sets .YES for one cycle to ensure that any active
  .MOVE, .FBRT, or .TOR is accepted before proceeding.
      If .Yes is set on entry to .FBRT, the whole foreground object 
  will be activated for FBRT. This may be useful for docking the
  foreground molecule against a background MOL object, and is much
  faster more a large molecule, since the program does not have to
  select which atoms to activate.
       If .No is set on entry to .FBRT, the transformation from the
  dials is connected to all AMOVE and MOVEXYZ defined in MOL. The
  foreground atoms are unaffected. This allows crystal packing etc
  to be explored. If the transformation is accepted with .Yes,
  the matrix and vector are written to the screen, and the RECOrd file
  is activated, in a form which may be reinput as a non-crystallographic
  symmetry operation. The coordinates are not changed.

1 .FIX
      Subsequently hit atoms are not allowed to move when they are
  next  subject to regularisation.  After regularisation, the atoms
  are set free.  With .NO set, fixed atoms are set free,  (this  is
  not  the  same  result as .STAT, since .STAT (or .YES/stat) makes
  the atom real, .NO/STAT makes it dummy whereas .NO/.FIX keeps the
  atomic status whilst freeing it).

1 .HBND
       Draws hydrogen bonds as part of the foreground atom display.
  If neither .Yes nor .No are set, the display atoms are searched
  for hydrogen bonds. The hydrogen bond search will not find bonds
  within the same residue, unless hydrogen atoms are present in the
  file. .Yes/Hbnd works like .Bond, hit 2 atoms and a bond appears
  between them. .No/.Hbnd deletes bonds (like .BoBr). These options
  remain active until cancelled by .NoDA: you can swap between adding
  and removing H-bonds by hitting .Yes or .No. The display of H-bonds
  remains until the foreground atoms are redrawn: this can be forced
  by the Chat command ATOM. 

1 .Labl
 	Changes the format of the atom label you get when you hit a
  foreground atom (cf Chat>LABL). .Yes/.Labl gives a label 
  atom-name//residue-name (eg CD1 203A), .No/.Labl gives 
  residue-type//residue-name (eg ARG 72B). If neither .Yes nor .No
  are set, the label type is switched to the other.


1 .LSQP
      Least squares plane calculation, using the  method  of  Blow
  (Acta  Cryst (1960) 13,168).  Subsequently hit atoms will be used
  in the calculation up to a maximum of  40,  until  .YES  is  set.
  Terminal   output  then  gives  information  on  the  plane,  and
  deviations of the atoms  from  the  plane.   More  atoms  can  be
  identified,  and their distance from the plane will appear in the
  text scratch area.  The PS300 version no longer forces other 
  commands off when .LSQP is activated.

1 .M1
      See Memories.

1 .M2
      See Memories.

1 .M3
      See Memories.

1 .M4
      See Memories.

1 .MOVE
      The subsequently hit atom is allowed to move. Its
  position is controlled by the .MOVE dials accessed by pressing
  '3' on the PS300 keyboard or right keypad. Bonds to this
  atom are 'rubber banded' as the atom moves, and a cross appears
  at the original position of the atom. If the atom was originally
  a cross, a cross will appear and move with the dials.
  The coordinates are not updated as the atom moves. .SET restores
  the atom to its starting position without deactivating .MOVE. Its
  position is accepted by .YES, or is restored to its starting
  position by activating .NO or .WAIT. Remember that for MOVE, 
  FBRT, TOR, THE COORDINATES ARE NOT WRITTEN TO COORD until
  explicitly told to via .SAVE, .POP, .CENT or .CHAT command SAVE. 

     Note that .MOVE sets .YES for one cycle to ensure that any active
  .MOVE, .FBRT, or .TOR is accepted before proceeding.

1 .NAYB
      Atoms which are within a certain distance (set by CHAT 
  command NAYB) from the next hit atom (or point) are identified on the
  screen, together with their separation. Contacts between the hit 
  atom and atoms in the same residue as the hit atom are not
  displayed. The command remains active and continuously updates
  neighbors to the last hit atom. Subsequently hit atoms become new
  centers for neighbor calculations. On the PS300 there is currently
  a limit of 20 contacts and the neighbors ARE NOT continuously
  updated. Also, since the host program only knows the static
  positions of atoms, atoms affected by .MOVE, .FBRT, or .TOR will not
  give legitimate distance values. This option is switched off by
  .WAIT or .NoDA (.NoDA also deletes the nayb object from the PS300) 
  
1 .NO
    With .YES, these are used to cause "events", and to pick options
  for a number of commands. Hitting one switches off the other.

1 .NODA 
    Clears the "continuous" functions: LSQP,XYZ,DIST,ANGL,NAYB,YES,
  NO,STAT,ALL,FIX,HBND,etc. Basically functions like .WAIT except .NO
  is never set.

1 .NOID 
    Clears the text scratch area, and the  text  on  the  atomic 
  positions.  If .NO is set, then only the text scratch area is
  cleared (but .No is not cleared: it may be cleared by .NoDA or .WAIT)

1 .ORIG 
      This shifts the screen center to the next hit atom or point.
  In the PS300 version it no longer forces a calculation of new
  atoms and bonds, and hence can be activated while any other
  function (e.q. TOR) is active. 

1 .PLOT
       The current display (excluding the menu) is dumped into a plot
  file for subsequent plotting. If no plotfile has been specified
  by the Chat command PLOT, the first .PLOT command will create a
  file called FROPLOT.PLT. Each subsequent use of this command will
  add another picture to the same plotfile, unless it is changed 
  by Chat>PLOT. See Chat> PLOT, PLPA and PLTI

1 .POIN
      Activates a displayed point, which may be moved by the dials on
  panel 3 as for .MOVE. The point position is accepted by .YES, or by
  .BADD and .BREL, and the point is deleted by .NO .  .NO/.POIN just
  clears the point. The point may be used for adding or removing parts 
  of map (see .BADD,.BREL and chat commands BADD,BREL), and for adding
  water molecules with .WATR: its coordinates are given by the Chat
  command NOW.

1 .POP
      The user must be in ZONE mode, and symmetry generation must be
  off (NOSYM), otherwise the operation is ignored. The action is to pop
  the display zone one unit along the linear sequence, writing the
  coordinates of what was the first residue in the zone to the COORD
  data set. If the last residue in the display zone is also the last
  residue in the coordinate data set, then the display zone is
  shortened by one unit. For proteins, the action is to move along the
  sequence from the N-terminal to the C-terminal. If .NO is not set,
  the coordinates of the new last residue in the display zone are read
  directly from the COORD data set.  If .NO is set, then a
  stereochemically correct connection is made for polypeptides,
  provided the added residue already existed on COORD with correct bond
  lengths and angles. The command is normally used in the early stages
  of fitting a model to a map. Note that the current origin is not
  shifted, but the density contours for the new residue will be
  downloaded if the auto-cover flag is ON. 

1 .RAMA
       Draw a Ramachandran plot for each residue hit. When you hit any 
  atom, the residue containing it is drawn on the plot, provided all the
  necessary atoms are present in the display zone. The display coordinates
  (not the disc coordinates) are used to calculate the angles. This option
  stays active until switched off by .No . It cannot be used when .Tor is
  active, since the coordinates may not be available.

1 .ROCK 
    In the PS300, .ROCK locally toggles rocking on and off, 
  using the angle and speed defined by the dials when '6' is pressed
  on the keyboard. Rocking slows many of the function 
  networks. The current speed (arbitrary) and the current half 
  angle (degrees) are displayed on the dial LED's when they are 
  activating by rotation. The rocking is about the screen vertical
  axis.  

1 .RSCL
  The identified fragment is  used  to  get  a  better  scale
  constant  to  bring the calculated density onto the scale of the
  map.  The result is shown on the terminal  and  the  user  must
  check the new value is reasonable.  This should be done twice when
  starting with a new map for the first time.
  On the PS 300, use .NO and .RSR together to achieve .RSCL.

1 .RSFX
  This is like RSR but only a rotational  search  is  carried
  out, using the identified atom as the origin.
  On the PS 300, use .YES and .RSR together to achieve .RSFX.

1 .RSR
  All atoms connected to the next identified atom  will  move
  as  a  rigid  group in my real space refinement algorithm.  They
  will undergo tranlational and (if there is more then  one  atom)
  rotational  refinement.   It is assumed that there exists a density 
  map data set and that the CHAT command RSR has been used  to  define
  suitable  constants.   The  calculated  density of all the other
  displayed atoms will be  subtracted  from  the  observed  density
  before starting the refinement.
       If .NO is set when the fragment is selected, then
  the identified fragment is  used  to  get  a  better  scale
  constant  to  bring the calculated density onto the scale of the
  map.  The result is shown on the terminal  and  the  user  must
  check the new value is reasonable.  This should be done twice when
  starting with a new map for the first time.
       If .YES is set when the fragment is selected, then
  this is like RSR but only a rotational  search  is  carried
  out, using the identified atom as the origin.

1 .RULE
       Activates a ruler on the screen, which is 5A long and calibrated
  in 0.1A intervals. The ruler is placed initially with one end on the
  last hit atom. It may be moved around using the FBRT dials. All active 
  manipulations and accepted before the ruler is activated. .NO 
  (or .YES or .WAIT) removes the ruler. The ruler may be moved to a new
  atom by hitting the atom and then .RULE, without removing the ruler first.

1 .SAVE
      Write the  coordinates  of  non-symmetry  generated  atoms  to
  disk. The menu commands  to manipulate coordinates only change the
  coordinates in memory,  and the new coordinates are not written to
  disk until you want. The user is  free to make any nonsense he likes
  on the screen, until .SAVE  is  set  (see  also .POP and .CENT) at which
  time the disk coordinates get overwritten. The Chat command SAVE does
  the same thing.

1 .STAT
      Is used to change the  atomic  status  of  subsequently  hit
  atoms.   Each  atom  carries  a  flag in its record in COORD which
  allows the atom to  have  4  states  -  REAL,  DUMMY,  FIXEDREAL,
  FIXEDDUMMY  (the  flag  is called IA and has values 1,2,3,4).  If
  the atom is hit with .NO set,then the atom is forced to be dummy.
  if  .YES (or not .NO) is set, the atom is forced to be real.  The
  command can be used to:

  1.  Reset incorrectly .FIX(ed) atoms.

  2. In connection with the .CHAT ADD option.

  3.  As a flag to  show  which  atoms  should  be  used  in  later
  structure  factor  calculations - see .SAM MAKEDIAM/MAKEPDB options.
  Note that once set, the .YES/.NO flags can be changed since they are
  mutually exclusive.

1 .TOR
      A maximum of 6 consecutive torsion angles can be defined, by 
  hitting a maximum of 9 atoms, or alternatively by hitting two atoms,
  in which case all intervening torsion angles are activated. Atom
  definition can be terminated after defining 2 atoms, or else a
  minimum of 4 atoms by hitting .YES.  Hitting N angles,therefore 
  requires hitting N+3 atoms.  The first atom should be connected
  to the second, the second to the third and so on. All atoms with
  connections to the first atom other then via the second atom will
   not move.  The  screen  connectivity determines  which atoms 
  move when one of the torsion A-D converters is changed. By
  applying suitable bond breaks, the user can limit the large
  long range movements caused by dihedral rotations. Care must be
  taken within ring structures, e.g.  one can change CHI1 and CHI2 of
  a PHE ring by defining N, CA, CB, CG, CD1, but to vary the angle 
  CB-CG-CD1-CE1 would first require breaking the CG-CD2 bond. 
  
     Pressing '4' on the PS300 keyboard or right keypad connects
  the dials to the torsion object.  Torsion angles can be changed 
  in any  order or simultaneously.   Pressing .SET  restores  the  
  initial  conformation,  keeping .TOR active. .YES keeps the  
  current  conformation,  .NO  or .WAIT restores  the
  starting conformation, and .TOR is switched off.  The torsion
  angles are displayed on the screen and are updated continuously
  in the PS300 by a local function network.

      The initial screen  connectivity  is  not  determined  by  a 
  bonding  dictionary.   This means that any molecule can be viewed  in
  the display without having to work out  a  rigid  connectivity  list.
  For all viewing options (and the MOL options), atoms within  a
  residue are joined by distance, 1.9A for most pairs,  1.3A for atoms
  beginning  with H and 2.5 A for S-S bridges. Residues are linked
  between the  atoms specified by the Chat command ZLNK (C and N for
  proteins),  provided that their distance is less than the value set
  in ZLNK (qv)

1 .VMM
       Go to DCL interface, for link with batch jobs. See full
  write-up, yet to be written. "v" on the keyboard does the same thing.

