JSME Help and
Basic Instructions
JSME Menu
shows molecule
SMILES
clears the editing area (or the current molecule,
if structure contains several parts)
starts new molecule component (when multipart option
or reaction input are enabled)
delete mode (click on atom or bond to delete it)
deletes functional group - choose this option and
then click bond connecting the group with the main skeleton
starts atom numbering or reaction mapping (when this
option is enabled)
query atom /
SMARTS
(when this option is enabled)
switches between allowed charged states on
clicked atom
reaction input (when reactions are enabled)
undo
redo
next ring will be added as a spiro ring
version information and link to the help page
input stereo bond, click existing stereo bond to
cycle through possible types (up, dowm, orientation)
powerful chain tool, allows creation of various
chains and rings; click single bond to change it to double
allows input of inorganic atoms or atoms in
nonstandard valence state (in this case enter the atom symbol enclosed in
[], for example the carbene carbon will be [C])
opens functional group popup menu
move selected atom useful when drawing crowded
structures (visible when enabled in options)
Basic Editing
Rings are added connected by a single bond (when not added to a
terminal atom); if you want to add a spiro ring press
Shift when adding it. An alternative way to add a spiro ring (that
may be used also on touch devices) is to press the
icon; the next ring will be then added as
spiro.
With single bond selected, a click on existing single bond changes it to
double.
With the powerful chain tool
you can draw
chains, saturated rings and by clicking on single bond change it to a
double bond.
Molecule may be moved by "dragging" free space and
rotated by pressing also the Shift key.
JSME Keyboard Shortcuts
If you are using JSME often, learn the following shortcuts. They will
speed-up your editing considerably.
ESC returns to the standard editing state (carbon, single bond)
d or Del starts delete mode
atoms C, N, O, P, S, F, L (for Cl), B (for Br), I, H, R
bonds - for single bond, = for double bond
rings 3..8 for 3 to 8 membered rings, 1 for phenyl and 0 for
furyl
groups a - COOH, y - NO2, z - SO3H, t - tert. butyl, ft - CF3
Stereochemistry
Stereochemistry at C4 centers, double bonds and allenes is supported. Use
the up / down wedge bonds to indicate stereochemistry at the C4 centers.
Remember, that only bonds with a "sharp point" towards the atom are
considered. When creating SMILES the editor tries to guess missing stereo
features, in unresolvable cases an error message is issued and the SMILES
without stereo information is created.
When the "autoez" option is set, SMILES with E,Z stereochemistry on all
non-ring double bonds will be generated automatically. Without this keyword
(or for ring double bonds) you have to mark a double bond as stereo by
clicking on it with the stereo bond button selected. The bond color will
change to magenta.
Stereochemistry may be completely disabled by the "nostereo" option.
Atom Numbering
Atom numbering (marking) is enabled by the option "number" (for reaction
input this is default). Button
appears in the menu.
To mark an atom the "numbering mode" must be on, selected by clicking the
123 button. The atom number is chosen by pressing respective keys on your
keyboard (i.e. 2 or 12); then atom(s) must be clicked. To delete the number
pres 0 at your keyboard and then click the atom.
Input of Multipart Structures
By default only non-disconnected structures may be entered. This may be
changed by a "multipart" option. A button
appears in
the menu. A new molecule may be started only after clicking this button,
then selecting a proper template (atom, ring or bond) and clicking free
space in the drawing area. Without clicking the NEW button first clicking
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 the
button deletes the last touched molecule.
Reaction Input
Reaction input is enabled with the option "reaction". Buttons
,
and
appear in the menu and arrow appears also in the
drawing area. Now simply draw reactant(s), product(s) and modulator(s)
(modulators have to be above the arrow) as explained in the description of
input of multipart structures. The arrow button enables simplified input of
reactions. After clicking it, the reactant will be copied to the product
(including atom numbering, if any).
Query Features
Query button
(when enabled in the options)
launches a query window that allows creation of SMARTS atom or bond queries
by combining various atom attributes. Select the SMARTS options in this
panel and then click the respective atom or bond in the molecule.
Copy and Paste
Right mouse click opens the Copy and Paste pop-up menu that allows to copy
the molecule as SMILES or MOL file or paste MOL , SDF, or RXN files into the
editor.
On supported touch devices, the menu can be opened by �touch and hold� on
the surface of the editor.
Keyboard shortcuts Ctrl C (for copy) and Ctrl V (for paste) are supported
on most browsers.
Drag and Drop of Files in the Editor
Some HTML 5 compatible browsers support the drag and drop of files. Starting
with version 2013-03-24, JSME accepts dropping of text files in the format
MOL, SDF and RXN.
To drag molecule from the editor into the appropriate destination (for
example Word or text document, or desktop) drag the icon in the lower right
corner of the editor.