How to draw
- Carbon atoms connected by
single bonds can be drawn when the
Bond button is down and its icon shows a
single bond.
- To select another bond type, hold the mouse button down on the icon
until a menu pops up.
- To change a single bond to double
(triple), select single bond mode, then
click on the bond once (twice).
- To change an atom,
press an atom button such as B,
N, O,
F, etc. and then click on the atom.
- To increase or decrease a charge,
select + or - and
click on the atom.
- Red underline means valence error.
Undo and Redo
- Operations can be reverted with Undo and
Redo.
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How to delete
- To delete the selection,
press Erase.
- To delete atoms or bonds one by one,
- be sure there is no selection,
- press Erase,
- click on the atoms/bonds
- To delete everything in a rectangle,
- press Erase,
- press and hold down the mouse button while selecting the rectangle
- release the button
- To delete a nonrectangular area,
- press Erase,
- click on the mouse button and move the mouse pointer around the fragment
- click again
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Selecting
- Press the Select button.
- To select an
atom,
bond or
group,
click on it.
- To select a fragment,
double click on an atom or bond of it.
- Lasso selection:
Click on the mouse button and move the mouse pointer around the fragment.
Click again when you are ready.
- Rectangle selection:
Hold the mouse button down while selecting.
- To increase or decrease selection, press
Shift while clicking on an
atom,
bond or
group.
- To unselect all the atoms, click on the sketchboard
somewhere outside the structure.
The More window
- Press More to bring up a window with a
periodic table,
query atoms, the SMARTS/Alias textfield
and a menu of abbreviated group,
- To choose a SMARTS query atom or property not found in the left button bar,
- write its SMARTS string into the textfield,
- press SMARTS.
- To define a set of fragments as R-group 5,
- select the fragments,
- press R5.
- To choose an attachment point on R-group 5,
- press R5,
- click on the atom.
- To select an abbreviated group, use the
Groups menu.
Graphics objects and text boxes
- To insert a (poly)line, rectangle or text box, choose it from the
Insert menu, point with the mouse to the
desired position, then click or drag. After putting a text box, you can
immediately use the keyboard to type a text.
- To change the contents of a text box, choose
Select mode, click on the box, then use the
keyboard.
- To resize or change the shape of an object, drag one of its points.
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Moving and Rotating
- To move an atom, drag it with the mouse in
Select mode.
- To move the selection,
- move the mouse pointer towards the center
until a blue rectangle appears,
- drag the selection by pressing and holding down the mouse button.
- To rotate the selection,
- move the mouse pointer towards the "edge"
until a blue gear appears,
- drag the selection by pressing and holding down the mouse button.
Drag & Drop
- Selections can be moved also between
different Marvin windows
- Molecule files from the file manager or the desktop can be dragged and
dropped in Marvin
Notes:
1. D&D only works in the Swing version, in Java 1.2 or later.
2. D&D does not work in the JMSketch applet running in a browser
window, because drop events are received by the browser in that case.
Hydrogen labels
- In the View menu, choose
Hydrogens to change the way implicit H labels
are shown.
If you do not see View and
Edit menus, put
the sketcher into a separate window by pressing the top left button (an
arrow pointing up).
Use the Edit menu to
- copy or paste,
- clean in 2D or 3D,
- aromatize or dearomatize,
- add or remove Hydrogen atoms,
- flip horizontally or vertically,
- specify the chiral flag
- set R-group query conditions
(R-logic),
- view or edit the Source
(Molfile, SMILES string, etc.)
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