1 .WAIT

      .NO is switched on for a single cycle then all flags are
  switched  off.   Since  the  commands  .MOVE, .FBRT,  .TOR  do
  not update the atomic coordinates in real time, this restores
  the original positions of atoms affected by these commands if
  they were active at the time.  .WAIT also removes any neighbor
  object from the display.

1 .WATR
       Adds or deletes waters from the COORD file.
       If .No is not set, the next available water atom will be put 
  at the position of the point. An active point will first be accepted.
  Available waters must have been activated by the SAM command WATER
  (qv)  This sets a pointer to the next available water and the last
  one.  An available water must be dummy and at the dummy position
  1500,1500,1500  it will then be made real and given the position of
  the point, and the  pointer incremented (provided it is before the
  last available water).  Note that when the pointer is incremented, it
  will step over any atoms which  are not in a water residue or not
  dummy. A new water will be drawn as a cross.
       If .No is set, the next hit atom, if it is a water atom (as
  defined  by SAM>WATER), will be 'deleted' ie made dummy at the dummy
  position  1500,1500,1500. The foreground atoms are then redrawn to
  remove this  atom. Such deleted water atoms may be reassigned
  positions if the  pointers are reset in SAM>WATER. 

1 .XYZ
      The current screen coords of a  subsequently  hit  atom  are 
 displayed  on  the screen.  A terminal listing is produced giving 
 all  the  information  that  exists  concerning  the  atom  (this 
 includes  atomic  temperature factor, weight and atom type .   Note 
 that  the dataset coordinates will be different  from the screen
 coords if the atom is symmetry  produced  or  has  been  moved 
 without  .SAVE(ing).   If the hit atom is moved (via  .MOVE, .FBRT,
 .TOR), then the new  position  is  updated  on  the  screen (NOT in 
  the PS300 version).

1 .YES
      With .NO, these are used to cause "events", and to pick options for  a
  number of commands.  Hitting one switches off the other.

1 ACEN
       The prompt expects a residue and  atom  name  to  define  the  next
  centre for selecting atoms (SPHE and (S)MIX ).  Omitting  the  atom name
  forces CA as default.  Error messages warn if the residue or atom does not
  exist in the current COORD data set.

1 ACON
       See ACEN

1 ADD
       This option must be used with care.  The  positions  of  all  dummy
  atoms  (IA=2,4)  are  calculated  from the dictionary connectivity, bond
  lengths and angles.  It is necessary to have 3 connected atoms somewhere
  in  the  RZON.   This  option is not required any more, having been made
  redundant by the REFI MODE options EXTD and RESI.(cf NOAD which switches
  it off)

1 ANCH
       This option applies an anchor at the ends of the RZON  to
  maintain  connectivity  along  the chain. The program asks you if you
  want to fix  the first residue in the RZON, the last residue, or
  both  ends. In fact it applies fixes to up to 3 atoms in the  first
  and last residues of  the RZON. These should be N CA, and CA C O  for
  protein molecules: the fixed atoms can be changed with the ZFIX
  command.  Note that this method of fixing ends is suitable for
  proteins since the bond linking residues is rigid. For nucleic acids,
  this is not true, and the atoms fixed must either fix more than is
  necessary, or allow bond angles to change at one end. (cf NOAN which
  switches it off) 

1 ANGL
       This   allows   one   to   guide   special   conformations   during
  regularisation  or  model making.  It can be used for example to force a
  piece of chain to adopt the phi and psi angles of an alpha helix  during
  the regularisation or can set free normally 'fixed' torsion angles (e.g.
  omega angles).  If this option is on, before  entering  the  regulariser
  the  user  gets  a message, requesting a four character option name.  By
  typing END or <cr> the program continues .  Other options are:

  1. ALPHA:  To define the phi and psi angles  for  an alpha  helix.   The
  program  then  prompts  for  a  zone of residues over which to apply the
  torsional restraint and for a weight.  The weight is the fraction of the
  fixed torsion angle weight at any time in the regularisation.  So typing
  1.0 ensures that the normally flexible phi and psi angles are treated as
  fixed torsion angles.

       The next 3 options produce the same prompt

  2. ABET:  To define anti-parallel pleated sheet angles

  3. PBET:  To define parallel pleated sheet angles

  4. PROL:  To define poly proline dihedral angles.

       The next 3 options have the same prompt.

  5. PHI:  The prompt is for a residue range,a value  and  a  weight.   The
  value refers to what value the phi angle should be restrained.

  6. PSI:  To define a value to a zone of psi angles.

       By using PHI and PSI the user can ,for example, define  main  chain
  angles for 3-sub-10 helices.

  7. OMEG:  To allow the  user  to  set  free  the  omega  angle  for  high
  resolution structures.

  8. TAU:  To allow the user to set free the tau angle (defined N-CA-C).

  9.  Unrecognized options are assumed to refer  to  torsion  angles.   An
  atom  must  be  defined which has 3 back chained atoms in the dictionary
  description of the residue.  These 4 atoms  define  the  torsion  angle.
  The prompt asks for residue, atom, value and weight.  As an example, one
  would define a CHI1 angle by  defining  the  CG  and  a  CHI2  angle  by
  defining a CD atom.

  (cf NANG which switches it off)

1 ATOM
       When GO is typed, new atoms are usually loaded from disk only if
  the atom selection has been changed. This command forces reloading of 
  atoms from disk. This may be useful if things have got screwed up.
  (qv NOATom which suppresses reloading)

1 ATTAch
       Reads the name of a MOL display object (previously created) which
  will be attached to the FBRT object whenever .FBRT is activated from the
  menu. This can be used to put a Van der Waals surface on a ligand to be
  docked into a protein.

1 AUTO
       Set or unset the auto-cover and auto-release flags. The main
  way of selecting the part of the map to display is to select those
  map bricks which cover the foreground atoms. Provided that map 
  display is enabled (see BACK and MAP commands), if the auto-cover
  flag is ON the atoms will be covered each time a new set of atoms is
  selected, subject to the setting of CRAD (qv). If the auto-release 
  flag is ON, those bricks which are not near an atom will be removed
  from the display when a new atom display is selected. The cover and
  release flags may be set explicitly for the next generation of the
  display only (ie when GO is next typed) by the commands COVR and
  RELS (qv). 
       Bricks are considered to cover an atom if they contain any of the 
  corners of a cube centred on the atom of half-width set by the command
  WIDTh (qv).
       However the bricks were selected, the program keeps a record of
  which bricks for each contour level and map have been downloaded to the
  PS300 in the current session, so that they need not be reloaded. The PURge
  command (qv) may be used to remove unused bricks if it is necessary to
  free PS300 memory. The map bricks will always be deleted at the end of
  a session.

1 AXES
  The F4 function key toggles an axes object in the corner of the screen 
  on and off.

1 BACK
       This enables the display of a contoured map when GO is typed. 
  This assumes the existence of a MAP data set. (qv NOBAck which suspends
  map display)

1 BADD
       When GO is next typed, add the map bricks in a cube centred on the 
  current point (if valid), of half-width set by the command WIDTh (qv).     

1 BKUP
       Backup coordinate file, ie copy the main coordinate file COORD
  to the backup file SAVE. This provides a backup and restore (RSTR)
  feature which if used correctly allows the user to let his
  imagination run riot when fitting his coordinates to a density.  As a
  precaution a prompt is typed on the terminal: answering anything
  other than 'Y' aborts the operation. The current screen coordinates
  are not affected, since the operation is a straight file to file
  copy. If the user requires more backup capacity, he must make use of
  system commands such as COPY to make copies of his coordinates. 

1 BREL
       When GO is next typed, remove the map bricks in a cube centred on the 
  current point (if valid), of half-width set by the command WIDTh (qv).     

1 BUFF
       Reset "vector buffer" size. With a 1MB PS300 on a fast interface
  (DMR, parallel or ethernet), the PS can suffer from indigestion
  caused by the host sending data too fast for the GCP to process it.
  It then stacks up in PS memory, often causing the whole system to
  crash. To avoid this problem, approximately every MXVCBF vectors
  Frodo waits until the previously sent data has been processed before
  sending the next bit. The BUFF command allows MXVCBF to be changed.
  It defaults to 2000 for 1MB systems on a fast line, otherwise 10000,
  but these numbers are guesses at suitable values.

1 CENT
       The prompt expects the coordinate to use as the next screen center  for
 atom selection (SPHE and (S)MIX ).  Typing  return  forces  the  position of
 the last identified atom as the  next center. 

1 CHAT 
       This describes the PS300 version on 5-Apr-1984

       The CHAT interface produces the prompt "Chat>" on the 
  terminal, and is entered from the display interface by typing <cr>. 
  The user can then type a four character command. Commands may
  be abbreviated or elongated provided they are unambiguous. An
  unrecognized keyword causes a listing of the current commands. 
  Input is free format. In most cases, the parameters to the command
  may be typed on the same line: if they are not, the user is
  prompted for the parameters. You can read commands from a file by 
  typing @filename (default extension .REC): all lines in this file are
  then treated as Frodo commands to any part of Frodo (but not input
  to SYS or HELP) until the end of file is reached. This is mostly
  useful for complicated MOL commands. See also the command RECOrd, to
  record all terminal input for later replay. A command beginning with
  "$" will be treated as a DCL command.

1 COLA
       Allows change of the atom type colours, in the same way as in
  MOL>ATCOL. The colour table is stored in the constants file.

1 COLB
       Allows change of the B-factor colours, in the same way as in
  MOL>BCOLOUR. The colour table is stored in the constants file.

1 COLQ
       Allows change of the occupancy colours, in the same way as in
  MOL>OCCOLOUR. The colour table is stored in the constants file.

1 CONT
       Now renamed CENT

1 COVR
       When GO is next typed, get all map bricks which cover the selected
  atoms, with a cube half-width set by WIDTh. This only has an effect the
  next time GO is typed: see AUTO for the auto-cover flag which is permanent.

1 CRAD
       Defines a radius for selecting maps. If it is zero, it has no
  effect. If atom covering is on (AUTO ON or COVR): if CRAD is positive,
  map bricks will be selected to cover atoms closer than CRAD to the
  current display origin; if CRAD is negative, the map will cover all atoms
  plus a cube of halfwidth abs(CRAD) centred at the origin. If atom
  covering is off, a cube of halfwidth abs(CRAD) centred at the origin
  will be selected.

1 DIALS
     There is currently only one set of 8 dials that must perform many
 functions.  In order to connect the dials to the different function 
 networks,  a number is pressed on the PS300 keyboard.  The keyboard
 must be in Graphics (KB) mode (press shift line/local on left keypad).
 The designations follow:

         1   VIEW Normal viewing mode, dials control view rotation and 
                  translation, scale and slab (front and back clipping)
         2   FBRT The dials now control the movement of the FBRT object
                  or the ruler
         3   MOVE The dials control the movement of the MOVE atom or POINT
         4   TOR  The dials control the pre-selected torsion movements.
         5   BRIT The dials control contrast, viewport for and aft intensity,
 		 and map intensity
         6   PARM The dials control character size (for all labels),
                  stereo half-angle, rock speed and rock
                  angle, and flash speed (for MOL FLASH option).
         7   COL1 The dials control the colour of 4 permanent objects:
 		 ATOMs, FBRT, ID and SATM (symmetry-generated atoms).
                  Each is specified by a hue and saturation.
 	8   COL2 The dials control the hue and saturation for MAP objects,
 		 MOL objects, and TOR objects. The selection of which element
 		 of these objects is connected to the dial is done by function
 		 keys F6, F8 and F10. Also hydrogen-bonds from the menu option
       		 .Hbnd.
         9   DGNL dial 8 controls the cycling through fragments generated by VMM
         0   COL3 the dials control colours (hue and saturation) which may
                  be explicitly connected to parts of mol objects.

    One can change the dials' function at any time, the current connection
  is shown on the display below the menu.  Also the dial LEDs change to 
  reflect the new assignments.

