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Edit menu
Undo
Restores the molecular structure changed by last modification; Redo
Restores the structure after Undo action; Add
atom
Adds a new atom to the displayed structure; Add
fragment
Adds a molecular fragment (ligand or radical) from the set of
standard fragments to current structure (see Working with molecular fragments). When radicals are added to the
molecule, H or X atoms of this molecule should be clicked, or the
heteroatoms to which the new fragment should be linked; Add/remove
bond
Inserts a single bond between two selected atoms, or removes the
existing bond; Select
all
Selects all atoms (to unselect them, right-click on the screen); Select
all atoms of specified type
Selects e.g. all C atoms; Deselect
all
Deselects all selected atoms; Expand selection Increases the amount of selected atoms according to atoms bonding; Invert
selection
After clicking, all selected atoms become unselected, and vice versa; Set
the types and captions of all selected atoms
Alters the selected atoms; Basic
editor options
These subitems duplicate double-clicks on atoms/bonds; Add
selected fragment to database Adds
the fragment of selected atoms to standard set of fragments. If the selected
fragment is a radical, the atom by which it is bonded to outer molecule must
be selected firstly. To delete the fragment from the set, or change its
directory, choose "Tools/Supporting/Edit fragments database". The
fragments database is stored in "fragments.bin" file; Copy
selected fragment to clip.
Remembers the fragment of selected atoms by copying it into the
clipboard (in text format); Paste
fragment from clipboard
Adds the fragment from the clipboard to displayed structure; Insert
dummy atom into center...
Places a dummy atom into coordinate center of selected atoms; Superpose
selected fragments
Places second selected fragment into coordinates center of first
selected fragment (the fragments are identified by bonds in molecule, and
there should be no common bonds between them); Unite
two groups
Before clicking this menu item, two dummy or hydrogen atoms belonging
to different bonded groups must be selected. These fragments will be united
into one molecule; Select
all atoms bonded to...
Selects all atoms, connected to selected atoms with bonds directly or
indirectly; Delete
selected
Removes all selected atoms or selected objects (lines, labels); Add
custom vectors and planes
Opens a window, in which the user can add vectors, planes with custom
coordinates to the molecule’s image; Translate
atomic coordinates
These subitems can be used for translating coordinates of all atoms
in molecule:
Move coord. center to sel. atom
Moves the coordinates of atoms so that the selected atom becomes
positioned in the coordinates center.
Move XYZ axis to 3 sel. atoms
Changes the coordinate system to place selected atoms in Z-matrix
orientation (first selected atom becomes the coordinate center, second
selected atom lies on Z axis, third in XZ plane);
Custom coordinates transform.
Opens a window which allows one to perform custom geometric
transformations of atomic coordinates in molecule (translation, rotation); Make
small random displacement
Adds a random shift to x, y, z coordinates of all atoms in molecule
(this possibility can be used to determine whether the structure is a local
minimum or a saddle point, when the second derivatives are too expensive to
be used); Update
atomic sequence by captions on atoms
Reorders the atoms in current structure according to labels on them.
After using this option, the atoms which have had digit labels will be
numbered corresponding to these labels. Non-labeled atoms will take
remaining numbers in old sequence; Rebond
Identifies bonds in displayed molecule, using the distance algorithm; Clear
bonds
Deletes all bonds in molecule; Clean
These subitems allow the positions of atoms in the whole molecule or
selected fragment to be adjusted to more closely match chemical intuition:
Set standard bond lengths
Positions the atoms to set standard values for bond lengths. The new
values are shown on the molecule's image; to hide them, right-click on the
screen;
Set standard bond angles
Positions the atoms to set standard bond angles;
Set all
Positions the atoms to set standard bond lengths and bond angles,
simultaneously;
In current version of the program, standard bond lengths are
estimated only for elements from H to I. The algorithm of estimation does
not take into account the p-coupling between bonds and can miss in some
cases. Besides that, cleaning does not work with rings. Set
point group
These subitems allow a symmetry point group to be applied to current
molecule. The program automatically finds appropriate group axes
orientations and allows the user to select an orientation; Set
principal axes
Changes the coordinate system so that the
X, Y, Z axes become the principal axes of current molecule. The
procedure also shows principal moments of inertia in the textbox at the
bottom; Drag
atoms
Toggles on/off the dragging mode, which allows the displayed
structure to be edited by "dragging" atoms in it; Dragging
type
Selects the type of mode in which the dragging will be performed (see
Constructing molecules); Rotate along selected Allows a fragment to be rotated along the line connecting two selected atoms; Copy image Copies the picture of the displayed molecule into the clipboard. Copy
current image without anti-aliasing
Does the same without drawing anti-aliased picture (usually anti-aliased
images are better, but with the 2d style the labels on atoms sometimes look
worse).
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