#
Steric
A program to calculate molecule cone angles and solid angles as measures
of molecule steric size
Programmed by B. Craig Taverner

Main menu options:
  file      - file options
  molecule  - molecule data operations
  symmetry  - perform crystallographic operations
  calculate - perform calculations
  plot      - plot graphs of profile results
  change    - change molecule and general calculation settings
  view      - view current molecule data and general settings
  help      - help facility
  exit      - exit from steric

In most cases preceding the command with an '&' character will result in
the required operation being performed on all data sets currently loaded.
Any commands not recognized by steric are passed to the operating system
shell from which steric was loaded, so one can list files, and edit data
sets without having to leave steric.  In the case where the shell command
required is recognized by steric, prepend it with the '!' character to
bypass steric's command interpreter.  If this is not enough, see the "file
shell" option.
Using the '>' character as the first character on the line will result in
the text output being redirected to the file which has it's name following
that character.  If no filename is given the output is directed at stdout.

Any arguments passed to steric on the command line are passed to the file
loader.  If they are recognizable atomic data files, they are loaded.  If
they are command files (starting with "#steric") they are used for command
input instead of the default "steric.ini".  If more than one command input
file is given on the command line, currently only the last one will be used.

#f
file
These are the main molecule data input and output options:
  load      - load molecule data
  save      - save molecule data
  svas      - save molecule data under different name
  shell     - open an operating system shell

#fl
file load
Enter the names of the files to be loaded as arguments.
Any number of files can be loaded with the same command.
The following file formats are understood:
 - command files containing normal steric commands starting with the line
   #steric
   will be executed.  Control is returned to the console after completion of
   execution, unless, of course, the last command was "exit".
 - steric data files starting with the line 'STERIC ...'
 - Biograph data files starting with the line 'BIOGRF ...'
 - Alchemy files in *.mol format
 - Biosym files in *.car format
 - Biograph conformer trajectory files in ascii format.  These files are
   only used in the "calculate conformer" command.
 - Schakal data files
 - Shelxl data files
 - CSDS GStat coordinate file (converted with 'calc coord frac')
 - Alchemy crystal data file
 - Xtal crystal data file.  Only 'atom', 'symtry', 'latice' and 'cell' lines
   are understood.
The Schakal, Shelxl, gstat cor, alchemy crystal and xtal files all have
fractional coordinates.  The Cartesian coordinates are calculated
immediately on loading, but the fractional coordinates are retained for
possible future symmetry operations (see the "symmetry" command).  Whenever
additional atoms are added by such symmetry commands, there Cartesian
coordinates are immediately calculated.  If a command is given the makes the
symmetry operators invalid (eg. "change origin"), the fractional coordinates
are discarded, and only the Cartesian coordinates are retained.  The
symmetry operators themselves are also removed from that particular data
sets memory space.

#fs
file save
Save the current molecule data in steric format.
All calculated data are included.

#fa
file svas
Save the current molecule data in steric format in specified file.
All calculated data are included.

#fe
file shell
Open an operating system shell.  This option is only available on some
operating systems.  Generally any commands not recognized by steric are
passed on to the operating system anyway.  If there is a command you wish to
use that steric also understands, then prepend it with the '!' character and
steric will pass it too the operating system unhindered.

#m
molecule
These are the main molecule data operations:
  view      - view the current molecule contents (see "view molecule")
  next      - make the next molecule in memory the current molecule
  previous  - make the previous molecule in memory the current molecule
  goto      - make particular molecule current
  kill      - mark atoms, atom types or groups as unusable in calculations
  close     - remove elements of the current molecule from memory

#mv
view molecule
The steric parameters calculated, as well as the current atomic contents
are displayed.

#mn
molecule next
Make the next molecule in memory the current one.

#mp
molecule previous
Make the previous molecule in memory the current one.

#mg
molecule goto
Make a particular molecule in memory the current one.  Enter the molecule
name or number on the command line, or it will be prompted for.  Note that
if a molecule has a number for a name, and you ask for a molecule with that
number it will find the one with the matching name.