1 Disclaimer
 	This software is a conversion of code provided to
  us by Dr. Alwyn Jones, the original program author.  The
  history of this code is something else again.  I believe
  it is mainly the VAX/MPS conversion of FRODO done by Dr.
  Bruce Bush at Merck & Co., Inc.  We have generally
  left code intact that did not require changes because of 
  different graphics systems, so that we can claim no respons-
  ibility for those parts. See the file history.txt for the 
  origin of this code.
          In addition, for the parts that have been modified 
  for the PS300, I would like to paraphrase Dr. Bruce Bush:

 	Neither the program author, nor the modifier, nor anybody
 	else, make any representations or warranties with respect 
 	to the correctness or usefulness of the program or docu-
 	mentation, either before or after modifications.

  I guess that's life.		J. W. Pflugrath  November, 1982

  Endorsed by Phil Evans and Rod Hubbard  April 1984


1 DIST
       This allows one to insert distant restraints between atoms  in 
  the  RZON and other atoms. When the DIST flag is set, REFI prompts for
  the residue name and atom  name of the moving atom, and then for the
  names for the fixed atom.  The  regulariser  treats  the  distance of
  the first atom (whose position may  change during the regularisation)
  to the position defined by the  second  atom  before  regularisation 
  (i.e.   it  does  not  change  during  the  regularisation) in the
  same way as a bond restraint on the first atom. 

1 END
       This ends the session. Current parameters are saved in the 
  constants file. All display objects are deleted. You should always exit
  Frodo with the END command, NOT with control/Y.
  

1 FCOL
       Changes foreground atom colouring style. The options are
  (a) NOCOlour  atoms are all drawn in the same colour, which is set
       by the dial on panel 7 (HUE ATOM)
  (b) ATCOlour  atoms are coloured by atom type. The atom type colours
       may be changed by the command COLA (or in MOL by ATCOLour).
  (c) BCOLour   atoms are coloured by temperature factor. The B-factor
       colours can be changed by COLB or MOL>BCOLOUR
  (d) OCCOLour  atoms are coloured by occupancy. The occupancy
       colours can be changed by COLQ or MOL>OCCOLOUR
  (e) CLASscolour  atoms are coloured by residue class
       The classes can be defined by the command SETC, and the current
       definitions printed with PRCL

       In all cases, symmetry-generated atoms are drawn all the same
  colour, which is set from a dial on panel 7.

1 FILE
       Change filenames of any files used by the program. The files are 
  identified by a logical stream name, as follows:-

   BACK
       A scratch data set which is used by the MOL  commands to create
  a background object.  The PS 300 version no longer  uses this data
  set for electron density vectors. 
   COORD
       The  coordinate  data  set (see the coordinate data set
  writeup for a description).
   DICT
       The name of the dictionary data set used by  the  regularizer 
  (see  the dictionary writeup for a brief description). 
   SCRATCH
       The name of a scratch data set. Used by REFI.
   SAVE
       The name of a coordinate data set used as the  backup/restore  data
  set (see the BKUP/RSTR description).
   NAMES
       The name of a data set  used  by  SAM  commands  ABINITIO,  INSERT,
  REPLACE.   It  is  a  source  data  set consisting of a residue type and
  number of atoms in the residue (format (A4,I5)) and then a list  of  the
  atom  names (format (18A4)).  The atomic order in this lists becomes the
  order in the data set.
   MAPn   n=1,4
       Up to 4 map files, used for contouring and real-space refinement.
  They may be either bricked density maps (created by MAPBRICK) or 
  pre-contoured vector maps (created by MAPCONT).

1 FKEYS

     The PS300 function keys are used generally to toggle the display
 of a named object.  The name of the object affected is shown on the LEDs
 associated with the function fkey.

2 MENU
     F1 toggles the menu on and off.

2 ID
     F2 causes the IDs to be toggled on and off without re-defining them.

2 ATOMS
     F3 toggles the ATOM, BOND and symmetry-generated bond objects on and off.

2 AXES
     F4 toggles the axes object on and off.  

2 NAYB
     F5 toggles the NAYB object on and off.

2 MAP
     F6 cycles through the current map elements (an element is a contour
  level in a map, labelled 'MmLl' where m is the map number and l is the
  contour level number), selecting which one is toggled by F7, and whose
  colour is controlled by dials on dial panel 8. The elements include 'ALL'
  which allows all contour levels to be toggled together by F7.

2 MOL
     F8 cycles through the current MOL objects (MOL1 to MOL8), selecting 
  which one is toggled by F9, and whose colour is controlled by dials on
  dial panel 8. The elements include 'ALL' which allows all MOL objects
  to be toggled together by F9.

2 TOR
     F10 cycles through the 6 torsion objects, changing the colour connections
  on dial panel 8.

2 RESET TR
     F11 resets the view translation to its last value sent from Frodo
  by options .CENT, .ORIG, ACEN, CENT

2 MONO/STEREO
     F12 cycles through the display styles: mono, flashing stereo, 
  left stereo and right stereo (for photography), split-screen stereo,
  and orthogonal views.

1 GO
       To exit from the CHAT interface (really to enter interactive graphics
  mode).  The  present  system  values  get written to the constants file.

1 HELP
       (VAX only) Enters VMS HELP routine for information on PSFRODO commands.
  Use it just like normal VMS HELP command.

  Format
       HELP     key1, key2 ...

1 JIMBOB
      Jimbob is responsible for programming this thing.
  He can be contacted at (713) 527-4872. This version was cooked
  up by Phil Evans (MRC LMB Cambridge) and Rod Hubbard (York).

1 KEYBOARD
     The PS300 keyboard is used to provide local changes in the
 function, such as change the dials function or toggle displays
 on/off.  See help for FKEYS and DIALS. 

2 CONTROL_R
     This forces reorthogonalization of  the rotation matrix applied
  to the view (shouldn't be necessary). After significant view 
  manipulation, the display loses its orthogonality because of matrix
  multiplication round-off error. The matrix is reorthogonalized 
  automatically from time to time. 

2 c
     Centres and scales the picture on the foreground atoms

2 o
     Restores the origin sent by Frodo (from .ORIG or ACEN etc) after 
     'c' has been used to centre the picture.

2 x
     Forces a view down the X axis 

2 y
     Forces a view down the Y axis 

2 z
     Forces a view down the Z axis 

2 p
     Rotates the view by 90 degrees about the X axis 

2 q
     Rotates the view by 90 degrees about the Y axis 

2 r
     Rotates the view by 90 degrees about the Z axis 

2 CLEAR,TERM,GRAPH
     On the left keypad, they perform their normal functions.

     CLEAR  clears the terminal emulator display
     TERM   toggles the display of the terminal emulator display
     GRAPH  toggles the graphics display 

1 LABL
       Changes the format of the atom label you get when you hit a
  foreground atom. The answer "A" gives a label atom-name//residue-name
  (eg CD1 203A), the answer "R" gives residue-type//residue-name
  (eg ARG 72B). This switch may also be done with the menu option .Labl

1 LINK
       This is used to look at a data set made  of  just  CA  atoms.   The
  connectivity  is  defined  so  that  the  first atom is connected to the
  second, the second to the third etc. An optional link distance may be given:
  atoms are not joined if they are further apart than this.

1 MAP
       This switches on or off any of the maps to be displayed. Up to
  four maps may be used, and they may be either precontoured vector maps,
  or bricked electron density maps. All maps to be displayed together must be
  on the same grid, cover the same volume, and be divided into the same size 
  bricks, whether they are precontoured or not.
       This option switches the specified map  ON or OFF, or SUSPENDs
  it. If a map is switched on,  the program asks for contour levels.
  For a vector map, these are the serial  numbers of the required
  vectors: for a density map, these are the actual  contour levels. In
  the case of a density map, if a contour level is changed,  all bricks
  associated with that level are deleted from the PS300. If a map is
  SUSPENDed, its current display is frozen and remains unchanged until
  it is turned ON or OFF with this command. A suspended map may still
  be toggled on and off by the function keys, and its colour changed
  from the dials. If a map is switched OFF, it is removed from the display
  and all its bricks are deleted from the PS300.
       Note that the colours of the map elements are just applied in order,
  so if a map element is deleted, the colours of subsequent ones will
  change.

1 Memories

      These are viewport memories holding a set of  parameters
  defining the current view (ROT X,Y,Z; TRANS X,Y,Z; SCALE, SLAB and
  CENTER.  The user can store a  current set or retrieve the stored
  set.  A loaded memory has  a  +  instead of a . next to the menu
  item.  To clear a memory hit .NO  then the memory. To load a memory
  it must  first  be  empty  and  then  hit.  In the PS300 version,
  these memories are valid only  for the current FRODO session. 
  Note that the + sign does not always appear properly on entry to
  the interactive part of the program.

2 .M1
      Memory 1.
2 .M2
      Memory 2.
2 .M3
      Memory 3.
2 .M4
      Memory 4.

1 Menu
      This describes the PS300 version on May 1984

  The User interacts via a  menu  on  the  screen  and  via  the PS300
  acting as a terminal.  The  menu  items are activated by moving a pen
  on the tablet on the desired  command  and  then  by pushing  the 
  pen into contact with the tablet. If  carried out correctly, the . 
  next to the command will become a *.  Likewise atoms are identified 
  by  pushing  the pen   into   contact  with  the  tablet. Type <cr>
  to return to Chat.
  
      The normal cursor (a cross) is changed when a menu option wants
  an atom to be picked (this change is not foolproof). Some commands
  which take some time to execute (.CENT, .POP, .RSR, .SAVE, .BADD, 
  .BREL, .CHAT) change the cursor to a square to indicate that the
  menu is inactive.

      Any number of commands can be active at the same time.  However,
  this is an event driven system and certain commands cause an exit
  (possibly just temporary) from the interactive overlay.  Some
  combinations although allowed in theory must not be done - in
  particular .TOR and .FBRT cannot be used together since both commands
  make use of the same array (Users can make very slight changes to the
  program to allow this to take place).  It is an advantage for the user
  to have some idea how the menu structure works.  Each menu item has a
  flag associated with it.  Each flag takes on values 0,1,2,3......
  where 0 signifies that the item is not active.  The value can then be
  used to signify what has been done and what is to be done next.  Each
  command is checked one after the other and so information gathered by
  one command can be made known to any other command, e.g.  .LSQP is
  used to determine least squares planes, and when activated has the
  initial value 1.  If .LSQP is on and there has been a successful
  atomic identification, then the atom is kept for use in defining the
  plane.  This carries on until the flag .YES is set.  .LSQP checks for
  this and when it happens it sets the .YES flag back to off and
  increments its own flag.  If enough atoms have been defined, it then
  calculates a least squares plane, and returns to wait for more ID's.
  When a subsequent atom is picked, the distance of the atom from the
  plane is calculated and displayed in the scratch text area.  The
  command stays active until cleared by .WAIT or .NODA. Note .ID is
  always on (and not visible on the screen as a menu item).  The menu
  commands are arranged in a more (or less) sensible order, which tends
  to change according to the personal preferences of the guy who knows
  the code.  If you want to know more, get a listing of INTER.FOR. 

      The order on the screen is the order  defined  in  the  data
  statement  filling  up  the  array  MENU.   The  array ICC is the
  important flag array, and JCC contains pointers to go  from  menu
  position  to  flag  index e.g.  the I'th menu item corresponds to
  the flag ICC(JCC(I)).


1 MIX
       A maximum of 10 zones plus a sphere can be  defined.   The  program
  continues to prompt for residue names until the user types END.  It then
  prompts for the sphere radius (if the user types 0.0 no sphere search is
  carried out).  The atoms in the specified zones are displayed only if
  they lie within the specified sphere. (This is different from MIX before
  JULY 1983.)

1 MODE
       The program prompts for one of four possible REFI modes: these 
  modes may also be selected on the REFI command.

2 MODL:  To carry out normal regularisation.  If an atom has  the  magic
  coordinate  (1500.,1500.,1500.)  given  by SAM to signify that it is not
  determined, an attempt will  be  made  to  place  the  atom,  given  the
  standard  dictionary  bond lengths, angles and torsion angles (which may
  be set by ANGL).  To be successful the algorithm  requires  at  least  3
  connected atoms.  For example, if SAM has been used to REPLACE a residue
  of type ALA for one of type PHE, then one requires one pass through  the
  regulariser to pick up the ring and the CG .
2 EXTD:  To extend the chain from the first residue in the  RZON.   This
  option  does  no regularisation, it is a model making option.  The atoms
  in the rest of the RZON  are  added  to  the  first  residue  using  the
  connectivity,  and bond lenths and angles defined in the dictionary data
  set, DICT.  By using the ANGL option one can define values  for  torsion
  angles to make any desired conformation.
2 BEXT:  this is like EXTD, but extends backwards from the last residue 
  in the RZON, instead of forwards from the first.
2 RESI:  To build a residue or zone of residues from scratch.   It  does
  not  require  coordinates  for  the  first  residue  in  the  RZON.  The
  algorithm searches for 3 connected atoms in the dictionary, it then puts
  the first atom at the current screen center, the second along the X-axis
  and the third in the X-Y plane.  The remaining atoms are added  as  with
  EXTD.

