1.36 symm

symm

Switches to the symmetry submenu of DISCUS. You can define a general symmetry operation in triclinic space such as a rotation around a general axis by a general angle. DISCUS performs a symmetry operation in general triclinic space according to the matrix notation:

r' = S*r + t

Here, r is the original position, r' its image, S the symmetry matrix and t the translation vector. There are no restrictions on the direction of the symmetry axis, the rotation angle or the translational part. You can use this feature to create a twinned crystal, to rotate a group of atoms around a general axis etc.

Further help topics are:

1.36.1 commands

Valid commands at this level are

@       ! Execute a macro file (see main help)
=       ! assigns the value to a variable (see main help)
angle   ! sets the angle of a rotation axis
asym    ! Shows asymmetric unit
calc    ! Calculates the symmetry transformation for a single point
chem    ! Shows the atoms present in the crystal
continue! Coninue a stopped macro (see main help level)
des     ! deselects atoms
echo    ! echo a string (see main help)
eval    ! Evaluates an expression for interactive check (see main help)
exit    ! terminates 'symm'
help    ! gives on line help for symmetry operations (see main help)
hkl     ! sets the symmetry axis in reciprocal space coordinates
incl    ! sets the range of atoms to be included in the symmetry operation
mdes    ! deselects molecules
mincl   ! sets the range of atoms to be included in the symmetry operation
mode    ! allows choice of creating a copy or replacing the atom
msel    ! selects molecules to be included in the symmetry operations
origin  ! sets the origin for the symmetry operation
power   ! sets the power of the symmetry operation
run     ! starts the calculation of the symmetry operations
sel     ! selects atoms to be included in the symmetry operations
show    ! shows the current parameters
stop    ! Stops execution of a macro (see main help level)
system  ! Executes operating system command (see main help)
trans   ! sets the translational part of the symmetry operation
type    ! Allows choice between proper and improper rotations
uvw     ! sets the symmetry axis in direct space coordinates
wait    ! Waits for user input (see main help)

1.36.2 angle

angle <value>

Sets the angle of the symmetry operation. The angle must be given in degrees. No limit applies to the numerical value.

1.36.3 asym

asym

Shows the content of the asymmetric unit. The names of those atoms, a number that is used as index for its scattering type, their position and temperature coefficient are listed. The number that is listed, is the number that refers to the scattering curve of that atom. It is contained in the variable m[<index>]. If a cell was read, all atoms are considered to be different, even if they are chemically identical and have the same temperature coefficient. If a whole structure was read, all atoms that are in the unit cell 0 <= xyz < 1, are chemically unique and have a different temperature coefficient are included in the asymmetric unit.

1.36.4 calc

calc x,y,z [,"d" | "r" ]

Calculates the symmetry transformation for a single point <x,y,z>. The current settings for the symmetry operation are used to transform the vector <x,y,z>. The result is displayed and stored in the result array "res". By default, or if the optional fourth parameter is set to "d", DISCUS assumes that the vector is a real space vector.i If the optional fourth parameter is set to "r" the vector is interpreted as a reciprocal space vector and the corresponding symmetry matrix in reciprocal space is used.

1.36.5 chem

chem

Displays the type of atoms present in the crystal. For each type of atom, its scattering curve number, its name and its temperature factor are listed. Warning, even, if all atoms of a particular type have been deleted, its scattering type will remain in the list. This list could therefore include more types of atoms than are actually present in the crystal.

1.36.6 des

des $\{$ "all" |<name>|<number>$\}$ [ , $\{$<name>|<number>$\}$ ...]

des "mic"

Deselects choices made by ==> 'sel' . Possible values for the parameter are mutually exclusively:

"all"     all atoms of the crystal are deselected.
"mic"     The selection of atoms that are inside a microdomain is canceled.
<name>    all the atoms called <name> of the crystal are deselected.
          This includes symmetrically not equivalent atoms.
<number>  all atoms of the crystal that are of scattering type <number>
          are deselected.

More than one atom may be deselected at once.

1.36.7 hkl

hkl <h>,<k>,<l>

Specifies the direction of the symmetry axis in reciprocal space coordinates. The corresponding direct space coordinates are calculated by the program. Alternatively you may specify the direction in direct space by the ==> 'uvw" command.

1.36.8 incl

incl $\{$<start>,<end>| "all" $\}$

The symmetry operation includes all atoms numbered <start> to <end> inclusively. All other atoms are ignored. If, instead of explicit numbers, the parameter "all" is given, the symmetry operation will include all atoms of the crystal. This holds even, if at a later time you include further atoms in the crystal. Thus, you can define a setup for the symmetry operations early in a lengthy macro, then modify the crystal and just run the symmetry operation later on. In addition you can define the atoms that are affected by the symmetry operation with the ==>'sele' and 'dese' commands.

1.36.9 mdes

mdes $\{$ "all" |<name>|<number>$\}$ [ , $\{$<name>|<number>$\}$ ...]

mdes "mic"

Deselects choices made by ==> 'msel' . Possible values for the parameter are mutually exclusively:

"all"     all molecules of the crystal are deselected.
"mic"     The selection of molecules that are inside a microdomain
          is canceled.
<number>  all molecules of the crystal that are of type <number>
          are deselected.

More than one molecule type may be deselected at once.

1.36.10 mincl

mincl $\{$<start>,<end>| "all" $\}$

The symmetry operation includes all molecules numbered <start> to <end> inclusively. All other molecules are ignored. If, instead of explicit numbers, the parameter "all" is given, the symmetry operation will include all molecules of the crystal. This holds even, if at a later time you include further molecules in the crystal. Thus, you can define a setup for the symmetry operations early in a lengthy macro, then modify the crystal and just run the symmetry operation later on. In addition you can define the molecules that are affected by the symmetry operation with the ==>'msele' and 'mdese' commands.