#mk
molecule kill
Remove the following from further calculations:
  atoms     - particular atoms located by name or number
  types     - all atoms of a particular type
  groups    - all occurances of particular groups
  numbers   - all groups of a given number or name
  restore   - undo the affects of any of the above options

#mka
molecule kill atoms
Disable particular atoms (based on name or number) from participation
in further calculations.

#mkt
molecule kill type
Disable all atoms of particular type from participation
in further calculations.

#mkg
molecule kill atoms
Disable all atoms of particular atomic groups from participation
in further calculations.  The groups are defined in the file steric.grp
Note the group must be clearly defined as being bonded to the origin
defining atom or the main atom (use 'molecule view' to check) before
it is identifiable as a group.

#mkn
molecule kill number
Disable all atoms of particular atomic group number from
participation in further calculations.

#mkr
molecule kill restore
Allow all atoms, excepting the origin defining atom, to be involved in
further calculations.

#mc
molecule close
Remove the following from memory permanently:
  atoms     - particular atoms located by name or number
  types     - all atoms of a particular type
  groups    - all occurances of particular groups
  numbers   - all groups of a given number or name
  molecule  - the entire molecule
If the command is followed by strings that are not recognized as one of
these options, then the strings are matched to group names, and any molecule
not containing all requested groups is closed down.  For example, "molecule
close water perchlorate" will remove from memory all molecules not
containing defined water and perchlorate groups.

#mca
molecule close atoms
Delete particular atoms (based on name or number) from memory.

#mct
molecule close type
Delete all atoms of particular type from memory.

#mcg
molecule close atoms
Delete all atoms of particular atomic groups from memory.
The groups are defined in the file steric.grp

#mcn
molecule close number
Delete all atoms of particular atomic group number from memory.

#mcm
molecule close molecule
Close the current molecule data.  Memory is deallocated.

#s
symmetry
These operation are only valid for molecular data for which the fractional
coordinates have been provided.  This allows the program to perform the
symmetry transformations provided in the data files, or by the user.  The
following operations can be performed:
  transform  - perform a single symmetry transformation
  expand    - expand data with current symmetry
  box       - expand data into predefined box of unit cells
  bond      - find all bonds in current data
  group     - find individual bonded molecular groups
  redundant - remove redundant atoms
  exclude   - exclude atoms outside group cavities
  shell     - use a radial profile to find the cavity radius
  volume    - calculate specific crystal volumes

#st
symmetry transform
A symmetry operator in the format used by the international tables can be
given on the command line or will be prompted for.  All atoms will have
their fractional coordinates modified by this operator, and then have their
Cartesian coordinates recalculated.

#sx
symmetry expand
All symmetry operators present are used to generate an expanded data set. 
The original data is not overwritten, and nothing is done to ensure the data
are all in the same unit cell.  Any symmetry generated copies of atoms on
special positions are removed.
If the space group is centrosymmetric the inversion centre is first used
to generate a double sized data set.  This is then operated on by the other
symmetry operators to generate a larger non-centred data set.  Any centring
operators present are then used to generate the full centred unit cell.

#sb
symmetry box
Pure unit cell translational symmetry is used to expand the current data
into the predefined box of unit cells.  Any concurrent identical atoms are
removed.  The size of the box is defined by one to six numbers on the
command line.  If none are given a single unit cell is assumed.  If three
are given a box from 0,0,0 to the three in units of cell dimensions is
created.  If they are negative the box is made from the negative values to
the positive values.  If more than three are given, the first three
represent the minima, and the last three represent the maxima.  If only one
is given three are assumed equal.  For example "symmetry box -2" will box
from [-2,-2,-2] to [2,2,2] and "symmetry box -1 0 2 3 4 5" will box from
[-1,0,2] to [3,4,5].

#sd
symmetry bond
Find all bonds in current data.  This algorithm uses the covalent radius of
the atoms to determine the existence of bonds.  The bond is determined to
exist if the distance between the atoms is between two fractions of the
radius, one larger than the radius and one smaller.  See 'change settings
bonding' for modification of these parameters.

#sg
symmetry group
Search for bonded molecular groups in the current data set.  All individual
bonded molecules are assigned separate group numbers, and matched against
the predefined groups in the steric.grp file so that they can be easily
identified later.