1 MOL
      Allows the user to make background objects from  the  COORD
  data  set.   A  flexible  set of user functions are available and
  defined below. MOL over-writes the atoms array so  you should save your
  changed coordinates before using MOL  (the program will prompt you if
  you forgot).
  
  The commands available are:
  
2 PICK
       This prompts for a set of atom names to be included in
  subsequent  display objects (CA, CG1 etc. ), terminate the list
  with <cr>, or  EXclude to exclude the atoms instead of including
  them. The character  '?' may be used as a wild card in any name.
  If only one atom is included  (eg CA), the atoms are linked in
  the order they are read, otherwise they  are linked by distance
  (cf CHAT/ LINK and NOLINK). The atom-picking  set up here
  applies to all subsequent atom-drawing options in the current 
  call to MOL (ie ZONE, RLIST, SPHERE, CENTRE, MIX, SURFACE but
  not  RESIDUE).  PICK is cancelled by ALLATOM (which is the
  default on  each entry to Frodo.  Alternative selections may be
  made by  MAIN, SIDE and CA (qv, CA is  equivalent to PICK CA) 

2 CA
       Pick CA atoms only. They will be linked in order of
  sequence, subject  to the maximum distance given by the chat
  command LINK. 

2 ALLATOM
       Reset atom-picking to include all atoms. This is the
  default on  each entry to MOL. 

2 MAIN
       Pick main-chain atoms (ie CA, C, N, O) for subsequent 
  atom drawing. The definition of main-chain atoms may be changed
  by the command SETMAIN (normally CA C N O OT)

2 SIDE
       Pick all atoms other than main-chain atoms for subsequent
  atom drawing. The definition of main-chain atoms may be changed
  by the command SETMAIN (normally CA C N O OT). The first main-chain
  atom (normally CA) will also be included in the side-chain.

2 SETMAIN
       Define which atoms are to be considered as main-chain. This
  definition may be used in the FCOL CLASS option, or in MOL. For proteins,
  normally  CA C N O [OT]. Note that MOL>SIDE will include the first
  main-chain atom (eg CA) as well as the side-chain atoms.
  
2 HBOND
       For all subsequent atom drawing commands  ZONE, RLIST 
  MIX, SPHERE, CENTRE, RESIDUE, draw hydrogen bonds between these
  atoms, instead of the covalent bonds. This search will not find
  H-bonds within the same residue unless hydrogen atoms are present
  in the file. BOND switches back to covalent bond drawing. 

2 BOND
       Draw covalent bonds in subsequent atom drawing commands
  RESIDUE, ZONE, RLIST, MIX, SPHERE, CENTRE, ie switch off HBOND.
  This is the default on first entry.

2 RESIDUE
       This prompts for a set of residue type names (ASP, GLN
  etc.),  terminated by END or <cr>, then you are prompted for a
  residue zone.  This option displays the residues with standard
  atom connectivity. 

2 ZONE
       This displays a single zone of residues with connectivity 
  determined by atomic position. The atoms will be individually
  coloured  by atom type or B-factor by using the commands
  ATCOLOUR (default)  or BCOLOUR before this command (see
  ATCOLOUR, BCOLOUR, NOCOLOUR).  Symmetry generated atoms will be
  displayed if the symmetry flag is  set (see SYMGEN, NOSYMGEN).
  ZONE * will give the whole molecule. 

2 RLIST
       This displays a list of up to 10 individual residues. The
  atoms will be individually coloured  by atom type or B-factor by
  using the commands ATCOLOUR (default)  or BCOLOUR before this
  command (see ATCOLOUR, BCOLOUR, NOCOLOUR). Symmetry generated
  atoms will be displayed if the symmetry flag is  set (see
  SYMGEN, NOSYMGEN). 

2 SPHERE
       This prompts for residue name and atomname to define a
  sphere  centre, and radius. The atom name defaults to CA. If the
  keyword  LABEL is typed on the same line as the  command, all 
  atoms of the  name given in response to the prompt  (default CA)
  are  labelled. The  atoms will be individually coloured  by atom
  type or B-factor by  using the commands ATCOLOUR (default)  or 
  BCOLOUR before this  command (see ATCOLOUR, BCOLOUR, NOCOLOUR). 
  Symmetry generated atoms  will be displayed if the symmetry flag
  is  set (see SYMGEN,  NOSYMGEN). 


2 CENTRE
       This is like SPHERE, except that the sphere centre is
  defined  by coordinates: it prompts for a sphere  centre, and
  radius. If the  keyword LABEL is typed on the same line as  the
  command, all  atoms  of the name given in response to the prompt
  (default CA) are  labelled. The atoms will be individually
  coloured  by atom type or  B-factor by using the commands
  ATCOLOUR (default)  or  BCOLOUR before  this command (see
  ATCOLOUR, BCOLOUR, NOCOLOUR).  Symmetry generated  atoms will be
  displayed if the symmetry flag is  set (see SYMGEN,  NOSYMGEN). 

2 MIX
       This is like the CMIX command, except that the centre is defined
  as an atom. Like the foreground MIX command, this draws atoms only if
  they  lie both in a specified sphere and in one of the specified
  residue  zones (up to 10). This option may be useful for example
  for drawing a  ligand site without the ligand. If the keyword
  LABEL is typed on the  same line as  the command, all  atoms of
  the name given in response  to the prompt  (default CA) are
  labelled. The atoms will be  individually coloured  by atom type
  or B-factor by using the commands  ATCOLOUR (default)  or 
  BCOLOUR before this command (see ATCOLOUR,  BCOLOUR, NOCOLOUR). 
  Symmetry generated atoms will be displayed if  the symmetry flag
  is  set (see SYMGEN, NOSYMGEN). 

2 CMIX
       This is like the MIX command, except that the centre is defined
  as xyz. Like the foreground MIX command, this draws atoms only if
  they  lie both in a specified sphere and in one of the specified
  residue  zones (up to 10). This option may be useful for example
  for drawing a  ligand site without the ligand. If the keyword
  LABEL is typed on the  same line as  the command, all  atoms of
  the name given in response  to the prompt  (default CA) are
  labelled. The atoms will be  individually coloured  by atom type
  or B-factor by using the commands  ATCOLOUR (default)  or 
  BCOLOUR before this command (see ATCOLOUR,  BCOLOUR, NOCOLOUR). 
  Symmetry generated atoms will be displayed if  the symmetry flag
  is  set (see SYMGEN, NOSYMGEN). 

2 SURFACE
       This generates dot surfaces at Van der Waals radius from
  specified  atom. It prompts for the residue range of atoms whose
  surface is to be  displayed, then for a range of context atoms.
  This context must include the  first range but may be as great
  as the entire molecule. eg. the surface of a  single residue in
  the context of just that residue is an enclosed shape  roughly
  like that of an isolated amino acid. Alternatively, the keyword 
  SPHERE may be given instead of a residue range, and the program
  prompts for a  residue name and atom name to use as a sphere
  centre, and a sphere  radius and  a border width (default 2A). 
  In this case, atoms are  selected they lie in the sphere, and
  the context  atoms are those  that lie between the sphere and a
  sphere larger by the border size.  It then prompts for what
  percentage  of the Van der Waals radius is  to be applied to all
  atoms. Radii may be reset by the VDWRADII command (qv)
       The program offers a selection of different icosahedral
  surface  lattices for drawing each atom, with different numbers
  of dots. They are  specified by the T (triangulation) -number,
  giving the following number of  dots: t=1, 12; t=2, 20; t=3, 32;
  t=4, 42; t=6, 60; t=7, 72; t=9, 92 ("t" = 2  and 6 are not
  proper triangulation numbers). t=7 is the default, but t=4 or 
  even 3 are useful for drawing large surfaces without overloading
  the machine.  t=1 and 2 are probably too sparse to be useful.
  For t=9 (92 dots) only, you  have a choice of surface texture:
  use S(single) normally but experiment with  others. They mean
  Double Triple density dots and alternative offsets of dots  A
  and B. 
       The atoms will be individually coloured  by atom type or 
  B-factor by using the commands ATCOLOUR (default)  or BCOLOUR
  before  this command (see ATCOLOUR, BCOLOUR, NOCOLOUR). 
  Symmetry generated  atoms will be displayed if the symmetry flag
  is  set (see SYMGEN,  NOSYMGEN). 

2 RIBBON
       This command draws a protein main chain as a smoothed ribbon,
  with the ribbon plane approximately parallel to the peptide plane.
  The algorithm use is related to that of Carson & Bugg, J Molec
  Graphics (1986) 4,121-122. The first prompt is for the residue
  range to be used. The way in which the ribbon is drawn is
  controlled by three parameters: the number of strands in the ribbon
  (1 to 5, default 2), the width of the ribbon in Angstrom 
  (default = 1.0) and the number of chords, ie the number of straight
  line segments between each pair of CA atoms (default = 3). This
  command uses the Bspline function of the PS300, ie the smoothing
  of the lines is done in the PS300. This means that after the
  structure containing the ribbon (eg MOL1) is closed, the PS300
  goes dead for up to 20-30 seconds: don't panic. The ribbon has
  no inherent colour, so will take its colour from colour dials
  or colour command. After this command, the atom picking (qv) is
  reset to select all atoms.
  Warning! This command seems to crash the PS300 sometimes.

2 TEXT
       Draw any text as a label to a given atom. The command prompts
  for the text, then the residue name and atom name (default CA) to
  label. The text can be up to 20 characters: if it includes spaces,
  it should be included in quotes ' '.

2 VECTOR
       This command reads in a vector list from another file and
  sends  it to the PS300 as part of the current open display
  object. At  present it reads a file as created by Arthur Lesk's
  ARPLOT program,  but does not use any colour changes (all
  vectors in the file are  drawn without explicit colour
  specification, as in NOCOLOUR). It  would be easy to change the
  routine to read other formats of vector  list, or a dot list. 

2 LATTICE
       This command reads in a set of vector lists (as written by
  MADNES option AUTJ>WRTVEC), and creates a number of dot or line
  objects from them. The user is asked for a suffix to append to
  the input name (this allows distinction between several files with
  the same object names), and the name of the file. The file is a
  formatted file containing, for each vector list, a header line
  consisting of the object name, list type, number of vectors, and
  a scale factor to multiply each vector (format 2A8,I5,F15.5),
  followed by x,y,z [,movedraw], vectors (format 3F10.5 [,I5])
  The movedraw flag = 0 for move, 1 for draw, and is only present
  for VECTORS & MVECTORS types.
 eg
 SCTVEC  MVDOTS    250     1000.00000
   -0.15209   0.10098   0.02049
   -0.06234  -0.21449   0.04445
 . . .
  For each list, a new object NAME Objectname//suffix will be created.
  List types are DOTS, LINES, VECTORS, MVDOTS, MVLINES, MVECTORS. 
  LINES types consist of alternate move & draw vectors, VECTORS have
  explicit move/draw flags. For types beginning MV, the vector 
  list will be preceded in the object by a MOVEXYZ node (qv) with a
  translation of 0,0,0. After creation of each object it is Instanced
  into MOL1 to MOL8 for display, but they may of course be re-instanced
  as you wish.
          For use with vectors from Madnes, the display centre
  should be 0 (Chat>Cen 0,0,0), and then .No/.Fbrt may be used to
  align the cell lattice on the observed vectors: .Yes then gives the
  "missetting" angles, rotations around x,y,z, which can be put back into
  Madnes.

2 LOCUS
       Draw circle representing the intersection between 2 spheres,
  for visual triangulation. The user is prompted for the xyz coordinates
  of the sphere centres (qv ALOCUS for spheres centred on atoms), then 
  for the sphere radii.

2 ALOCUS
       Draw circle representing the intersection between 2 spheres,
  for visual triangulation. The user is prompted for the residue and
  atom names for the sphere centres (qv LOCUS for spheres centred at
  xyz positions), then for the sphere radii.

2 DOTS
       This command reads in a molecular surface from a file 
  previously specified by MSURFACE (qv). The whole surface file
  is read, and drawn in the same colour (with colour taken from
  the dials or previous COLOUR commands), unlike drawing the
  surface with the other drawing commands (see MSURFACE).

