Moloc: Molecular Modelling on UNIX Workstations: 7 Display Geometry Data [geo]
Display Geometry Data [geo]
Geometrical data can be printed to the text port or be
displayed on the structure. The displayed values are
continuously updated. The items to be picked to generate the
mentioned display are indicated after the semicolon.
a: atoms: atom
Pick an atom to get a display of coordinates, tempera
ture factor and occupation number. Picking with the
shift-key pressed results in the presentation of a text
box to insert arbitrary text which will be displayed.
b: bonds: bond
Pick a bond to get a display of its length in pm.
v: valence angles: center
Pick an atom to get a display of all valence angle val
ues at that atom in degrees.
t: torsion angles: 4 atoms
Upon picking four atoms a display of the corresponding
torsional angle value (in degrees) is generated.
p: pyramidalities: center
Pick an atom to get a display of all pyramidality values
at that atom. The pyramidality is the signed volume
spanned by the unit vectors pointing from the central
atom to the ligands. For tetrahedral arrangement p =
0.77.
d: distances: 2 atoms
a: angles: center, 2 atoms
Provides the possibility to display values of single
angles. The picked atoms need not be connected by
bonds.
q: pyramidalities: center, 3 atoms
Provides the possibility to display values of single
pyramidalities. The picked atoms need not be connected
by bonds.
k: type coordinates
By picking an atom, its coordinates and additional data
are printed. When the shift key is also pressed during
picking, the data of the whole entry are given.
r: Ramachandran plot for Calf structure
Upon picking a Calf structure a two-dimensional Ram
achandran plot is generated, in which each amino acid
is represented by a dot in the plane of phi-psi angles.
c: clear geometry display
This option clears all geometry displays!
w: written data
Upon choosing this option the program digresses to the
following menu:
7.1 Written geometry data [gw]
Geometrical data which are normally displayed on the
graphics screen can be written to the dialog window. In most
cases, when the shift key is also pressed during picking, the
data of the whole entry are given.
b: bonds: bond
v: valence angles: center
t: torsion angles: bond
p: pyramidalities: center
d: distances: 2 atoms
n: angles: center, 2 atoms
Provides the possibility to display values of single
angles. The picked atoms need not be connected by
bonds.
f: phi-psi of Calf: Calf
h: helicity: 2 Calfs
A value for the helicity of the stretch between the two
Calfs is calculated and printed.
s: beta strand: 2 Calfs
A value for the beta strand weight of the stretch
between the two Calfs is calculated and printed.
k: type coordinates
By picking an atom, its coordinates and additional data
are printed.
g: geometry data of set of atoms
Given are: position of centroid, radius of gyration,
rotational volume, root mean square distance from and
normal vectors of second-moment principle-axes planes.
If this option is used repeatedly, distances of consec
utive centroids and various other quantities specifying
the mutual geometry of the two atom sets are printed in
addition, for example the Euler angles between consecu
tive second moment tensors. In this example the theta
angle is the dihedral angle between the two approximat
ing planes (with lowest root mean square distance) for
the two sets.
a: accuracy threshold for data of atom sets
This threshold determines when a second moment tensor
is considered to be axial or spheric. This means, that
if the difference between two eigenvalues, divided by
the root mean square distance, is smaller than this
threshold, the two eigenvalues are considered to be
equal.
m: dipole moment with current charges
The electric dipole moment is calculated, using the
charges held currently in the atomic charge fields.
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