Drawing structure query
JSME Help and Basic
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
delete mode (click on atom or
bond to delete it)
group - choose this option and then click bond connecting the group with the
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)
next ring will be added as a spiro ring
version information and link to the help
input stereo bond, click
existing stereo bond to cycle through possible types (up, dowm,
powerful chain tool,
allows creation of various chains and rings; click single bond to change it to
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
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
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
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
rings 3..8 for 3 to 8 membered rings, 1 for phenyl and 0
groups a - COOH, y - NO2, z - SO3H, t - tert. butyl, ft -
StereochemistryStereochemistry 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 NumberingAtom 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 StructuresBy 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
Reaction InputReaction input is enabled with the option "reaction".
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 FeaturesQuery 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
Copy and PasteRight 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 EditorSome 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.