2 CELL
       This command draws the crystallographic unit cell,
  provided that  symmetry information is present in the COORD file
  (see SAM/SYMMETRY) 

2 LINE
       Draw a line between two points x1,y1,z1 and x2,y2,z2. This
  may be  useful for drawing axes etc 

2 POINT
       Draw a point (tetrahedron) at point x,y,z. this may be
  useful for  marking positions. 

2 SYMMETRY
       This command inserts a specified symmetry operation into 
  the current display object, to apply either to the rest of the 
  object, or if an object name is given as the second argument to
  the command, to the named object, which will be instanced (ie 
  displayed) with this symmetry operation. The named object must 
  have previously been created (see NAME). The permanent objects
  BOND (foreground bonds), FBND (FBRT object bonds) and HBND
  (foreground atom hydrogen bonds) may be instanced as well as
  objects created by MOL. Symmetry information must have been
  placed in the COORD file with the SAM command SYMMETRY. 
       The symmetry operation is specified by  a character string
  (with no included spaces) made up of some of the following
  elements  (in any order). 
       (i)   Sn  the n'th crystallographic symmetry operation
       (ii)  Ln  the n'th non-primitive lattice translation
       (iii) Nn  the n'th non-crystallographic symmetry operation
       (iv)  +-na,+-nb,+-nc  + or -n cell translations along a,
                b, or c 

  eg S2,  S3+a-2c, S1L1N5-B

  SYMPRINT may be used to find the serial numbers of each symmetry
  operation.

2 INSTANCE
       Instance (ie display a copy of) a previously created
  display  object into the current display object. This can be
  used for example  in conjunction with instancing with the
  SYMMETRY command, to build  up oligomers of proteins. eg to
  display a dimer, the subunit could  be created as a picture with
  NAME SUB,  ZONE *, and then the dimer  could be created by NAME
  MOL1, INSTANCE SUB, SYMMETRY S2 SUB  using in this case the
  second crystallographic symmetry operation  to create the dimer.
  The permanent objects BOND (foreground bonds), FBND (FBRT
  object bonds) and HBND (foreground atom hydrogen bonds) may be
  instanced as well as objects created by MOL. 

2 SYMGEN
       This command sets a switch for subsequent molecule drawing
  commands (except ZONE) such that atoms are selected in the
  specified  sphere using symmetry operations to bring the atoms
  into the sphere if  necessary. The given symmetry operation may
  either be ALL, in which case  all symmetry operations including
  cell translations are used (as for  the foreground SYMM option),
  CRYS for just crystallographic, NONC for just non-crystallographic 
  operations, or may be a single operation specified as for SYMMETRY
  (qv). The SYMGEN switch is off at the start of each Frodo session, 
  and may be turned off by NOSYMGEN. 

2 HELP
       (VAX only) Enters VMS HELP routine for information on
  MOL commands.  Use it just like normal VMS HELP command. 

2 FLASH
       This command asks for the name of one or two previously
  created  display objects, and flashes it or between them. The
  flash speed is  controlled by dial 8 on panel 6. 
  The permanent objects BOND (foreground bonds), FBND (FBRT
  object bonds) and HBND (foreground atom hydrogen bonds) may be
  instanced as well as objects created by MOL. 

2 ANIMATE
       This command asks for the name of a number of previously
  created  display objects, and cycles the display between them. 
  This is like FLASH, except with more than 2 objects. 
  The speed is  controlled by dial 8 on panel 6. 
  The permanent objects BOND (foreground bonds), FBND (FBRT
  object bonds) and HBND (foreground atom hydrogen bonds) may be
  instanced as well as objects created by MOL. Only one ANIMATE
  structure may exists at a time.

2 PEARLS
 	This generates a display of CA-atoms, with animated dots
  running along the CA-CA bonds from N to C terminus. 
  The command asks for a residue range,
  the number of dots/residue (default=4), and the number of intervals
  between these dots to give the animation effect (default=5). Note that
  this command closes the current display object, and creates several
  sub-objects: the sub-objects will be deleted when the main object is
  deleted. Several PEARLS structures may exist, but they must be
  in different NAMEd objects, and will all be constrained to have the 
  same animation interval.
  The speed is controlled by dial 8 on panel 6, as for FLASH and ANIMATE. 
  The idea for this display was cribbed from Klaus Mueller.

2 DELETE
       Deletes a named display object. A list of currently
  defined  background objects may be obtained with NOW. DELETE *
  deletes all  MOL objects: they are also all deleted on exit from
  Frodo (Chat/END). 

2 NOW
       Shows the current state of MOL. The setting of the five
  switches  which affect molecule drawing are shown. 
       (a) colouring mode (atom type ATCOLOUR, B-factor BCOLOUR,
            CLASSCOLOUR, or colour unspecified NOCOLOUR) 
       (b) symmetry generation (SYMGEN or NOSYMGEN)
       (c) atom picking (PICK, CA, MAIN, SIDE)
       (d) the style of drawing: covalent bonds (default, [BOND]);
           hydrogen bonds [HBOND], or molecular surface from file
           [MSURFACE]
       (e) labelling options [LABEL]

  Also given are the names of display objects which have been
  created,  and the name of the current open object (if any). 

2 SYMPRINT
       Prints all symmetry operations present in the COORD file
  (if any).  This is useful to find the serial numbers of the
  symmetry operations  that you want for SYMMETRY or SYMGEN
  commands. 

2 VIEW
       This closes any open display object and shows the new
  display.  The dials and function keys are then active, but the
  menu options are not.  This is probably only useful if you work
  with the PS300 as the terminal  as well. 


2 LABEL
       This sets the flag for generating atom and residue labels 
  for all the drawing commands (ie ZONE, RLIST, SPHERE, CENTRE,
  MIX, SURFACE and RESIDUE) . The prompt is for atom names
  (CA,CG2 etc.). Terminate with END or <cr>, and then you are
  prompted for a residue range, and a residue interval, eg you
  can label every 10'th residue. 
       The special atom name ALL causes labelling of all atom
  names  in the residue. The first designated atom name receives
  the residue  name and type as a label. The rest get name labels.
       Labelling is turned off by hitting <cr> in response to the
  first prompt, ie setting no atoms for labelling.

2 MSURFACE
       This sets the flag for drawing molecular surfaces from a
  precalculated file. you are prompted for the filename (<cr> to
  to leave unchanged) and whether you want to select exposed or
  buried surface, or both (if you have calculated them, see
  write-up for surface-calculation SURFACE.TXT). After this
  command has been typed, any of the atom drawing commands
  (ie ZONE, RLIST, SPHERE, CENTRE, MIX and RESIDUE) will select
  the appropriate atoms and then load the corresponding parts of 
  the surface from the file, coloured according to the colouring 
  switches ATCOLOUR, BCOLOUR, NOCOLOUR. Alternatively, the whole
  surface may be drawn uncoloured from the file with the command
  DOTS. You can switch back to drawing bonds with the command
  BOND. Note that the surface dots in the file are identified by
  an atom number, so that the atoms used to generate the surface
  must be in the same order as the atoms in Frodo, and the atoms
  in Frodo must not have been altered in order by any rebuilding:
  you may have to unload all atoms to a formatted file and reload
  them. 

2 COLOUR
       The colour of MOL objects is controlled in three basic
  ways: if individual atom colouring (by type or B-factor) is
  used, this overrides other colours. Otherwise (if NOCOLOUR is
  set, or for the options  RESIDUE, LABEL, and CELL), the colour
  of objects is normally controlled through the  dials selected by
  hitting "8" on the PS300 keyboard and function key  8. This
  command COLOUR can be used to change the colour at any  point in
  the MOL object, to be applied to subsequent parts of the same
  object.  The colour of all vectors defined before defining 
  COLOUR will be altered by the MOL dials.
  The colour on the COLOUR comand may be specified in three ways:
   (a) as RED,GREEN,BLUE,MAGENTA,YELLOW,CYAN or WHITE 
   (b) as a hue number (0 to 360) and optional saturation (0 to 1)
       the hue is 0=360 = blue, 120=red, 240=green, specified as
       100*hue + 10*saturation (eg 12010 is red)
   (c) as a dial connection to a dial on panel 9: this is
       specified as D1 to D4. 

2 ATCOLOUR
       This command sets the atom-type colouring switch, so that 
  subsequent drawing commands will colour atoms by type. This
  remains  active until cancelled by NOCOLOUR or BCOLOUR. ATCOLOUR
  is the default  on each entry to Frodo, and the switch setting
  is not saved between  sessions. 
       The command also allows you to redefine the atom type
  colours.  The colours are specified as 100*hue + 10*saturation
  (eg 010 is blue,  12010 is red, 24010 is green, 36010 is blue
  again, 0 is white). These  colours are saved in the constants
  file. The atom types used must be defined in the atom-type list,
  controlled by SAM>ATOMTYPE.

2 BCOLOUR
       This command sets the atom colouring switch such that 
  subsequent drawing commands will colour atoms by B-factor. This 
  remains  active until cancelled by NOCOLOUR or ATCOLOUR. Note
  that  ATCOLOUR is the default  on each entry to Frodo, and the
  switch  setting is not saved between  sessions. 
       The command also allows you to redefine the B-factor
  ranges and  the colours.  The colours are specified as 100*hue +
  10*saturation  (eg 010 is blue,  12010 is red, 24010 is green,
  36010 is blue again,  0 is white). These  colours are saved in
  the constants file. 

2 OCCOLOUR
       This command sets the atom colouring switch such that 
  subsequent drawing commands will colour atoms by occupancy. This 
  remains  active until cancelled by NOCOLOUR, BCOLOUR or ATCOLOUR.
  Note that ATCOLOUR is the default on each entry to Frodo, and the
  switch setting is not saved between  sessions. 
       The command also allows you to redefine the occupancy
  ranges and  the colours.  The colours are specified as 100*hue +
  10*saturation  (eg 010 is blue,  12010 is red, 24010 is green,
  36010 is blue again,  0 is white). These  colours are saved in
  the constants file. 

2 NOCOLOUR
       This command sets the atom colouring switch such that 
  subsequent drawing commands draw all atoms in the same colour:
  they  will then take there colour from the MOL colour dials
  (panel 8) or  COLOUR commands. This switch remains active until
  cancelled by  ATCOLOUR or BCOLOUR. Note that ATCOLOUR is the
  default on each entry  to Frodo, and the switch setting is not
  saved between sessions. 

2 SETCLASS
       Set classes for the CLASSCOLOUR option: these may also be
  set from CHAT>SETC
       You can define up to 10 colour classes, each containing a list
  of possible residue types (ie GLY, PHE etc), or alternatively MAIN
  (all main-chain atoms), SIDE (all non-main-chain atoms), or REST
  (everything not otherwise defined). Each class is assigned a colour,
  as a hue/saturation or colour name, or ATCOLOUR, BCOLOUR or NOCOLOUR.
  If any class is assigned ATCOLOUR or BCOLOUR, all other classes will
  be automatically reassigned to NOCOLOUR, since only one colour table
  can be active at one time. This CLASSCOLOUR option can be used to
  colour particular types of residues in different ways, and also to
  distinguish main-chain and side-chain, eg MAIN/NOCOLOUR,
  SIDE/ATCOLOUR. 
       Note that one set of class assignments are stored in the
  constants file. If you want several alternative sets, use the
  RECORD/playback facility.

2 CLASSCOL
       Set colouring option to colour by residue class. The classes are
  defined by the commands Chat>FCOL CLASS or MOL>SETCLASS. Use PRCLASS
  to print the current class assignments.
       
2 PRCLASS
       Print current CLASSCOLOUR definitions (even if this option is not
  selected)

2 VDWRADII
       This command allows Van der Waal radii to be set for any
  atoms in the SAM>ATOMTYPE list. The values are saved in the
  constants file.

2 GO
       This closes the  last named MOL object (MOL1 if the NAME 
  command has not been used in  this call to MOL) and exits from
  MOL  back to Chat. Control/z (end-of-file) does the same thing. 

2 NAME
       This starts a new MOL object. The default is MOL1.  Names
  that the PS300 recognises are MOL1 to MOL8: these are 
  automatically displayed. Other named objects can only be
  displayed  if they are instanced into an object called MOL1 to
  MOL8 by the  commands INSTANCE, SYMMETRY, or FLASH (or refenced
  by the Chat option  ATTAch). Drawing commands following the NAME
  command add extra  bits of picture to this object until it is
  closed by another NAME  command, or by VIEW, GO or ABORT. If a
  drawing command is given  without a preceding NAME command, an
  object called MOL1 is  automatically opened. 