#sr
symmetry redundant
Remove any redundant atoms that are present from boxing atoms on special
positions.  See "change settings mode" for automating this.

#se
symmetry exclude
This option is present for the purpose of speeding up the "symmetry volume
group/cavity" calculations.  The name of a group, or group type is specified
on the command line, and all atoms not overlapping the group volume radius
defined for that group (see "change molecule group") or for at least one
matching group, are not only excluded from further calculations but removed
from memory entirely.  This dramatically speeds up the crystal calculations
which can sometimes involve many thousands of unimportant atoms.  Note that
further calculations that require the entire data set will involve the
reloading of the data.

#ss
symmetry shell
This option is used to find the radial size of the cavity in which a defined
group is present.  The third argument on the line defines the required
steric parameter to be used, and can be one of the following:
  oldleach  - the solid angle calculated using the original Leach algorithm
  ryan      - the solid angle calculated using the Ryan/Leach multiple
              overlap algorithm
  craig     - the solid angle calculated using the Craig multiple overlap
              algorithm
  vertexO   - the sum of all vertex angles of overlap between all pairs
              of atoms
  solidO    - the sum of all solid angles of overlap between all pairs
              of atoms
(see "calculate total ..." for further details on each one).
Any further arguments describe the groups of interest.  This calculation
moves the origin to the main atom of the required group, and so any data
sets that have fractional coordinates loose the use of those coordinates, as
well as any symmetry operators present.
The technique used involves the calculation of the radial profile (see
"calculate profile") of the data set centred at the required group, and
excluding that group, so as to get the steric profile of the group cavity. 
A cutoff steric value (see "change settings accuracy") is used on a smoothed
profile (see "change settings size") to determine the radius at which the
cavity ends.  This radius is used to calculate a spherical cavity volume
and is stored for possible use in the normal cavity volume calculation (see
"symmetry volume cavity").
Note:  If the radial profile never reaches the specified cutoff value, then
the radius at the maximum profile value is used.

#sv
symmetry volume
Certain crystallographically interesting volumes can be calculated:
  free      - the free volume in the unit cell
  group     - the volumes of all groups that match the named groups
  cavity    - the volume of the cavity occupied by named groups

#svf
symmetry volume free
The volume of all unoccupied space in the unit cell is calculated.

#svg
symmetry volume group
All groups named on the command line are searched for and the volume of each
instance found is calculated.

#svc
symmetry volume cavity
The volume of all named groups in the command line is calculated in terms of
it's cavity volume.  This means that the volume of a predefined sphere
around the group is calculated excluding all space occupied by groups other
that the group of interest.  See the "steric.grp" file for definition of the
enveloping sphere.

#c
calculate
There are currently three sets of calculations possible
  total     - calculate the total value of the specified steric parameter
  conformer - calculate the conformer averaged value of the specified steric
              parameter
  profile   - calculate the profile of the specified steric parameter
  volume    - the molecular volume is calculated in cubic angstroms
  area      - the molecular area orthogonally projected onto a plane
  volume    - the molecular volume is calculated in cubic angstroms
  area      - the molecular area orthogonally projected onto a plane

#ct
calculate total
The following steric parameters can be calculated as a total value for the
entire molecule
#cc
calculate conformer
The following steric parameters can be calculated and averaged over all
molecular conformers in the relevant ASCII trajectory file (extension '.trj')
#cp
calculate profile
The following steric parameters can be calculated as radial profiles
The cone angle can have it's angular profile calculated as well  
At the end of the calculation, the maximum value reached, as well as the
area under the curve are output.
#p
plot
Seven plots can be performed:
  orthog    - orthogonal view of atomic outlines
  molecule  - perspective view of atomic outlines
  cartesian - any profile is plotted on cartesian axes
  polar     - any profile is plotted on polar axes
  steric    - the results of particular steric calculations are output for all
              molecules
  contour   - the contour data from the numerical solid angle calculation
              are plot using the external script 'contplot'
  profile   - the radial profile contour is plotted in three dimensions

#pn
plot contour
The contour data from the numerical solid angle are plot using the script
'contplot'.  The molecule can be rotated about the z axis by a specified
angle (see 'change settings rotation').  If the numerical solid angle
profile calculation is done, the plot should represent the surface of the
molecule.  In both the total and the profile calculations the data are plot
in three dimensions.
The plot can be done in two modes: perspective (atoms further from the origin
are reduced in size) and cartesian (true cartesian coordinates are used,
all atoms are sized correctly).

