2D Workspace Panel

Summary
Opening the 2D Workspace Panel
Using the 2D Workspace Panel
2D Workspace Panel Features
Related Topics

Summary

In this panel you can sketch a molecule in 2D, save it as a project entry, either in 2D or in 3D, and save an image of the molecule.

Opening the 2D Workspace Panel

To open the 2D Workspace panel, you can:

Choose Edit → 2D Sketcher in the main window.
Click the 2D Sketcher button on the Edit toolbar in the main window.

Using the 2D Workspace Panel

To start drawing, click the Draw button

Drawing creates a carbon-atom framework. You can change the element with the element buttons, either during drawing or after you have finished drawing.

The first atom is placed by clicking in the drawing area. It is shown as CH₄. After placing the first atom, you can draw in several ways:

Click on an atom to place a new atom and draw a bond to it from the clicked atom. The bond is placed in a default orientation with respect to existing bonds.
Drag from an atom in a particular direction, to place a new atom and draw a bond from the clicked atom to the new atom in the chosen direction.
Drag from an atom to another atom to create a bond between the two atoms.
Hold down shift and drag from an atom to add a linear chain to that atom.
Click on a bond to increase its bond order.

The "active" atom—the one to which a new bond will be attached— is indicated by a gray filled circle. Likewise, the active bond is indicated by a thicker gray line. The active atom or bond changes as you move the pointer over the atoms or bonds.

You can also start your drawing with a ring: click on the ring in the toolbar, then click in the drawing area to place the ring. Likewise, you can start drawing with a custom fragment by clicking on it in the User defined fragments toolbar, then clicking in the drawing area.

To draw bonds with a particular stereochemistry, click the Wedge Bond or Dashed Bond button,

and draw in the drawing area. Clicking on a bond changes its stereochemistry; clicking on an atom adds a new atom with the selected orientation.

To add rings to your system, click on one of the ring buttons, then click in the drawing area. When you move the pointer into the drawing area, the ring is shown in blue. As you move the pointer in the drawing area, the ring "snaps" to positions that show a potential attachment of the ring to the structure. Clicking when the ring is in one of these positions places the ring at that position, and its color changes to black.

To replace functional groups, pause the pointer over the atom you want to replace with the group, then type in the group name or a SMARTS pattern and press Enter. Many common functional groups are recognized: the list is given below with the corresponding SMARTS patterns. You must ensure that the valence is properly satisfied by the group you choose.

To add functional groups, pause the pointer over the atom you want to add the group to, type - then type in the group name or a SMARTS pattern and press Enter. Many common functional groups are recognized: the list is given below with the corresponding SMARTS patterns.

me	C
et	CC
pr	CCC
ipr	C(C)C
nbu	CCCC
ibu	CC(C)C
sbu	C(C)CC
tbu	C(C)(C)C
nhex	CCCCCC

ph	C(C=C1)=C-C=C1
bz	CC(C=C1)=C-C=C1
chex	C(CC1)CCC1
cp	C(C=C1)C=C1
ome	OC
oet	OCC
cooh	C(=O)O
coome	C(=O)OC
cooet	C(=O)OCC

coo-	C(=O)[O-]
no2	[N+](=O)[O-]
so2	S(=O)=O
so2n	S(=O)(=O)N
so3	S(=O)(=O)[O-]
po3	P(=O)([O-])[O-]
con	C(=O)N
nco	NC=O
cn	C#N

To change the element, you can do one of the following:

Pause the pointer over the atom, then type the element symbol.
Click the button for the desired element on the toolbar, then click an atom in the structure.
Type the element symbol, then click an atom in the structure.

The last two of these choices allow you to click on multiple atoms to change the element; the first operates only on the active atom.

To assign a formal charge, click the Increase Charge button or the Decrease Charge button,

then click on an atom. The formal charge is given next to the atom, and any hydrogens are also shown that are needed to complete the valence for the atom; or a red underline is shown to indicate that the valence is not satisfied. You can also pause the pointer over an atom and type in the formal charge. Any combination of numbers and + and − are accepted.

To move a group, first select the group by drawing around it with the Lasso tool

If you want to translate it, just drag it to the new location. If you want to rotate it, click the Rotate button,

then drag it to the new orientation. The angle is displayed as you drag.

To save a structure as a project entry, provide a title in the Entry title text box, then click Create Entry. If you have a LigPrep license, you can convert it to 3D by selecting Convert to 3D; otherwise it is added as a 2D structure, and you must convert it to 3D if you want to use it for calculations.