2 AMOVE
       Set up a transformation node (ie a rotation matrix and a
  translation vector) in the current display object (default MOL1)
  which can be altered from the menu option .No/.FBRT (qv). A residue
  name and atom name (default CA) are given to define the coordinates of
  the centre of rotation. The command MOVEXYZ (qv) is similar but takes
  the x,y,z coordinates of the centre of rotation. This can be used eg
  for exploring crystal packing, by creating a basic object including
  a transformation node (AMOVE or MOVEXYZ), then instancing this object
  with different symmetry operations. Then when .No/.FBRT is used, the
  transformation is applied to the basic object, and the symmetry-related
  objects move in symmetry-related ways. Several MOVE nodes way be created,
  but not more than one in any display object.

2 MOVEXYZ
       Set up a transformation node (ie a rotation matrix and a 
  translation vector) in the current display object (default MOL1) 
  which can be altered from the menu option .No/.FBRT (qv). The x, y,
  z values are given to define the coordinates of the centre of
  rotation. The command AMOVE (qv) is similar but takes a residue and
  atom name to define the coordinates of the centre of rotation. This
  can be used eg for exploring crystal packing, by creating a basic
  object including a transformation node (AMOVE or MOVEXYZ), then
  instancing this object with different symmetry operations. Then when
  .No/.FBRT is used, the transformation is applied to the basic
  object, and the symmetry-related objects move in symmetry-related
  ways. Several MOVE nodes way be created, but not more than one in
  any display object. 

2 WAIT
       Wait for the specified number of seconds (maximum 106secs).
  This may be useful in MOL command files to allow the PS300 time
  to digest data sent to it over a fast link.

2 ABORT
       This aborts the current open display object and deletes it.

1 MSUR
       Activates or cancels the display of accessible surface with
  foreground atoms. The surface is precalculated and stored in a file
  (see SURFACE.TXT). The first keyword is ON (to switch on the display
  of both exposed and buried surface), OFF (to switch off the display),
  EXPOsed (to display exposed surface), BURIed (to display buried surface),
  or SUSPend to leave the current display unaltered. Further prompts are
  for the file name (the same as that for MOL>MSURFACE); a selection radius
  from the origin SRAD; a colour type code NOCOlour (ie all the same colour,
  taking colour from the MOL dial), ATCOlour (atom-type colour), or BCOLour,
  (temperature factor colours); and an MOL object name MOL1 to MOL8 to be
  used for the display. If this display is switched ON (or EXPOsed or
  BURIed), when the foreground atoms are selected, all the surface dots
  belonging to thes atoms are selected for display, provided they are
  within a radius of SRAD of the origin: if SRAD = 0, no radius check
  is done. Atoms generated by symmetry are not covered. The display uses 
  one of the MOL objects, as specified. Note that if the object name is 
  changed, the previous one remains unless deleted in MOL.

1 MUVA
       This is used to move atoms to new positions.   The  program  prompts
  for  residue  and  atom  names,  and then for the new coordinates.  This
  continues until the user presses just a return at the first prompt.   If
  the  atom  name  is  not  typed,  the  program  defaults to CA.  The new
  coordinate values get written to the COORD data set.  If the user  has  a
  large  list  of  data,  it  may be more convenient to use the SAM option
  UPDATE which can also define the IA flag.

1 MWT
       The regularisation requires 4 starting weights and 4 final weights.
  The  weights  correspond to the shift from the starting coordinates, the
  bond length error, the bond angle error and  the  torsion  angle  error.
  During  each  cycle, the weights get updated according to an exponential
  function, starting with the initial values and finishing with the final
  values.   The  program  prompts for the 4 starting values (I use 1., 1.,
  1., 1.), and then for the the 4 final values (I use 1., 30., 20., 10.).

1 NANG
       Switches off the ANGL option.

1 NAYBR
       This sets the contact distance for the display .NAYB command.

1 NCODe
       Set orthogonalisation code NCODE: this is a number 1 to 5 which
  defines the relation between orthogonal cartesian axes in Angstrom
  (used for atoms) tocell axes (used for maps)

 	1   orthogonal axes x,y,z along		a,   c* x a,   c*
 	2					b,   a* x b,   a*
 	3					c,   b* x c,   b*
 	4				      a+b,   -a+b,     c*
 	5				       a*,   c  x a*,  c

  1 and 5 are the most useful: 1 is the Brookhaven standard convention,
  5 is as defined by Rollett, Computing methods in Crystallography, and
  has also been widely used. 4 may be useful for trigonal and hexagonal cells.
  2 and 3 are probably useless.

1 NCYC
       The method of minimization requires a number of passes through  the
  RZON.   during  each  pass  the atoms are shifted to satisfy their local
  conditions.  After each  cycle  there  is  a  listing  on  the  terminal
  defining  the  largest  shift from the starting coordinates, the largest
  error in bond lengths, bond angles and torsion angles found in  the  last
  cycle.  One also gets an internal count for which atom had the error.  I
  normally use 10 cycles on my Pdp11/34.

1 NOAD
       Switches off the ADD option.

1 NOAN
       Switches off the ANCH option.

1 NOATom
       When GO is typed, new atoms are usually loaded from disk only if
  the atom selection has been changed. This command suppresses reloading of
  atoms from disk (qv ATOM which forces reloading)

1 NOAX
       No axes are drawn on the screen.  This is not used by the 
  PS300 program, but the shift F1 function key toggles an axes object 
  on and off.

1 NOBA(ck)
       This prevents the calculation of a contour vector list. There is no need
  for a MAP data set.

1 NODI
       Switches off the DIST option.

1 NOLI
       This is the normal option.  The  connectivity  is  then  formed  by
  various distance criterion.

1 NOREcord
       Closes the RECORD file, and switches off recording of commands:
  see RECord.

1 NORHyd
       Omit hydrogen atoms from REFI refinement. (qv RHYD)

1 NOSYM
       This switches off the symmetry checking.

1 NOW
       This causes a listing on the terminal of the present values of the
  important system parameters. Most of these are printed next to the Chat
  commands which define them: the Chat commands are printed in square
  brackets [].

2 FILES
       Produces listing of current file designations.

   Format:
       NOW FILES

1 PICK
       This option allows the user to display only  certain  named  atoms.
  After  the  prompt,  specify  up to 10 atom names.  Pressing just
  carriage return ends input. The atom names may include the wild card 
  character '?', which will match any character, thus C??? will match
  any carbon atom. If the list is ended with the keyword EX[clude], the
  listed atoms will be excluded.

1 PLOT
       Defines a plotfile name and optional title for use with the menu
  command .PLOT. The default filename is FROPLOT.PLT. Each use of the
  menu command .PLOT will add another picture to the plotfile, until
  it is closed by answering the prompt from PLOT by cntrl/z, changing
  to a different filename, or when you leave Frodo by typing END. Each
  picture may have two titles, the first one given here or with the
  command PLTItle, the second one giving the picture number in the file,
  and the time and date of creation. The titles may be suppressed by
  answering the title prompt with cntrl/z. The form of the plotfile
  and how to plot it will depend on the implementation: at the MRC
  it is a PLOT84 file. The simulation of intensity by line thickening
  is controlled by parameters set with the PLPA command.

1 PLPA
       Define parameters which control the way in which intensity variation
  (depth cueing) is simulated in plots from the .PLOT command. Lines
  are thickened by drawing several parallel lines depending on intensity.
  This is controlled by 4 parameters PLTTHR (threshold), PLTSTP (intensity
  step), ITMAX (maximum number of lines), JOSTEP (offset between lines)
  The number of lines is given by 1+(intensity-PLTTHR)/PLTSTP, subject to
  being at least 1 and not more than ITMAX.
  Suggested values are 0.5, 0.1, 6, 5

1 PLTI
       Give a title for the pictures plotted by .PLOT . A reply of
  cntrl/z suppresses all titles.

1 POINt
       Define a displayed point, which may be used for adding or removing
  parts of map (see BADD,BREL). The coordinates of the point may be given,
  or the keyword ATOM which puts the point on the last hit atom. If no
  argument is given, the point is removed from display. The coordinates
  of a valid point are printed by NOW.

1 PRCL
       Print current definitions of residue classes for colouring atoms.
  These will be used by the CLASSCOLOUR option for foreground atoms
  (FCOL CLASS) or background atoms (MOL CLASSCOLOUR), if activated.
  
1 PURGe
       Delete from PS300 memory all map bricks which are not currently 
  displayed. This may be useful to clear out the PS300 memory from time
  to time.

1 REAL
       All atoms are made real after regularization.  I use this  only  at
  the  very  beginning  since with SAM command ABINITIO all atoms are made
  dummy, and i like to make atoms dummy when not  fitting  density  rather
  then making them real when they do (optimism ,maybe).

1 RECOrd
       Reads a file name (default RECORD.REC, default extension .REC)
  to define a file into which all subsequent commands are copied,
  until the NOREcord command. This file may be 'played back' later by
  typing @filename to read commands from the file. This may be useful
  for creating complicated MOL objects. 

1 REFI
      Initiates entry to model building or regularization options. The
  user has access to the CHAT interface to redefine constants such as
  refinement zones, guide angle options, etc. The model building options
  allow the user to build exact conformations such as alpha helices, by
  extension from an existing residue (REFI modes EXTD and BEXT,or from
  scratch with mode RESI). The regularization is done by the method of
  Hermans and Mcqueens Acta. Cryst A30 (1974), 730. I call this method the
  molten atom method, since each atom moves by itself to satisfy it's local
  conditions (provided it is not FIXed).  It is probably not the most
  efficient method available but is usually well behaved. All bond lengths,
  angles and torsion angles are guided to preferred values without any
  rigid constraints. This ensures that large errors do not build up at any
  point in the chain. Prompts are issued on entry to remind the user that
  he may need to redefine the RZONE and also to define which REFI option is
  active. 

1 RELS
       When GO is next typed, release all map bricks which do not include
  any of the selected atoms, within a cube half-width set by WIDTh.
  This only has an effect the next time GO is typed: see AUTO for
  the auto-release flag which is permanent.

1 RHYD
       Include hydrogens in REFI (qv NORH)

1 RIGI
       This allows one to apply a rotation  /translation  operation  to  a
  zone  of  residues which best fits the current COORD coordinates to a set
  of guide coordinates.  The least squares algorithm was  written  by  Jim
  Remington.   The program prompts for residue and atom name, and then for
  the guide position.  Input is terminated by typing END.   A  maximum  of
  100  atoms  can  be  used in the matching process.  If the user does not
  wish to apply the transformation, he should answer the  prompt  TO  WHAT
  RESIDUE RANGE IS IT APPLIED ?  with END.

1 RSR
 This is used to define the constants used by the real space
 refinement  options  on  the  display menu.  The program prompts with
 the present values and then asks if they  are  to  changed, only  the
  answer  NO  is  recognised.   The first prompt is the map number to
 be used for the refinement: it must be a density map. The next prompt
 is for number of cycles and the shift size (note that  the  shift 
 size also determines the angular search range).  I (Alwyn) normally
 use the maximum of 5 cycles with shifts of 0.5, 0.4, 0.3, 0.2, 0.1. 
 The next  prompt  is  for  the grid sum radius (I use 2), the atomic
 radius  (I  use  1.2)  and  the  scale  constant  to  bring  the
 calculated  density  onto the scale of the map (if you do not know
 this number you must define something positive, e.g. 1.0 and then use
 the menu option .NO/.RSR =.RSCL to calculate the scale factor).   The 
 last  prompt is for the Z-values of the atom types. The standard
 method of assigning Z values (atomic numbers) to atoms uses the
 atomtype codes stored in the COORD files (usually, Diamond types) and
 translates them according to the values provided by the user in the
 CHAT command RSR.  Alternatively, the Merck and PS 300 versions
 provide a default: if the atomtype codes exceed 99, they are assumed
 to indicate atomic numbers directly: 
 	Zatom = atomic number = integer part of(ATOMTYPE/100).
 The numerical atomtype codes may be reset with SAM commands
 ATOMTYPE or SETATYPE.
 One can have up to 10 different Z-values.

1 RSTR
       Restore backup coordinate file, ie reverse the effect of BKUP,
  copy the backup coordinate file SAVE to the main coordinate file 
  COORD. As a precaution a prompt is typed on the terminal: answering
  anything other than 'Y' aborts the operation.

