Moloc: Molecular Modelling on UNIX Workstations: 8 Forge: Coordinate Changes [frg]
Forge: Coordinate Changes [frg]
This tool allows the user to make coordinate changes of
atoms or residues by various means. Some of the options are
specific to all-atom or to Calf structures. In cases, where
it is unambiguous which type of structures are handled, the
non-applying options may be inaccessible.
s: select set
Several options work on whole sets of atoms. The set to
be handled must first be defined here (set tool).
m: move set
A predefined set of atoms can be moved around. The move
ment is invoked by pressing a shift key and operating
the mouse as if the view was to be changed. The speci
fied set of atoms then moves correspondingly. The zoom
action does not make sense here and is replaced by a
rotation about the axis perpendicular to the screen.
r: rotate set about axis (2 atoms)
A predefined set may be rotated about an axis. This axis
is first defined by picking two atoms. Rotation takes
place when the shift key is pressed and the mouse moved
sideways with the left-hand button down.
d: drag set
The drag option works like the move option, but atoms
outside the set are dragged along by reduced amounts,
depending on the topologigal distance from the set.
a: move single atom
The atom to be moved is first picked and than moved with
the help of the mouse while the shift key is pressed
(see option m, rotation is inactive.).
t: drive torsions
Torsions are driven by first picking a bond. If the bond
is highlighted in white rotation about it can be per
formed by pressing the shift key and moving the mouse
sideways. If the left-hand mouse button is pressed, the
smaller substituent (indicated by a mark at the bond
end) moves. The middle button causes the larger sub
stituent to move. Press the shift key and both middle
and left mouse button to reset the torsion to the orig
inal position.
l: turn peptide links
Peptide links are turned in Calf structures by first
picking the link. Pressing the shift key and the left-
hand mouse button and moving the mouse sideways turns
the link. To see any action the peptide display (,
option) must be generated for that structure. This dis
play is continuously updated in this case.
h: drive chi angles
By picking a residue in a Calf structure, the corre
sponding side chain is displayed with the current val
ues of the chi's. These values can be altered in two
ways: 1. Toggling through a set of Ponder-Richards rot
amers (J.Mol.Biol. 193, 775 (1987)) is induced by keep
ing the control button pressed and hitting the middle
mouse button. The number of the rotamer and its chi
angles appear on the printout. 2. Continuous change of
chi angles is induced by rolling the mouse sideways.
Pressing the shift key and the left-hand or middle
mouse button affects chi 1 or chi 2 respectively,
pressing the alt key in addition affects chi 3 or chi 4.
v: invert stereo centers
By picking a chiral atom, its stereochemistry is
inverted. In the case of a three-coordinated atom,
picking with the left-hand (middle) mouse button moves
the shortest (second-shortest) substituent.
e: enantiomer (mirror structure): pick it
A picked structure is changed to its enantiomer. If an
atom is picked central inversion about that atom is
performed. Picking a bond leads to axial inversion with
respect to the picked bond.
k: coordinate transfer
Coordinate values can be transferred from one set of
atoms to an other one. For each corresponding atom pair
one atom must belong to an active entry the other to a
visible one. The active atoms will be moved to the posi
tions of the visible ones. Pair specification can be
done by atoms, by residues, or by entries.
w: worry set of atoms or structure
This option involves random shifts of the atoms of a set
by an amount that can be given and monitored interac
tively. If a set has been defined in the set option 's\q,
all atoms of this set will be affected, otherwise the
user is asked to pick an entry. In the latter case all
atoms of the picked entry will be affected.
p: peptide secondary structures on sets
For predefined sets on Calf structures (most sensibly
loops) secondary structure arrangement can be induced.
A possibility to relocate the sets is included.
c: clear settings
Any (display) setting produced during the forge proce
dure can be cleared here (e.g. axis of rotation).
f: flat (principle axis orientation)
The picked entry will be rotated to present is flattest
face towards the user in the current view, i.e. the axis
of smallest eigenvalue of the second moment of atomic
positions is rotated in viewing direction, the axis of
the largest eigenvalue to the right. The centroid
remains unchanged.
i: ab initio conformation
Moloc has an algorithm to generate a from-scratch con
formation which is applied here to the picked entry.
q: generate stochastic conformation
For a picked Calf structure a stochastic conformation
is generated by choosing appropriately weighted random
values for phi and psi of each residue. For Calf struc
tures, if a sequence file is given in which the #p
records contain an indication for secondary structure,
such as H or S, phi and psi of the corresponding residue
are set to the standard values of the indicated struc
ture type.
-> Table of Contents