1.36.11 mode

mode $\{$ "copy" | "repl" $\}$ [ , $\{$ "new" | "old" $\}$ ]

The symmetry operation can have two different effects on the current atom. In the "copy" mode, the symmetry operation creates a copy of the current atom. In the "repl" mode, the symmetry operation moves the current atom from its old position to the new position.

The optional second parameter has only an effect if molecules are used. It determines if the new molecule created by the symmetry operation has is of the same type as the original ("old") or is treated as a new molecule type ("new").

1.36.12 msel

msel $\{$ "all" |<number>$\}$ [ , <number> ...]

msel "mic",$\{$ "all" | "eve" | "non" |<number>$\}$

This command executes two different functions. It serves to select those molecules that will be modified by the symmetry operation and secondly it can set the microdomain status.

First function:

Defines which molecules are included in symmetry operation. Possible values for the first mandatory parameter are mutually exclusively:

"all"     all molecules of the crystal are included.
          This includes the empty molecules in the structure, which are
          stored as scattering curve number zero.
<number>  all molecules of the crystal that are of type <number>
          are included.

More than one atom may be selected at once.

Second function:

Defines how molecules inside any microdomains are to be treated. The second parameter serves to distinguish different possible values of the status.

"mic"     selects whether molecules that are inside a microdomain are to be
          modified by the symmetry operation or not.
          The kind of molecules to be included are to be chosen by an
          additional 'sel' command.
          Second parameter:
          "all"    molecules inside any microdomain are selected, all
                   molecules outside all microdomains are not included.
          "eve"    Disregard microdomain status of an molecule. Molecules
                   in the host structure and inside any microdomain are
                   included alike.
          "none"   Only molecules outside all microdomains are selected.
          <number> Only molecules inside microdomain type <number> are
                   selected.

The selections made stay valid until explicitly deselected!

The selection of molecules by 'msel' and atoms by 'sel' are mutually exclusive. The symmetry operation uses either atoms or molecules.

1.36.13 origin

origin <x>,<y>,<z> [, $\{$ "mol" | "cryst" $\}$ ]

Specifies the origin of the symmetry operation in direct space coordinates. The symmetry axis intersects this point and has the direction specified by ==> 'hkl' or 'uvw'. If the symmetry operation is an improper rotation, the center of symmetry is at <x>,<y>,<z>.

In case of molecules to be transformed, the optional last parameter specifies if the given origin is relative to the origin of the molecule ("mol") or the crystal ("cryst"). Note that the first atom within a molecule has to be on the molecules origin (see manual).

1.36.14 power

power <n>$\{$, "multiple" | "single" $\}$

Sets the power of the symmetry operation. The symmetry operation is applied <n> times.

If the ==> 'mode' of the symmetry operation is "repl", the second parameter is meaningless. The symmetry operation that applies in this case is :

       n         n
 r' = S  * r  + t

The atom is moved to the new position that results from an <n> fold application of the symmetry operation.

If the ==> 'mode' of the symmetry operation is "copy", <n> new atoms are created. The position of the first atom results from a single application of the symmetry operation, the position of the second from a twofold application etc.

1.36.15 run

run

Starts the symmetry operation.

1.36.16 sel

sel $\{$ "all" |<name>|<number>$\}$ [ , $\{$<name>|<number>$\}$ ...]

sel "mic",$\{$ "all" | "eve" | "non" |<number>$\}$

This command executes two different functions. It serves to select those atoms that will be modified by the symmetry operation and secondly it can set the microdomain status.

First function:

Defines which atoms are included in symmetry operation. Possible values for the first mandatory parameter are mutually exclusively:

"all"     all atoms of the crystal are included.

This includes the "voids" in the structure, which are stored as scattering curve number zero.

<name>    all the atoms called <name> of the crystal are included.
          This includes symmetrically not equivalent atoms.
<number>  all atoms of the crystal that are of scattering type <number>
          are included.

More than one atom may be selected at once.

Second function:

Defines how atoms inside any microdomains are to be treated. The second parameter serves to distinguish different possible values of the status.

"mic"     selects whether atoms that are inside a microdomain are to be
          modified by the symmetry operation or not.
          The kind of atoms to be included are to be chosen by an
          additional 'sel' command.
          Second parameter:
          "all"    atoms inside any microdomain are selected, all atoms
                   outside all microdomains are not included.
          "eve"    Disregard microdomain status of an atom. Atoms in the
                   host structure and inside any microdomain are included
                   alike.
          "none"   Only atoms outside all microdomains are selected.
          <number> Only atoms inside microdomain type <number> are selected.

The selection made stay valid until explicitly deselected!

1.36.17 show

show

Shows the current parameters of the symmetry operation.

1.36.18 trans

trans <t1>,<t2>,<t3>

Sets the translational part of the symmetry operation. The translation is applied after the rotation according to the matrix notation:

r' = S*r + t

Here, r is the original position, r' its image, S the symmetry matrix and t the translation vector.

1.36.19 type

type $\{$"proper" | "improper" $\}$

A general rotation may be either a "proper" or an "improper" rotation. An improper rotation is a normal rotation followed by an inversion. To create, for example, a mirror operation specify a 180 degree angle and an improper rotation.

1.36.20 uvw

uvw <h>,<k>,<l>

Specifies the direction of the symmetry axis in direct space coordinates. The corresponding reciprocal space coordinates are calculated by the program. Alternatively you may specify the direction in reciprocal space by the ==> 'hkl" command.

terminates 'wave' returns to the normal discus prompt