1 RZON
       The regularisation is over a zone of residues.  There is  an  upper
  limit of 200 atoms in the VG, MMSX programs and 150 in the PS program.

1 SAM
       SAM exists as a standalone program and as an exit from  the
  main  graphics  overlay in FRODO.  Its function is to manipulate
  the COORD data set in various ways.  It  is  used  to  create  an
  initial  empty  data  set,  to  fill  it  with data from various
  external formats, to list the atoms or sequence in the data  set
  and other things.

       As for Chat, commands may be abbreviated provided that they 
  are unambiguous, and parameters may optionally be given on the same 
  line.

2 Stand-alone
       When running the stand alone program, the user is  prompted 
 for  the  name  of  the  FRODO random access coordinate data set 
 which he wishes to work with, and  then  for  the  name  of  the 
 'names'  data  set (this must be defined if one uses ABINITIO, 
 REPLACE, or  INSERT).  When running FRODO, these prompts are not
 issued since  the data sets are already known (COORD, and NAMES). 

2 EMPTY
       This is to  allocate  a  fixed  amount  of  space  for  the
  controller  record, the sequence records, and the extra records.
  Once made they cannot be expanded.  The  program  allocates  one
  record  for  the  controller,  and  then  prompts  for  how many
  sequence records are to be allocated and then for how many extra
  records  are  to  be  allocated.  The number of sequence records
  must be greater then the number of  residues  in  the structure.
  Every  time the user does an INSERT, a sequence record gets used
  up.  When one does a DELETE, the free sequence record  will  not
  be used later by an INSERT.  REPLACE uses the existing record.

       If there are N  sequence  records,  then  the  user  should
  define  at  least  (N+4)/5  extra records.  If the user wants to
  define SYMMETRY, he must also allow space for (2*nsymop+2)  more
  records, where Nsymop is the number of symmetry operations.

2 ABINITIO
       This allows one to generate from scratch a file with atomic
  records  corresponding  to  a  given  sequence.   One  record is
  generated for  each  atom,  the  coordinate  is  (1500.,  1500.,
  1500.),  it  is  dummy (IA=2).  The program prompts as for EMPTY
  and then asks for the data set  containing  the  sequence.   The
  data  set  must contain the residue types, left justified with a
  reference to this type in the 'names' data set.  The  format  is
  (18a4),  and a line is terminated by a blank name.  If a residue
  type is not defined in the 'names' data set, an error message is
  printed,  but  the  program  continues checking through the full
  sequence.  However the file is of no use.

       There are limits of  1000  residues  in  the  sequence,  50
  residues  in  the  'names'  file, and 1000 atoms in total in the
  'names' file.

2 READDIAM
       To read in  my  modified  form  of  R.Diamonds  Real  Space
  Refinement coordinates.  The format of my 'Diamond' file is :

  1. Three header records, the 2nd being a title

  2.Atomic records, one atom per record.  I do  not  use  Diamonds
  non-atomic  records.   Each  record  contains the coordinates in
  Angstroems along the cell edge ( or orthogonal), a temperature
  factor,  an  atom  type  (IDW  in  Diamonds  nomenclature, by default
  the record is skipped if  this values is less or equal to 0), an
  internal  residue  count  (NO  in  Diamonds  nomenclature,  i  do not
  store it) ,an entry  number ,a weight, a residue type, a residue name
  and  an  atomic  name.   The  format is (4F10.0,3I5,F9.0,2A4,T76,A4).
  Input will  be terminated by end of file. 


       This option by default over-writes the current contents of 
  the data set COORD: alternatively it may be used to update a
  dataset, or append new data to the end of an existing COORD file
  (beware of non-unique residue names). Before issuing this option, an
  empty data set must have been created either by EMPTY or ABINITIO. 
  Once the command has been issued, any number of Diamond data sets
  can be combined into one new COORD data set. The first prompt
  issued by the program is for the name of the Diamond data set,
  typing END or <cr> terminates the option. The program lists the 
  title found in the data set. It then prompts for 2 residue names, and
  only atoms between these 2 residues are added to the COORD data 
  set.  The program lists on the terminal each residue name, its
  type, the disc address for the coords for that residue and the 
  pseudo sphere center and radius for the residue (this is a
  standard WRITE statement in subroutine PUTSEQ and is called when 
  any program updates the COORD sequence records). The program returns
  to the first prompt when it is finished. 

2 READWH
       This option allows one to read  in  any  formatted  list  of
  coordinates.   The  I/O list specifies the residue type, residue
  name, atom name, X, Y, Z and temperature factor.  If this is not
  the  order in the file, remember the use of T format (MMSX users
  cannot use T format on their Texas 980) which allows one to  set
  the  position on the record from which to read (e.g.  if we have
  a formated file X, Y, Z, B, res.  type, res.   name,  atom  name
  with   format   (4F10.3,3A4),   we   can  define  a  new  format
  (T31,3A4,T1,4F10.0)).

       The program first prompts for the file name containing  the
  coordinates.   It then prompts for the unit cell constants to be
  used on the input coords.  (typing return defaults  to  1.,  1.,
  1.,  90.,  90.  , 90.  i.e.  to orthogonal Angstroems).  It then
  asks if the input residue types are  in  the  standard  1-letter
  code.   The next prompt asks if the input format is the default.
  If the user types  NO  he  will  be  asked  for  a  new  format.
  Otherwise the atoms will be read with Wayne Hendrickson's PROLSQ
  format, (3X,3A4,4F10.0).   The  program  returns  to  the  first
  prompt to define another input data set.  This can be terminated
  by typing END in answer to this prompt.

2 PDB
       Same as READPDB.
       This option allows one to read in coordinates which are  in
  the  standard Protein Data Bank format.  The program prompts for
  the name of the PDB data set.  The user gets the PUTSEQ  listing
  on the terminal.

2 READPDB
       Same as PDB.
       This option allows one to read in coordinates which are  in
  the  standard Protein Data Bank format.  The program prompts for
  the name of the PDB data set.  The user gets the PUTSEQ  listing
  on the terminal.

2 READATOM
       This option is to read in free format a list of atoms.   It
  does  not  make  a  fully operational data set since it does not
  read in the residue type.  The free format coordinates must have
  one  line  for  each atom with X, Y, Z, Residue name, Atom name,
  and an IA flag.   The  program  prompts  for  the  data  set  of
  coordinates,  and  then  for the unit cell of the coordinates in
  the prepared data set (typing just a  return  defaults  to  1.0,
  1.0,  1.0,  90.,  90.,  90.).   In a later version, this will be
  updated to include the residue type.

       If the user needs to read in coords in some  other  format,
  he  should  list  a subroutine called READRD and use this to see
  how to add a new option.

2 SSBRIDGE
       This option is used to define di-sulphide  bridges  in  the
  COORD data set.  The option updates the IB flag so that it points
  to the record of the equivalent atom in  the  di-sulphide  ,i.e.
  if residues 100 and 200 are have a di-sulphide, CA of 100 points
  to CA of 200, and CA of 200 points to CA of  100,  and  likewise
  the  CB  and SG atoms.  The program checks that the residues are
  of type CYS or  CYH.   Having  defined  these  connections,  the
  bridge atoms will be used in regularization.

       The program prompts for 2 residue names to define the pair.
  Typing END OR <CR> causes an exit.  The program issues error
  messages if  the residues are of the wrong type and if the expected
  atoms are  not in the residues. 

2 SYMMETRY
        Crystallographic symmetry can be encoded in the COORD data set.
  The program prompts for the lattice symmetry, or the space group name
  or number: if a space group name (eg P212121) or number (as in
  International Tables eg 19) is given, the file with logical name
  SYMOP is searched for this space group. If it cannot be found, the
  symmetry operations may still be input explicitly. Alternatively, the
  lattice symmetry is given as one of P, I, R, F, A, B, C. The program
  then prompts for the 6 unit cell parameters (angeles default to 90).
  Note that if your coordinates have no crystallographic cell, dummy 
  cell dimensions must be given which are at least as large as the
  molecule in each direction. If no space group was given, it then
  prompts for symmetry operations until the user types <cr> . The
  symmetry operations are given of the form shown in International
  Tables vol. 1, i.e. X,Y,Z or -X,1/2+Y,-Z  etc. One must include the
  self operation. Several operations may be given on each line,
  separated by '*'. Finally, the program prompts for
  non-crystallographic symmetry operations: these are given as a 3x3
  matrix followed by a translation vector, such that x' = Rx + t  . 
  The first operation must be the identity operation. Remember that input
  lines may be continued with '-' or '&' at the end of the line.
        Each symmetry operation uses up two records, and the lattice
  and cell  dimensions one record, in the extra area in the COORD data
  set. If  this area gets filled an error message is issued. Nonsense 
  symmetry will be rejected with an error message. The command SYMPRINT
  may be used to print the symmetry operations stored in the file.

2 SYMPRINT
       Prints all symmetry operations present in the COORD file (if any).

2 SYMERROR
       This option can be used to correct any errors introduced by
  the user in defining the SYMMETRY operation.  For each parameter
  the program prints the present value and asks if it is  correct.
  Typing NO allows one to input the correct data.

2 UPDATE
       This option allows one to update  the  coordinates  and  IA 
 flag  of  an  existing  atom  in  the  COORD  data  set.  The new 
 coordinates are read in free format with data for each  atom  on  one
 line.  This data is X, Y, Z, Residue name, Atom name, and optionally
 atom type, residue type and IA. The first prompt is for the file 
 containing  the  new  coordinates.   The  coordinates   must be
 orthogonal.  The  atoms can take on new IA values, and the program
 prompts  for  a  number  to  define  the  desired option.  Typing 0
 means use the  flag in the update file, 1 makes all the UPDATE  atoms
 real,  2  makes  them  dummy,  3 makes them fixed real, 4 makes them
 fixed  dummy. 

       This option is normally used  when  using  the  'explosion'
  method  of  making an initial model.  The UPDATE coordinates are
  then guide coords read from a mini-map and should  include  data
  for  the  CA  and  at least one side chain atom.  One would make
  these atoms fixed and real ,i.e.  type 3.  The  user  must  have
  previously  made  a  data  set  using ABINITIO, READDIAM, PDB or
  READATOM.

2 PSEUDO
       This options updates the pseudo sphere  center  and  radius
  for  any  part  of the COORD data set.  The program prompts for a
  residue range, typing ALL forces the update of all  residues  in
  the  data  set.   If the sphere center or radius is greater then
  0.5 Angstroems from its expected position, we issue a message.

2 RESXYZ
       Same as PSEUDO

2 ATOMTYPE
       In the coordinate file, each atom should be assigned an atom
  type number. This is used by the RSR option to identify the electron
  count Z, by the MOL options for colouring atoms differently, for 
  linking atoms, and by MAKEDIAM for writing Diamond files. For atoms
  read from a Diamond format file, this atom type number is that read
  from column 5 of the file, provided that it is .gt. 0. For other
  external inputs, and for atoms created internally (ABINITIO, INSERT,
  REPLACE), the atom type number is generated using a table of up to 
  19 different 1- or 2-character atom type labels, in order of type 
  number.
       This command allows this table to be changed: the table is 
  preserved between sessions in the constants file. The program prints
  the current table, and prompts for a new one. It then asks if you 
  want to update the atom types of all atoms in the file [All], just
  those which are unset with type .le.0 [Unset], or none <cr>.

2 DELETE
       This deletes a residue from the data set,  by  removing  it
  from  the  sequence  area  of  the  COORD  data set.  The program
  prompts for the residue name, and is re-issued  until  the  user
  types END or <cr>.

2 REPLACE
       This replaces a residue of one type by a residue of another
  type.   If  the 2 residues have atoms having the same name, then
  the information for those atoms is  kept  in  the  new  residue.
  Otherwise,  new  atoms  are  placed  at (1500.,1500.,1500.), are
  dummy, and of appropriate atom type (see ATOMTYPE).

       The program first prompts for the name of the residue to be
  replaced  and  then for the new residue type.  A new residue can
  contain a maximum of 100  atoms.   If  successful,  the  program
  returns to the first prompt.  The user terminates by typing END
  or <cr>.