To save an image of the structure in PNG, JPEG, or BMP format, press Ctrl+Alt+P (⌥⌘P). A dialog box opens, in which you can specify the size of the image and the background transparency. When you click OK, a file selector opens, in which you can navigate to the location and name the file. The image type is determined by the file extension.

To save a structure for drawing, press Ctrl (⌘) and drag the structure to the User-defined fragments toolbar. If you want to delete it, click the structure on the toolbar and press Delete or Backspace.

Menu bar

File menu
Edit menu
View menu

File menu

Save Screenshot (Ctrl+Alt+P, ⌥⌘P): Save an image of the structure in a file. The image can be saved in PNG, JPG, or BMP format.
Close (Ctrl+W, ⌘W): Close the window.

Edit menu

Preferences: Set display preferences. Opens a Preferences panel, in which you can make settings. In the General tab you can make settings for the drawing of the structure and the background; in the Selection tab you can make settings for the selection of atoms in the structure, and in the Ligand Interaction Diagram tab, you can make settings for the representation of objects in the Ligand Interaction Diagram.
Undo (Ctrl+Z, ⌘Z): Undo the last action. Can be performed multiple times. Same as the toolbar button.
Redo: Redo the last action that was undone. Can be performed multiple times. Same as the toolbar button.
Copy (Ctrl+C, ⌘C): Copy the selected atoms (or the entire structure, if there is no selection) to the clipboard as a SMILES string.
Paste (Ctrl+V, ⌘V): Paste the SMILES string from the clipboard onto the drawing area as a 2D structure. The structure is placed in the center of the drawing area.
Select All (Ctrl+A, ⌘A): Select all atoms in the structure. The atoms are outlined in yellow.
Deselect (Ctrl+D, ⌘D): Clear the atom selection.
Cleanup: Clean up the structure (2D coordinates) and normalize orientation and arrangement of groups. If you have atoms selected, only those atoms are cleaned up. Same as the toolbar button.
Input SMILES String (Ctrl+S, ⌘S): Specify a structure by using a SMILES string. Opens a dialog box, in which you can enter the SMILES string. When you click OK, the structure is added to the drawing area, at the center.
Common or IUPAC Name Search (Ctrl+P, ⌘P): Run a PubChem query (on the web) on the name provided and add the first result as a 2D structure to the drawing area, at the center. Opens a dialog box, in which you can enter the name.

View menu

Flip Vertical (Ctrl+Alt+F, ⌥⌘F): Flip the structure from top to bottom.
Flip Horizontal (Ctrl+Alt+H, ⌥⌘H): Flip the structure from left to right.
Fit to Screen (Ctrl+F, ⌘F): Zoom in or out so that the structure fills the visible part of the drawing area.
Blackboard View (Ctrl+I, ⌘I): Display the structure in white on a black background, like drawing on a blackboard.
Selection Display Mode (Ctrl+Alt+S, ⌥⌘S)
Stereochemistry Labels (Ctrl+L, ⌘L): Label chiral atoms with R or S.
Color Heteroatoms (Ctrl+T, ⌘T): Color atoms other than carbon (N is blue, O is red, S is yellow, and so on). If this option is deselected, all atoms are colored black if the background is white, or white if the background is black.
Scene Title (Ctrl+T, ⌘T): Display the title above the structure.
LID Legend: When displaying a ligand interaction diagram, display the legend below the diagram.
User defined fragments: Display the User-defined fragments toolbar. By default it is placed below the menu bar, but you can move it to another location. This toolbar contains custom fragments, which you can use for drawing structures.

Toolbar

The main toolbar has three sets of buttons. The first set of buttons is for performing actions, which are described below. The second set is a collection of rings that you can add to the structure. The third set is a collection of elements, which you can use to change atoms to a chosen element. The selection of the element can also be done by typing the element symbol (case insensitive).

In addition to the main toolbar, there is a User-defined fragments toolbar, which you can display from the View menu. To add a structure to this toolbar, hold down Ctrl (⌘) and drag the structure to the toolbar. To delete a structure from this toolbar, click on the button for the structure and press Delete or Backspace. You can use the structures on this toolbar in the same way as the ring fragments on the main toolbar: click the button, then click in the drawing area.