#po
plot orthogonal
An orthogonal view of the outlines of all atoms in the current molecule is
plotted for the purpose of observing the nature of the overlaps involved.
This is particularly useful for the analytical area calculation.

#pm
plot molecule
A perspective view of the outlines of all atoms in the current molecule is
plotted for the purpose of observing the nature of the overlaps involved.
This is particularly useful for the multiple overlap solid angle calculation
(see "calculate total craig").

#pc
plot cartesian
The following steric parameter profiles are plotted on cartesian axes.
#pp
plot polar
The following steric parameter profiles are plotted on polar axes.
#cp pc pp
  angular   - the angular profile of the semi-vertex angle of the molecule
              about the origin-main atom bond direction
#ct cc cp pc pp
  tolman    - the tolman cone angle of the molecule
  cone      - the maximum vertex angle of the molecule
  oldleach  - the solid angle calculated using the original Leach algorithm
  ryan      - the solid angle calculated using the Ryan/Leach multiple
              overlap algorithm
  craig     - the solid angle calculated using the Craig multiple overlap
              algorithm
  numerical - the numerical solid angle calculated using the cone angle
              angular profile algorithm
  vertexO   - the sum of all vertex angles of overlap between all pairs
              of atoms
  solidO    - the sum of all solid angles of overlap between all pairs
              of atoms
#ct cc
  volume    - the molecular volume is calculated in cubic angstroms
#ct cc pc pp
  area      - the molecular area orthogonally projected onto a plane

#ctt cct cpt pct ppt
The Tolman Cone Angle:
This is calculated based on the groups defined during the loading of the
data sets, or after any major change.  If there is no origin defining atom,
no groups are defined.  If the origin defining atom has several bonds the
the groups are defined as those molecular fragments bonded to the origin
defining atom.
If the origin defining atom has only one bond, then the atom bonded, called
the 'main atom' has the groups defined about it, and it itself is allocated
to the zero group.
This last case is clearly useful for the calculation of the Tolman Cone
Angle, which is simply the average of the cone angles of the groups present.
If there are three or more groups about the 'main atom' then the zero group
is not used in the Tolman cone angle calculation.  If however, there are
less than three groups bonded to the main atom, the zero group, which
represents only the cone angle of the main atom itself, is also used in the
tolman cone angle calculation, so that the cone angle still represents the
steric 'distribution' about the main atom.

#ctc ccc cpc pcc ppc
The Cone Angle:
This is calculated at the maximum vertex angle about the origin-main atom
bong vector, and should correspond to the maximum value obtained in the
angular profile calculation.  It is calculated very simply as the theta
angle of the atom with the greatest theta angle from the main atom bond (the
bond from the origin defining atom to the ligand atom) plus it's semi-vertex
angle, and then doubled to be consistent with the Tolman cone angle.

#cto cco cpo pco ppo
The Old Leach Solid Angle:
This is the original algorithm used in the calculation of the molecule solid
angles in the program "CONE".  It involves summing the solid angles of pairs
of atoms, followed by subtracting the extra single atom solids angles that
result.  This does not take into account the possibility of multiple
overlaps of order three or above.  In order to reduce this error, the
counting of pairs of atoms has been done in a specific way to reduce the
occurances of erroneous missing multiple overlaps.  For many molecules
this works quite well, but unfortunately it can be shown that, since not all
possible double overlaps are taken into account, this algorithm very rarely
gives the exact solid angle, excepting in the radial profile calculations,
where multiple overlaps are relatively rare, or at least very small.
In the case of total solid angles unfortunately, in no case but the simplest
two atom data sets, can it be said for sure that the solid angle calculated
will be exactly correct.
An additional problem was found in the actual integration of the solid angle
of two overlapping regions: due to the particular choice of origin, it
occasionally occured that segments were left out of the calculation.  The
correction algorithm employed for this has since been shown not to be bug
free, and therefore this correction is optional (see 'change settings
mode').  An alternative to the original segment correction is the option to
use one of the new features in the multiple overlap calculations to perform
the correction (see 'change settings mode').

