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;

Operations with all selected atoms

   Set the types and captions of all selected atoms          Alters the selected atoms;

   Remove bonds involving the selected atoms          Removes all bonds between 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);

Delete all atoms except selected        Removes all non-selected atoms; 

Custom vectors and planes        These subitems allow the user to add custom vectors on planes with coordinates described by selected atoms;

    Add vectors, planes and labels by...     This menu item allows the user to add custom vectors, planes and labels with coordinates specified in text format;

     Examine geometrical parameters    These menu items provide the possibility to estimate the angle and distance between two planes, or two vectors, or a plane and selected atom, etc. For appliing this feature, the user must firstly add e.g. two planes to the molecule's image, or one plane and one vector, etc;

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);

  Align two selected atoms along...         Changes the coordinate system to place two selected atoms on X, Y or Z axis;

  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).

BACK