2 INSERT
       This allows one to add a new residue to the COORD data  set.
  The first prompt asks AFTER WHAT RESIDUE DO YOU WANT AN INSERT ?
  If the user wishes to insert a residue at the start of the  data
  set  he  should  enter ????  which is the name of a non existent
  residue which is always in the data set.  The second  prompt  is
  to define the name of this new residue (e.g.100A), and the third
  prompt is to define the type of residue (e.g.  ALA).   The  user
  then  returns  to  the first prompt and can terminate input with
  END or <cr>

2 RENAME
 	This allows the residue names (numbers) of residues to be
  changed. Type pairs of 'old-name' 'new-name'.

2 TITLE
       Allows the title in the COORD file to be replaced.

2 WATER
       Allows insertion of new water residues, and sets pointers to
  the next available water for use with the menu option .Watr.
       You are first prompted for the water residue type (eg WAT):
  the NAMES file is then searched for a residue of this type, and this
  is used for all subsequent definition of waters. Note that this
  residue type may contain one or more water atoms. The current
  coordinate file is then searched for all residues of this type, and
  you are given a summary of the water residues present. You are
  then asked if you want to insert an new waters. These can be
  inserted anywhere in the file, and are named with a number and a
  1-character chain identifier (eg 1W to 100W). They are created as
  dummy entries in the file, that is they have coordinates 1500,1500,1500
  and IA=2. Finally you are asked to update the pointers to the next
  available water for .WATR and the last available one. (see .Watr)
  The command NOWATER inactivates the .Watr command

2 NOWATER
       Switches off WATER (.Watr)

2 LISTA
       Same as LISTXYZ
       This produces a listing on the terminal  of  all  the  data
  held  concerning  the  atom.   It  lists  the  data  set  record
  number,IA, IB, Internal residue  count,  X,  Y,  Z,  Temperature
  factor,  Weight, Atom type, Residue name.  It then lists all the
  data concerning each of the residues:   The  name,  the  residue
  type,  the  2 record pointers to the coordinate data, the pseudo
  sphere center and radius.
       The program prompts to define the zone.   Typing  just  ALL
  or <cr> lists everything in the data set. ? (or ????) may be used
  to indicate the first residue, $ (or $$$$) the last residue, and
  . (or ....) the next or previous 15 residues.

2 LISTXYZ
       Same as LISTA
       This produces a listing on the terminal  of  all  the  data
  held  concerning  the  atom.   It  lists  the  data  set  record
  number,IA, IB, Internal residue  count,  X,  Y,  Z,  Temperature
  factor,  Weight, Atom type, Residue name.  It then lists all the
  data concerning each of the residues:   The  name,  the  residue
  type,  the  2 record pointers to the coordinate data, the pseudo
  sphere center and radius.
       The program prompts to define the zone.   Typing  just  ALL
  or <cr> lists everything in the data set. ? (or ????) may be used
  to indicate the first residue, $ (or $$$$) the last residue, and
  . (or ....) the next or previous 15 residues.

2 LISTR
       Same as LISTSEQU. This produces a sequence listing, all the
  data concerning each of the residues: The name, the residue type,
  the 2 record pointers to the coordinate data, the pseudo sphere
  center and  radius. 
       The program prompts to define the zone. Typing just ALL  or
  <cr> lists everything in the data set. ? (or ????) may be used  to
  indicate the first residue, $ (or $$$$) the last residue, and  . (or
  ....) the next or previous 15 residues. 

2 LISTSEQU
       Same as LISTR. This produces a sequence listing, all the data
  concerning each of the residues: The name, the residue type, the 2
  record pointers to the coordinate data, the pseudo sphere center and
  radius. 
       The program prompts to define the zone. Typing just ALL  or
  <cr> lists everything in the data set. ? (or ????) may be used  to
  indicate the first residue, $ (or $$$$) the last residue, and  . (or
  ....) the next or previous 15 residues. 

2 ISITMADE
       This checks for the occurrence of  coordinates  at  (1500.,
  1500., 1500.) and reports it on the terminal.

2 DISABLE
       Set the residue's pseudo-sphere centre to ridiculous values
  so that it will not be selected by the SPHERe options.

2 ENABLE
       Recalculate the residue's pseudo-sphere centre to restore it
  to its proper value.

2 MAKEDIAM
       This makes my version of Diamond's data set from  the  COORD
  data set.  The first prompt asks for the name of the data set to
  be made.  The second prompt is DEFAULT  IS  ALL  ATOMS  ,  O.K.?
  ,typing  NO  allows  one  to select specific atoms from the COORD
  data set.  The prompt then asks for the atom names one per  line
  until  one  types  END,  up  to a maximum of 20.  Continuing the
  program asks if one wants a default temperature factor: this will
  be used to fill in zero B values.  The next prompt is  for  the
  unit  cell  angular  constants to be applied, typing just return
  defaults to (90., 90., 90.).  The program always forces A= B= C=
  1.   Angstroems.   The program then prompts for a residue range,
  typing ALL causes everything in the COORD data set to  be  copied
  out.

       Atoms with IA=2 or 4 are written out as dummy atoms with  a
  weight of 0.0 .  

2 MAKEPDB
       This makes a list of coords in Brookhaven Data Bank. This 
  option has the same prompts as MAKEDIAM. The temperature factor is
  written out in this version. 

2 MAKEWH
       This makes a list of coords in Wayne Hendrickson's  format.
  This  option has the same prompts as MAKEDIAM.  Note that PROLSQ
  expects  integer  residue  names.   The  temperature  factor  is
  written out in this version.

2 GO
       In the stand alone version of SAM this halts  the  program.
  In FRODO, control is passed back to the display.  Control Z and STOP
  also work in the PS300 version.

2 STOP
       In the stand alone version of SAM this halts  the  program.
  In FRODO, control is passed back to the display.  Control Z and GO
  also work in the PS300 version.

2 HELP
       (VAX only) enter VMS help for SAM  options

2 SYS
       (VAX only) Causes user to enter an interactive VMS shell with
 all of  the environment characteristics of the parent process.  Type 
 LOgout to return to SAM. 

1 SAVE
       This is meant for forgetful people.  It does  the  same  thing  as
  .SAVE ,i.e.  it writes the current screen coords to the COORD data set.

1 SETClass
       Set classes for the CLASSCOLOUR option: these may also be
  set from MOL>SETCLASS. Current settings are printed by PRCLass.
       You can define up to 10 colour classes, each containing a list
  of possible residue types (ie GLY, PHE etc), or alternatively MAIN
  (all main-chain atoms), SIDE (all non-main-chain atoms), or REST
  (everything not otherwise defined). Each class is assigned a colour,
  as a hue/saturation or colour name, or ATCOLOUR, BCOLOUR or NOCOLOUR.
  If any class is assigned ATCOLOUR or BCOLOUR, all other classes will
  be automatically reassigned to NOCOLOUR, since only one colour table
  can be active at one time. This CLASSCOLOUR option can be used to
  colour particular types of residues in different ways, and also to
  distinguish main-chain and side-chain, eg MAIN/NOCOLOUR,
  SIDE/ATCOLOUR. 
       Note that one set of class assignments are stored in the
  constants file. If you want several alternative sets, use the
  RECORD/playback facility.
       
1 SETMain
       Define which atoms are to be considered as main-chain. This
  definition may be used in the FCOL CLASS option, or in MOL. For proteins,
  normally  CA C N O [OT]. Note that MOL>SIDE will include the first
  main-chain atom (eg CA) as well as the side-chain atoms.

1 SETView
       Set view matrix to that typed in. The matrix will be checked for
  its determinant = +1.0, and is orthonormalized before being used.
  If the determinant is not +1.0, the matrix is not used. The 9 numbers
  may be typed on several lines, or on one.

1 SHIF
       This defines the maximum allowed shift during each cycle.   If  the
  program  calculates  a  larger shift during refinement, then the applied
  shift is in the calculated direction but is equal to the  value  defined
  by SHIF.  I normally use 1.0 Angstroem when using the 'explosion' method
  of building an initial model, otherwise i use 0.3 Angstroems.

1 SMIX
       As MIX but gives you all atom which EITHER lie in a specified 
  sphere, OR are part of a "mixture" of up to 10 specified residue
  ranges (zones). When its SPHEre RADIUS is set to 0.0, it just shows
  the desired ZONES; or when the first response to the prompt for
  ZONE: is "END", it just shows a SPHEre. 

1 SPHE(re)
       This is the normal working mode.  The  prompt  asks  for  a  sphere
  radius.   All atoms in the data set within this distance from the current
  screen center are displayed.  If an atom is not connected to  any  other
  atom on the screen, it appears as a 3-D cross.  The user must be careful
  when modifying large groups of atoms on the edge  of  the  screen  since
  large  discontinuities  can be introduced in the coordinates in the COORD
  data set, e.g.  if the user applies .FBRT to a piece of  a  Lysine  side
  chain  where  the  NZ  atom is outside the sphere radius, then the CE-NZ
  distance could be very large.

       The program decides on which atoms  are  in  the  sphere  by  first
  checking if the residue center is in the sphere, in which case it checks
  all the atoms in the residue.  (FRODO no longer creates forests of imagi-
  nary bonds between residues that happen to lie near or on top of one an-
  other; bonding is done one residue at a time in all display modes.

1 STAY
       There is no change in the atomic status after regularisation.

1 SYMM
       This forces the program to check if symmetry related atoms 
  occur within the viewing sphere, for options ZONE, MIX and the 
  sphere part of SMIX. The COORD data set must have been updated 
  with SAM option SYMMETRY. The symmetry-generated bonds will be drawn
  in a different colour (see SATM on dial panel 7). The 
  symmetry-generated atoms may be picked for labelling and for
  distance and angle calculation, but they may not be manipulated
  (.FBRT, .TOR, .MOVE, .RSR) and their coordinates are not saved. 
  The program can use all symmetry operations (default is symmetry
  on), just crystallographic or just non-crystallographic operations.
  It may be useful for instance if two or more nearly identical subunits
  are present explicitly in the file: the non-crystallographic symmetry
  operations which superimpose them can then be stored in the file for
  use in MOL but be excluded from the foreground symmetry generation.

1 SYS
      In Version V3.0 of VMS on a VAX, this spawns a subprocess 
  attached  to the terminal. Enters an interactive VMS shell with all 
  the environment characteristics of the parent process.  One can then
  perform any VMS  command, including  changing the PS300 function
  network.Type  LOgout to return to PSFRODO.    For  non-VAX users,
  this should  be implemented in its most primitive  form to a copy
  from the terminal  to the PS300 command  interpreter, allowing one
  to modify the function  network from  FRODO. 

1 TCOL
       Set the colour for the terminal emulator, 0-360 to define the
  hue. For people who can't stand green.

1 TERM
       Tells the program whether you have a separate terminal for
  Frodo, or whether you use the PS300 as a terminal as well.

1 VIEW
      Gives the current view matrix which may be used in other
  plotting programs to give pictures from the same viewpoint.
  If commands are being RECOrded (qv), the matrix is written to the
  record file, from which it may be edited, or read back in with the
  SETView command.

1 WIDTh
       Sets the half-widths in Angstrom of cubes for covering atoms with
  map bricks, covering the point with map bricks (BADD), and releasing
  bricks around the point (BREL). When the program is covering atoms or
  the point, bricks are selected for display if they lie between the
  eight corners of this cube centred on the atom or point, subject to
  CRAD (qv) for atoms. It may be useful to set the half-widths for BADD 
  and BREL to different values, so that you can add large blocks, and
  release smaller ones.

1 ZFIX
      Defines the atoms to be fixed in the first and last residues of the
  RZON in REFI, when the ANCHor option is on. For proteins, these should
  be N & CA for the first residue (used to be N CA CB, but the CB should 
  really be free), and CA C O for the last residue.

1 ZLNK
       In all modes the program forms a bond between a named atom  in
  one  residue  and  another  in  the  next  residue.  These two atoms are
  defined with ZLNK.  The program first prompts for the atom in  the  i'th
  residue and then the (i+1)'th residue.  For proteins, these are C and N.
  Two pairs of link atoms may be defined, thus C N   O3' P will link both
  proteins and nucleic acids. After the link atoms, the program prompts for
  the maximum distance between the two link atoms  (eg 2.5A).

1 ZONE
       The prompt requires the alphanumeric names of 2 residues, the first
  must  be  before the second in the linear sequence.  The connectivity is
  made on a residue to residue basis and with ZLNK connections.   This  is
  normally  used  at  the  start when working with the initial isomorphous
  map, later one normally works in SPHE(re) mode.  The atoms can be picked
  from  disk  more  quickly in ZONE mode then any of the other modes.  SYM
  has no affect when in this mode.