#ctr ccr cpr pcr ppr
The Ryan/Leach Multiple Overlap Solid Angle
In order to solve the problems that occur in the Old Leach Solid Angle due
to it's not taking multiple overlaps of order higher than two into account,
Peter Leach developed further equations for the calculations of solid angles
of regions of multiple overlap.  These were developed into an algorithm and
coded by Ryan Lemmer.

#ctg ccg cpg pcg ppg
The Craig Multiple Overlap Solid Angle
In order to solve the problems that occur in the Old Leach Solid Angle due
to it's not taking multiple overlaps of order higher than two into account,
Craig Taverner developed a set of vector based equations for the calculations
of solid angles of regions of multiple overlap.
These equations also replaced much of the maths used in the Old Leach Solid
Angle algorithm, leaving only the equations for the ellipse parameters by
Peter Leach.
The Algorithm was developed and coded by Craig Taverner.

#ctn ccn cpn pcn ppn
The Numerical Solid Angle
This is calculated simply by integrating over the angular cone angle
profile.
The cone angle values at all phi angles can be output to a file for use in
molecular contour plots (see 'change settings mode').
Currently there is a bug in the code which results in most solid angles
being overestimated in all but the highest symmetry cases.
This will be resolved as soon as possible.

#ctv ccv cpv pcv ppv
The Vertex Angle of Overlap
This is the sum of all the vertex angles of the overlap regions found
between all overlapping pairs of atoms.  It can be used as a means of
estimating steric congestion.
It's main advantage is in the simplicity of the calculation:
 VAO = alpha + beta - chi
Using the non-bonded overlap option (see "change settings mode"), only
non-bonded interactions are taken into account.
Using the no inter-group overlap option (see "change settings mode"), only
interaction between atoms of different groups are taken into account.
See "calculate total tolman" for a description of the group definitions.

#cts ccs cps pcs pps
The Solid Angle of Overlap
This is the sum of all the solid angles of the overlap regions found
between all overlapping pairs of atoms.  It can be used as a means of
estimating steric congestion.  It is not as simple as the vertex angle of
overlap calculation because it uses calculations from the Craig multiple
overlap algorithm, but is a more quantitative measure of steric overlap.
It is intended for future versions to give the solid angle of the total
region of overlap as opposed to the current simple sum.  Since this will
count all orders of overlap as equal, it will only be implemented as an
option, because the current version clearly gives a greater emphasis on
multiple overlap.  This is considered desirable.
Using the non-bonded overlap option (see "change settings mode"), only
non-bonded interactions are taken into account.
Using the no inter-group overlap option (see "change settings mode"), only
interaction between atoms of different groups are taken into account.
See "calculate total tolman" for a description of the group definitions.

#cv ctl ccl
The molecular volume
This calculation is a simple numerical calculation of the volume of the
molecule.  Two methods are provided:
 1 - A box enveloping the entire molecule is divided into a three
     dimensional grid and then all elements of the grid that are within
     the molecule have their volumes added to the total.  See 'change
     settings volume' for help on modifying the grid.
 2 - Monte Carlo approach in which the points inside the box are sampled at
     random, and the molecular volume calculated from the ratio found inside
     the molecule.  See 'change settings volume' and 'change settings
     accuracy' for relevant settings.

