Displays activated viewer for the Query Attributes, which displays
the attributes for a node or bond at the current cursor position.
The display changes as the cursor is moved over different nodes
Allows you to improve the appearance of rings or chains drawn
freehand. If you do not like the appearance of the smoothed
structure use the Undo command.
Enlarges and centers the drawing on the screen. If the structure
expands out of the current viewing port, use the scroll bars to
view it. One or more discrete fragments can be selectively
expanded. Use the Selection tool to select the fragment(s)
before using the Expand option.
Reduces the size of the drawing on your screen and centers it.
One or more discrete fragments can be selectively contracted.
Use the Selection tool to select the fragment(s) before using the
Displays a shortcut in its reverse form. For example, an "OH"
group with a horizontal bond extending to the right is usually
drawn as "HO". Select the shortcut to be reversed then select
Reverse Shortcut from the Display menu. Where possible, the
bond is drawn to the relevant node in the shortcut.
Rotates a structure about an atom or bond on the screen. Select
the structure or fragment that you want to rotate. Then choose
Rotate command. The cursor changes displaying a curved
arrow around a dot which shows the direction of rotation. Click
and move the cursor in a clockwise or counter clockwise
direction. The fragment will be rotated in that direction about a
Makes a left-right rotation of a structural fragment through 180
degrees. The structure is rotated about a vertical axis creating a
Makes an up-down rotation of a structural fragment through 180
degrees. The structure is rotated about a horizontal axis creating
a mirror image.
Show a grid in the structure drawing window.
Snap to Grid
Select a set of nodes or a fragment, then use this command to
snap the nodes to the nearest grid position.
Select a set of bonds or a fragment and use this command to
snap the bonds to the nearest compass position.
Structure Drawing Menus
Window Menu in Structure Drawing
Several query structures can be open at the same time. Each open file is displayed
in a separate window; the open windows can be tiled, cascaded, or displayed as
icons. All open windows are listed in the Window Menu. The current window is
checked. The Window Menu provides options for the appearance of structure
How it works
Causes all open windows to be
cascaded, with the current window on
top. Clicking on any window in the
cascade makes it the active window
and brings it to the top of the cascade.
Causes all open windows to be tiled
horizontally so that several queries can
be displayed and modified
simultaneously, e.g., fragments can be
copied and pasted between windows.
Causes all open windows to be tiled
horizontally or vertically
This option becomes active when an
open window has been minimized.
Each open window can be minimized
(displayed as an icon) by clicking on
the down arrow on the header bar of
that window. The down arrow is
displayed only when windows have
been cascaded or tiled. Arrange Icons
displays all open window icons at the
bottom left of the drawing screen.
Click, hold and drag on an icon to
move it. Click once on an icon and
then on the Restore option to redisplay
the window in either its tiled or
cascaded form. The Maximize option
maximizes that window so that it fills
the structure drawing screen.
Closes all open drawing windows.
Drawing a Reaction Query
To draw a reaction query:
1. Open the Structure Drawing window by clicking on the Prepare Query button
on the Main Menu Toolbar or selecting Prepare Structure Query from the
2. Click the Reaction (Rxn) button on the Structure Drawing Toolbar or select
Show Reactions from the Display menu. The Structure Drawing window is
displayed in Reaction mode, and the Reaction Drawing tools are activated on
the Tool Palette:
Reaction Arrow tool - to set up a chemical reaction between structures
Reaction Role tool - to specify the roles of the participants in a reaction
Reaction Site Tool - to specify a reaction site label for a specific bond
Atom Mapping Tool - to specify a correspondence between atoms in the
reactant and atoms in the product
Using Functional Groups in a Reaction Query
To use Functional Groups in a Reaction Query:
1. Open a new window by selecting New/Standard from the Structure Drawing
File menu or clicking the New/Standard button located on the Toolbar.
2. Click the Functional Group button on the Toolbar in the new Structure
Drawing window. The following reaction drawing tools and the functional
group drawing tools on the bottom of the Tool Palette are activated:
OR tool for Functional Groups
Creating WPI structures
To create a structure for searching in the WPI databases:
1. Create a structure in the Structure Drawing window and save it as a standard
structure. The .str extension is automatically applied, e.g., pyraz.str.
