JME Molecular Editor

Basic Instructions


Editor is intended to be used without any special documentation or training, but there are some tricks which can help you to work with it more efficiently.

Menu Buttons

D-R deletes functional groups - choose this option and then click on the bond connecting the group with the main skeleton.
UDO - undo last editing step.
QRY button (if enabled in the param tag) allows easy specification of atomic queries for substructure searches.
Stereo bonds - the type of stereo bond (up, down) may be changed by clicking on the already created stereo bond; this cycles through two / four possible stereo bond types.
Atomic charges may be changed by the +/- button. Editor enables modification of charges only in "reasonable" cases. If you are not satisfied with the editor's inteligence (concerning charges and the explicit number of hydrogens) you can force your will by using the X button.
"Non-organic" atoms or atoms with nonstandard valence may be entered with help of X button by specifying atomic SMILES (without [] brackets, i.e. Si, Fe++, NH3+).

Keyboard Shortcuts

Most of the commands may be accessed also by keyboard shortcuts. It is possible to :
change atom type by pressing C N O S F L (for Cl) B (for Br) I P H X R and clicking the respective atom
choose bond order - for single bond, = for double bond
choose ring type by pressing 3 4 5 6 7 8 9 or 1 for phenyl, 0 for furyl
start delete mode by pressing D or Del and return to the standard state (carbon, single bond) with Esc
common functional groups may also be added by keyboard shortcuts, use t for t-butyl, ft for trifluoromethyl, lt for trichloromethyl, a for COOMe, z for SO2Me and y for nitro, and then click the atom where the group should be connected.

Moving and Rotation

You can move molecule by "dragging free space" with the left mouse button and rotate it by using the left mouse button and shift key (or left and right mouse buttons together).

Adding rings

When a ring template is selected and multivalent atom is clicked, a new ring will be created connected by single bond to this atom. When spiro ring is required, the Shift key must be pressed when clicking on the atom. Spiro ring may be added only to atom with 2 single bonds.

Multivalent nitrogen groups

Multivalent nitrogen groups, such as nitro, azide, N-oxide, nitrile etc, should be drawn with a pentavalent nitrogen as shown below.

N(=O)=O

Input of Multipart Structures

Creation of a new molecule may be started only after clicking the NEW button, selecting a proper template (atom, ring, bond) and clicking free space in the drawing area. Without NEW button the click on the free space has the same effect as in the standard mode (i.e moving or rotation of the last touched molecule). In the multipart mode CLR button deletes the last touched molecule.