#ca ctp ccp
The orthogonally projected molecular area
This calculation is a fully analytical calculation.  Firstly the entire
molecule is orthogonally projected onto a plane, by default the xy plane.
It then uses a procedure similar to that used in the multiple overlap
solid angle calculation (see "calculate total craig") to cut the
molecular projection up into sections representing single atoms, regions of
overlap of two atoms, regions of triple overlap, regions of quadruple
overlap, etc. up until either no higher order of overlap exists in the
particular data set, or the maximum level of overlap allowed is reached. 
The default for this is 10.  The total area is calculated analytically by
summing the areas of all odd orders of overlap, including single atoms, and
subtracting all even orders.  Each region of multiple overlap has its area
calculated using simple trigonometric formulae to decompose the region into
subregions of segments of circles and simple triangles.
With no arguments this command calculates the area of the molecular
projection onto the plane defined in "change molecule plane", or (0,0,1)
(ie. xy plane) if not defined.  For more complex calculations the following
arguments can be given:
  theta     - projected areas verses a range of theta rotations of the plane
  phi       - projected areas versus a range of phi rotations of the plane
  map        - projected areas versus both theta and phi rotations

#cat
calculate area theta
The plane of projection is rotated stepwise (see "change settings size")
through the theta range specified in "change molecule plane" from the
defined position, and the projected area onto the plane at each step is
calculated and stored in the profile array (see "plot cartesian area" and
"plot polar area").

#cap
calculate area phi
The plane of projection is rotated stepwise (see "change settings size")
through the phi range specified in "change molecule plane" from the
defined position, and the projected area onto the plane at each step is
calculated and stored in the profile array (see "plot cartesian area" and
"plot polar area").

#cam
calculate area map
The plane of projection is rotated stepwise (see "change settings size")
through both the theta and phi ranges specified in "change molecule plane"
from the defined position, and the projected area onto the plane at each
step is calculated and stored in the profile array (see "plot cartesian
area" and "plot polar area").

#a
change
The folling data can be modified
  molecule  - current molecule data
  settings  - the general calculation settings
  origin    - origin for all cone and solid angle calculations
  parameter - the data in the atomic parameter table

#am
The following molecular parameters can be changed
  group     - group specific data
  plane     - plane onto which projections are made

#amg
change molecule group
The cavity volume radius and the groups aliases can be changed

#amp
change molecule plane
Up to 10 arguments can be given.  If any are omitted, they are left
unchanged.  All arguments will be read as double precision floating point
numbers and mean the following:
  1 to 3    - vector defining perpendicular to plane (z in plane system)
              default (0.0,0.0,1.0) in normal coordinates
  4 to 6    - vector defining phi=0 in plane system (x in plane system)
              default (1.0,0.0,0.0) in normal coordinates
  7, 8      - minimum and maximum values of theta for rotation of plane
              default 0 and PI
  9, 10     - minimum and maximum values of phi for rotation of plane
              default 0 and 2*PI
The "calculate area" command uses only the plane defining vector to
calculate the area of projection onto.
The "calculate area theta" command uses both vectors and the theta range to
calculate the projected area over a one dimensional range.
The "calculate area phi" command uses both vectors and the phi range to
calculate the projected area over a one dimensional range.
The "calculate area map" command uses both vectors and both ranges to
calculate the projected area over a two dimensional range.
All three maps are stored in the one dimensional array used for double
precision array storage.  None can be in memory simultaneously.

#as
change settings
The settings of the following can be changed
  order     - change maximum order of multiple overlap considered in
              Craig multiple overlap solid angle calculations
  range     - the general angular and radial profile ranges
  rotation  - the contour plot rotation
  size      - the profile array sizes, and the size of the numerical solid
              angle integration array
  mode      - the general calculation modes are changed
  accuracy  - the maximum error in the leach algorithm calculations, and the
              Monte Carlo volume
  plot      - the parameters for the molecule plot
  volume    - the grid used in the numerical volume calculation
  bonding   - the settings used in the bond search can be changed

#asm
Several settings can be changed:
- The profile ranging mode can be set so that the profile ranges are either
taken from the general settings range, or from the individual molecule
ranges.
- The improved G positioning feature used in the Craig and the Ryan solid
angle calculations can be set to be used in the Oldleach solid angle
calculation as well.
- The oldleach solid angle calculation can be set to either use the segment
correction algorithm or not.  The default is not to use it, because it was
found to be inaccurate.
- The vertex angle of overlap and solid angle of overlap calculations can be
set to consider only overlaps occuring between non-bonded atoms.
- The vertex angle of overlap and solid angle of overlap calculations can be
set to consider only overlaps occuring between atoms in different groups.
- The numerical solid angle calculation can be set to output the
angular-radial contour data involved.
- The contour plot can be set to perspective mode.
- van der Waals radii can be used in all calculations.
- the Monte Carlo method can replace the default fixed grid in volume
calculations.
- dummy unit cell atoms can be allowed to be visible to the "view molecule
atoms" command.
- the unit cell can be automatically boxed in the group and cavity volume
calculations.