2. Open the standard structure in the Structure Drawing window. In the Open
Query dialog box click WPI under Convert to and click Open. The structure
is displayed in the Structure Drawing window and is identified as a WPI
structure, e.g., pyraz.str *WPI.*
3. To insert superatoms into a WPI structure, select Ring Superatoms, Chain
Superatoms, or Other Superatoms from the Draw menu and make your
To include non-structural codes and sugar codes for your WPI Fragmentation code
1. Select Include WPI Other Code Concepts from the Query menu.
2. Select the codes you want by clicking Select Codes, then on the appropriate
descriptor(s) from the menus. Selected codes appear in the lower window,
with the definitions in the upper window. To combine codes using Boolean
AND or OR, click on the menu heading to toggle between them. Use Delete
Last or Delete All to erase your selection.
3. Select Leave OCC or minimize the OCC window to return to the main STN
Express menu. If you have not yet drawn your structure, you can do it now;
the selected non-structural codes will remain active. When you have drawn
and saved your structure, leave structure drawing and return to the main STN
To generate WPI fragmentation code strategy from your structure, select Generate
WPI Strategy from the Query main menu.
Ring Superatoms for WPI Queries
To use Ring Superatoms:
Select Ring Superatoms from the Draw menu in order to insert a ring
superatom into a WPI structure query only.
In the Ring Superatoms dialog box, click the button next to one of the
Click Single Use or Multiple Use.
Insert the ring superatom at the desired location in your structure.
Options for Ring Superatoms are:
CYC: Cycloaliphatic - Carbocyclic, optionally fused
ARY: Aryl-Carbocyclic, optionally fused, containing at least one
HEA: Heterocyclic - Aromatic, Monocyclic (5 or 6 ring atoms)
HET: Heterocyclic - Non-aromatic, Monocyclic
HEF: Heterocyclic - Fused, optionally aromatic
HEO: Heterocyclic - containing metal, halogen, or B, Si, P, or As
Other Superatoms for WPI Queries
To use Other Superatoms:
1. Select Other Superatoms to insert a superatom other than a chain or a ring
superatom into a WPI structure query.
2. Click the radio button next to one of the "other" superatoms in the Other
Superatoms dialog box.
3. Click Single Use or Multiple Use.
Options for Other Superatoms are:
AMX: Alkali (ne Earth) Metal
A35: Group IIIVa Metal - Al, Ga, In, Tl, Ge, Sn, Pb, Sb, Bi
TRM: Transition Metals excluding Lanthanum
LAN: Lanthanide (including Lanthanum)
ACT: Actinide (including Actinium)
MX: Metal, any
TX: O, S, Se, Te
UX: O, S, Se, Te, N
ZX: B, Si, P, As
TM1: First series transition metals
TM2: Second series transition metals
TM3: Third series transition metals
Other Code Concepts for WPI Queries
The Other Code Concepts in the STN Express Query menu is used to include non-
structural codes and sugar codes in your Fragmentation code strategy. These codes
can be selected before or after drawing your structure, by choosing the Include WPI
Other Code Concepts from the STN Express Query menu.
To use Other Code Concepts:
1. Select the codes you want by clicking Select Codes. On the appropriate
descriptor(s) from the menus selected codes appear in the lower window,
with the definitions in the upper window.
2. Codes can be combined using Boolean AND or OR. Click on the menu
heading to toggle between them. Use Delete Last or Delete All to erase
your selection. It is not possible to select truncated codes directly, but you
can include them by selecting a specific code, generating the strategy, and
then editing the strategy.
3. When you have finished selecting codes, select Leave OCC or minimize the
OCC window. This returns you to the main STN Express menu. (If you have
not yet drawn your structure, do so now - the selected non-structural codes
will remain active. When you have drawn and saved your structure, leave
structure drawing and return to the main STN Express menus.)
4. Select Generate WPI Codes from the Query menu, and select the name of
the saved structure. Click in the checkbox labeled Include, to mark it with an
x, and click on Generate. The selected non-structural codes will be included
in your strategy.
Documents you may be interested
Documents you may be interested