	Undo Undo the last action. Can be performed multiple times.
	Redo Redo the last action that was undone. Can be performed multiple times.
	Lasso Select atoms by drawing around them ("lassoing"). The selected atoms can be moved, rotated, deleted, copied.
	Move Move (translate) the selected atoms or the entire structure. Drag in the drawing area to move the structure. Drag the selection to move the selected atoms. (This is the default action for dragging a selection, so you do not need to click this button before dragging it.) You can also move the structure by dragging with the right mouse button.
	Rotate Rotate the selected atoms or the entire structure. Drag in the drawing area to rotate the structure. The angle through which the structure has been rotated is displayed near the center of rotation while you are rotating it. If rotation does not seem to be working properly, check whether you have other structures in the drawing area that are not visible. You can also rotate the structure by dragging with the middle mouse button.
	Cleanup Clean up the structure (2D coordinates) and normalize orientation and arrangement of groups. If you have atoms selected, only the selected atoms are cleaned up.
	Draw Draw a single bond. Click on an atom to draw a bond to a new (carbon) atom, click on a bond to add another bond between two atoms.
	Erase Delete atoms or bonds. Clicking on a carbon atom deletes it; clicking on a non-carbon atom changes it back to carbon, then clicking again deletes it. Clicking on a bond removes one bond.
	Wedge Bond Draw a wedge bond. Clicking on an atom draws a wedge bond to a new (carbon) atom; clicking on a single bond converts it to a wedge bond.
	Dashed Bond Draw a dashed bond. Clicking on an atom draws a dashed bond to a new (carbon) atom; clicking on a single bond converts it to a dashed bond.
	Increase Charge Increase the formal charge on an atom by 1.
	Decrease Charge Decrease the formal charge on an atom by 1.

Drawing area

The drawing area shows the structure and is used to build or edit structures. You can pan the view with the right mouse button, and rotate it with the middle mouse button. You can zoom in and out with the mouse wheel, and you can scroll the drawing area with the scroll bars. The area is large, so it is possible to place a number of structures in it.

When the pointer is over an atom, it becomes the active atom, to which drawing operations are applied: bonding to a new carbon atom, changing element (by typing the element symbol), adding or replacing the functional group (by typing a group name or SMARTS string and pressing Enter).

When the pointer is over a bond and you are drawing with one of the three bond types, the bond becomes active. You can change it to a wedge or dashed bond, or increase the bond order, depending on the bond type.

When a ring is selected, the ring is shown in blue. As you move the pointer in the drawing area, the ring "snaps" to positions that show a potential attachment of the ring to the structure. Clicking when the ring is in one of these positions places the ring at that position, and its color changes to black.

Right-clicking on an atom displays a shortcut menu that allows you to make settings for that atom:

Set stereochemistry to R—Set the stereochemistry at this atom to R. This option is only available for chiral centers. The appropriate bonds are changed to wedge or dotted to reflect the stereochemistry.
Set stereochemistry to S—Set the stereochemistry at this atom to S. This option is only available for chiral centers. The appropriate bonds are changed to wedge or dotted to reflect the stereochemistry.
Set allowed atoms—Enter a list of atoms that are allowed at the current center in the Edit Atom dialog box, which opens when you choose this item.
Set as any wildcard—Allow any atom to be present at this center. The atom symbol is set to Qn, where n is a numerical suffix to distinguish different "wildcard" atoms. A text label is also placed in the Workspace reading "Qn = Any atom".
Set as any wildcard—Allow any atom to be present at this center. The atom symbol is set to Qn, where n is a numerical suffix to distinguish different "wildcard" atoms. A text label is also placed in the Workspace reading "Qn = Any atom".
Add unpaired electron—Mark the atom as a radical, and place a dot next to the atom.
Set R group—Mark the atom as an R group. The submenu has items for R1 through R6, and an Rn item to set the index if needed to a value greater than 6. You can label more than one center with the same R group label.

You can add a structure to the User-defined fragments toolbar by holding down Ctrl (⌘) and dragging the structure to the toolbar. If the toolbar is not displayed, choose View → User defined fragments.

Entry creation controls

These controls enable you to create an entry from the structure in the sketcher. When you do so, any "wildcard" atoms or bonds are converted using the first member of the list for the atom or bond.

Replace Workspace button
Create New Entry button
Update Entry button
Replace w/ Workspace button
Convert to 3D option

Replace Workspace button: Replace the Workspace with the sketched structure, as a scratch entry.
Create New Entry button: Click this button to create a project entry from the structure in the drawing area, with the title specified in the Entry title text box. Hydrogens are added to the structure; it is converted to 3D if Convert to 3D is selected.
Update Entry button: Click this button to update the project entry from which the structure was taken with the updated structure in the drawing area. Hydrogens are added to the structure; it is converted to 3D if Convert to 3D is selected.
Replace w/ Workspace button: Replace the contents of the sketcher with the Workspace contents.
Convert to 3D option: Convert the structure to 3D, using LigPrep, when creating an entry. The conversion uses the stereochemical information provided, and produces a single 3D structure. You must have a LigPrep license to use this feature. If you do not select this option, a 2D structure is created, and must be converted to an all-atom, 3D structure to be used by other applications.