#ao
change origin
The origin can be changed in three ways:
  atom      - the atom defining the origin can be changed
  group     - the origin can be changed to the main atom of a group
  distance  - the origin distance from the main atom can be changed

#aoa
change origin atom
Entering either the origin atom name or number as an argument will result
in all atomic coordinates changing to place that atom at the origin.
All distances and semi-vertex angles are recalculated.
The new origin atom is marked to be excluded from further calculations.
The groups present are reassigned.

#aoa
change origin group
Entering either the group name or number as an argument will result
in all atomic coordinates changing to place that groups main atom at
the origin.
All distances and semi-vertex angles are recalculated.
The new origin atom is marked to be excluded from further calculations.
The groups present are reassigned.

#aod
change origin distance
Entering a distance in angstroms as an argument will result in all atomic
coordinates changing so as to move the origin to that distance from the
main atom, along the vector direction from the main atom to the original
origin.
All distances and semi-vertex angles are recalculated.

#ap
change parameters
The contents of the atomic parameter table can be modified.

#v
view
the following data can be viewed
  molecule  - atomic data of the current molecule
  parameter - the atomic parameter table
  settings  - the current general calculation settings

#vm
view molecule
This command can be given with the following arguments:
  atoms     - The molecules atom list is displayed
  groups    - The molecules group list is displayed
  symmetry  - The molecules symmetry operator list is displayed

In any case, even if no argument is given, the following is displayed:

The steric parameters calculated, as well as the current atomic contents and
group assignments are displayed.
Steric Parameters:
- The original tolman cone angle calculated when the data set was loaded.
If you have modified the group assignments this is likely to no longer be
the correct value.  Use "calculate total tolman" to find the correct value.
- The total value, conformer average, maximum profile and profile area are
displayed for all steric calculations.
Group Assignments:
- The groups found for the current molecular configuration are listed.  If a
zero group exists, it is because the groups are defined about the main atom
bonded to the origin defining atom, and this atom has been assigned to the
zero group for special Tolman cone angle calculations (see "calculate total
tolman").  The semi-vertex angles in each case are used for the Tolman cone
angle calculations.

#vma
view molecule atoms
All the important parameters pertaining to the atoms present are listed. 
This includes number, group, position (cartesian and polar), radius and
semi-vertex angle.  The origin defining atom is indicated with a 'o'
character, and the main atom with a '*' character.  The semi-vertex angle
present is the one last used in a calculation, and therefore may change (eg.
in the profile calculation the semi-vertex angle changes constantly).

#vmg
view molecule groups
The listing of individually defined groups is given.  Groups are defined
either as separate molecules, or as separate ligands bonded to the origin
defining atom, or as individual branches on the ligand if only one ligand is
present.

#vms
view molecule symmetry
The list of symmetry operators loaded with the current molecule is
displayed.  Normal symmetry is listed as "SYMM" while centring conditions
are listed as "CENT".

#vp
view parameters
The contents of the atomic parameter table are displayed.
This table currently contains only the van der Waals and covalent radii
found in the 'steric.par' file.

#vs
view settings
The current general settings are displayed.

#h
help
Help can be obtained on each command by entering that command as an argument
after help.
for example:
  help file      - gives help on the file options
  help file load - gives help on the file loading option

All commands are also associated with single characters, most often the
first character of the command.
for example:
  'help file load' can be replaced with 'h f l'.
The spaces are obligatory.

When more than one command in the same menu level starts with
the same character, another character from the word has been assigned as the
shortcut character.
for example:
  'calculate total craig' is 'c t g'

#x
exit
Exit the steric program

#mkg mkn mcg mcn
The groups are defined by their numbers (or names).
Note the group must be clearly defined as being bonded to the origin
defining atom or the main atom (use 'molecule view' to check) before
it is identifiable as a group.

