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Moloc: Molecular Modelling on UNIX Workstations: 16 Surfaces and Loci [srf]
Surfaces and Loci [srf]
Surfaces can be calculated or generated, either as dotted
surfaces or as polyhedra, according to the users choice. By
default, van der Waals surfaces are taken, but an additional
solvent radius can be added (option r). Included are all
visible entries, but a surface is only generated or
calculated for the atoms chosen in the set menu. If only a
fraction of the visible atoms is chosen, one has the choice
of counting overlaps between all atoms of an entry, or only
between atoms belonging to the set. The generated surfaces
are associated entries to the one containing the central
atoms. They can be deleted in exactly the same way as normal
entries. Upon moving the central atoms, the coordinates of
the surface are not updated. The surface calculation is
approximative and improves with increasing number of points
per atom.
Further options related to surfaces are: generation of
loci, calculation of free energy of solvation, estimation of
free energy of binding, and location of voids.
t: type of surface
Two modi of displaying surfaces are available. The con
ventional way is to distribute dots on the atomic
spheres. In this case, the number of dots per sphere can
be chosen. The second option is to draw the edges of a
suitable polyhedron for each sphere. This option
requires comparatively little drawing resources and
gives an acceptable impression of the surfaces. Con
nolly surfaces are dotted and calculated as described
in M.L.Connolly, J. Appl. Cryst. 16, 548-558 (1983).
Connolly surfaces differ from the Lee-Richards ones in
the treatment of accessibility of the probe sphere.
e: define center and radius of an environment
If the surface is only needed in a restricted volume,
such a volume can be specified by picking an atom and
fixing a radius of a sphere around it. This option does
not work for Connolly surfaces.
r: set radii
Two parameters can be defined here. The first is a fac
tor by which the van der Waals radii are multiplies to
yield the atomic radii for the surface. The second is a
solvent radius which is added to each atom radius to
yield the surface radii.
s: calculate surface
This option only calculates surfaces without generating
a display. It always uses the dot-algorithm and simply
counts dots to obtain a surface value (also atom-wise).
The accuracy is limited by the number of dots chosen as
well as by the evenness of distributing them on a
sphere.
g: generate surface
When generating a surface, the first step is to define
the set of atoms for which a surface display is needed.
After leaving the set tool, the color of the surface
display is specified. Then, the user is asked whether
the surface is meant for the set or for all atoms. In
the first case a single atom get a full sphere even if
it is bound to other atoms not in the set. In the second
case the parts of the surface that are inside atoms not
belonging to the set are not displayed. If a set con
tains atoms of several entries a separated associated
entry is generated for each entry containing atoms from
the set.
a: calculate partial atomic charges
For the selected entries partial atomic charges are
calculated (see MAB force field).
l: generate loci
A locus is a set of points generated by the positions an
atom will assume if one performs rotation about one or
several bonds in a molecule
h: hydration
The free enthalpy of hydration is evaluated atom-wise.
The resulting values for the atomic contributions
replace the charge values of the atoms!
b: scoring function
This option takes all visible entries together as
receptor entity and the active ones as the actor entity
(inhibitor, agonist, etc.). An empirical formula of the
type used by Boehm (J-CAMD 8, 243, 1994, JACS 114,
10697, 1992) is applied to give an estimate for the free
enthalpy of binding of the complex.
v: find voids
Empty regions in a molecular complex are searched. The
user has to specify the entries that are included in the
search. If several entries are specified, a single one
has to be identified which will be adjacent to the
voids. Voids that are not in contact with this entry are
not searched for. The user is asked to specify a criti
cal void distance, which specified the minimal distance
from a void position to the neighboring atoms above
which the void is considered to be relevant and is kept.
Voids having distances to neighboring atoms below the
critical one are discarded.
Loci of points can be generated. The points correspond to
positions which specified atoms assume under rotation about
specified bonds. The labels of the points indicate the state
of the rotation, that generated the point. Each character
indicates the number of rotation steps performed about a
bond, where the first character corresponds to the bond
nearest to the atom. For step numbers above 10 the letters of
the alphabet are used. The loci are either displayed as dots
or as a net of bonds connecting each pair of points separated
by a single rotation step (default).
n,d: net, dots
This switch toggles between displaying of the locus as
a net of bonds, or as marked dots.
r: reset specification
All specifications of bonds to rotate about and of the
root of the locus are removed.
b: specify rotatable bonds
To specify a bond as being rotatable, it has to be
picked, whereupon its color turns to white. This indi
cates that the user needs to also specify the end of the
bond that should rotate, by picking the corresponding
atom. That done, the bond color is reset.
s: define set of atom (root of the locus)
The root of the locus is the set of atoms for which
points are generated on the locus. In most cases this is
just one atom. The case of several atoms is identical
with the set of loci generated from each of the atoms
alone.
l: generate the locus
If bonds and a root are specified, the locus is gener
ated and the program returns to the calling menu. All
specifications are removed.
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