Getting Started

Structure and Substructure video

Not all Beilstein and Gmelin substance records include structures. A structure search will eliminate such records. MDL CrossFire Commander 7.0 may be set to use three different structure editors: MDL ISISDraw, MDLDraw, and CrossFire Structure Editor. All UW-Madison Libraries Crossfire 7 pages illustrate MDL CrossFire Structure Editor.

1. Click on OPTIONS in the MDL CrossFire Commander window.
   
2. Select the preferred structure editor.
   
   
3. Select either Beilstein or Gmelin or both databases.
   Note: It is possible to search Beilstein and Gmelin simultaneously. If both databases are selected, only structure, text, and fields common to both databases may be searched.
4. Click on CLEAR to delete a previous structure or fact search.

Basic Procedure

Toolbox:

1. Begin search in the CrossFire Commander window.
2. Click on CLEAR to delete a previous STRUCTURE or FACT search .
3. Double-click in the STRUCTURE window to switch to Structure mode.
4. Click on EDIT in the Toolbox.
5. Draw the structure with the currently active atom (default is C) and bond (default is single), or select one of the ring templates.
6. Click on an existing atom to open the atom dialog box to modify it.
7. Set the number of free sites (default is none) and other specifications.
8. To merge individual structures, select the structure with LASSO or SELECT. Drag the square in the middle of the bond to the target bond or drag the square at the atom node to the target atom. Drag the square at the atom to merge it with another atom.
9. Click on to return to COMMANDER.
10. (Optional) Select STRUCTURE QUERY OPTIONS.
11. Click on START SEARCH.

Drawing Atoms and Bonds

The default view atom view within the Structure and Preaction modes is set to view structures without displaying Carbon when using EDIT. C will only appear when using SELECT. Hydrogen is implied.

Atoms

1. Click on EDIT (pencil) to draw structure(s) and bond(s).
2. Click in the Structure Editor window. The default atom, C, will appear.
3. Place the pencil over the atom. An "A" will appear on top of the pencil.
4. Double-click to open the Atom Attributes window.
5. Select the desired atom or generic group from the drop-down symbol menu or type the element symbol in the Symbol box.
6. (Optional) Set Free Sites to desired number to specify a substructure search,. This will permit substitution at this atom node.
7. (Optional) Set Valency or other attributes.
8. Click on OK.

Bonds

1. Place the pencil over the atom. The "A" will appear.
2. Click-and-drag the pencil to draw a bond.
3. Place the pencil over the bond. A "B" will appear on top of the pencil.
4. Double-click to open the Bond Attributes window. If the bond is unknown, select ANY.
5. Click on OK.
   

Merging Atoms and Bonds

1. Click on SELECT or LASSO.
2. Select the structure to be merged.
3. Drag the atom handle to the target atom to merge atoms or drag the bond handle to the target bond to merge bonds.
   

Predefined Atom Lists and Generic Groups

A substituent can be defined using predefined atoms, predefined groups, user defined atoms, or user defined groups.

1. Double click on an existing atom or draw and double click a new atom to open the Atom Attributes window.
2. Select Generics in the drop-down Symbol menu.
3. Select a predefined atom or group. Place your cursor over the abbreviation to display full name. Refer to Help for group contents.
4. Click on OK.
   

User Defined Atom Lists

Create user defined atom lists to define specific atom substititions.

1. Double click on an existing atom or draw and double click a new atom to open the Atom Attributes window.
2. Select Generics in the drop-down Symbol menu.
3. Choose a number in the Userdefined A drop-down menu (e. g. A1)
4. Click on OK to place the A1 symbol in the structure.
5. Click on An in the Toolbox.
6. Select the correct Atom List Number.
7. Click OK to open a periodic table.
8. Click on the desired elements to define the list.
9. Click on OK to accept the chosen elements.
10. Define additional atom lists in the same query by repeating this procedure for A2, A3 etc.

User Defined Generic Groups (Markush)

Create generic groups to define structure/substructure fragment substituents.

1. Double click on an existing atom to open the Atom Attributes window.
2. Select Generics in the drop-down Symbol menu.
3. Choose a number in the Userdefined G list (e. g. G1)
4. Click on OK to place it in the root structure.
5. Draw the desired structure fragments for the generic group in the Structure Editor.
6. Click on SELECT or LASSO.
7. Lasso or click-and-drag to s elect all the fragments.
8. Click on Gn on the Toolbox
9. Choose the Gn number.

1. Click on EDIT.
2. Place the pencil over the fragment's atom to be attached to the parent structure.
3. Click to open the Atom Attributes window.
4. Click on ATTACHMENTS.
5. Select the appropriate attachment number(s).
6. Click on OK in the Attachment Points window.
7. Click on OK in the Atom Attributes window.

Template Files

Group template files are included with the MDL CrossFire installation. Personal User template files may be created by drawing structures and saving the files in your local template directory.

To access Group or User template files:

1. Click on FILE in the Structure Editor.
2. Click on GROUP TEMPLATE... (for standard structures supplied with database client) or USER TEMPLATE... (created by user). Group template files are located in MDL CrossFire Commander 7.0\group\template . User template files are located in C:\Documents and Settings\username\My Documents\MDL\Commander\template .
3. Select the appropriate directory to view a list of files.
4. Double-click the desired template file to view contents of files.
5. Double-click on the desired structure to place it in the Structure Editor window.

To create a personal User Template file:

1. Draw desired structure in the Structure Editor.
2. Click on FILE.
3. Click on SAVE COPY AS....
4. Select the destination user template .bsd file (or create a new .bsd file).
5. Click on BROWSE.
6. Click on an "Unused" structure box.
7. Click on FILE in the Save INO window.
8. Click on SAVE.

Query Options

1. Select query options in the Commander 7 window.