The Quick Reference Guide (Commander Version 2.1 and higher)

1 Starting CrossFire

Open the Commander from any platform you are using Select from the menu Application: CrossFire or click the -button Fill in the login-box See 5.2 in this guide for problems with the login procedure

1.1 General Settings

Database: The name of the loaded database is displayed in the listbox; other databases can be chosen here if there are any available

Context: The display mode of hits can be chosen from the listbox:

• Substances: The hitset is displayed as substances
• Reactions: The hitset is displayed as reactions
• Citations: The hitset is displayed as references

The default is Automatic Context Selection (menu Options); e. g. the display context is chosen by the kind of search that is performed, but you can change the context manually.

The target display context has to be chosen before performing a search!

1.2 Searching Procedure

• Starting a search is only possible from the Commander!
• From all other tasks (Structure or Fact Editor, Display Hits) switch to the Commander using the -button or the F7-key
• To start a search within the Commander click the -button or use the F7-key

1.3 Opening the Structure or Fact Editor

• Choose from the menu Task: Structure Editor or Fact Editor

or

• Double click on either Fact or Structure Editor window

or

• Click the task function bar buttons (Structure Editor) or (Fact Editor)

2 Structure Editor

Windows-type Menu Atom, bond and template buttons Short-cut buttons for some features of the Menu Toolbox Keys: edit select lasso erase rotate magnify reduce

2.1 Drawing/Editing Atoms

• Activate the edit tool and choose one of the atom buttons (Function Bar)
• Draw the structure with the currently active atom (and bond)
• Click on an already existing atom to open the atom dialog box to change it (edit mode)

Atom buttons

Further choice of atoms as well as generic groups:

Atoms: H, F, Cl, Br Atom lists: A (any atom), M (any metal), X (any halogen) Elements...: Opens periodic table from which you can choose any atom Generics...: Opens table of generics from which you can choose predefined atom lists, predefined generic groups, user-defined atom lists An and user-defined generic groups Gn (see 2.8 and 2.9)

2.2 Drawing/Editing Bonds

• Activate the edit tool and choose one of the bond buttons
• Draw the structure with the currently active bond (and atom)
• Click on an already existing bond to open the bond dialog box to change it (edit mode)

Bond buttons: single, double, triple

Further choice of bonds:

Drawing steric bonds (up , down ) for stereogenic atoms Defining Z/E-isomers (double steric ) for double bonds Allowing groups of bonds (any , double/triple , steric unknown ) Selecting user-defined bonds

Stereo information will only be taken into account in a search if the Structure Query Options (see 2.7) have been set to absolute stereo search

2.3 Drawing Rings

Clicking one of the -buttons pastes the corresponding ring into the structure window

Annelated rings: drag the square in the middle of the bond to the bond you want to fuse Spiro-fused compounds: drag the square at the atom to merge it to another atom

2.4 Template Files

Template files contain pre-defined molecules, substructures as well as functional groups

1. Choose from the menu File; Template... and select a template file
2. You can view the contents by using the browse-button, but you cannot pick a molecule and paste it in the structure window from this menu
3. Use the template button to browse the chosen template file and select the desired (sub)structure by double click

2.5 Functional Groups

Make sure you follow the structure conventions used in the Beilstein database (see manual); if you are not sure how to draw a functional group choose it from the template file "residue.bsd".

2.6 Setting Atom Attributes (individual attributes)

On clicking at an atom (edit mode) an atom dialog box appears; further atom specifications such as number of free sites, charges, radicals, exact mass, set attachment points etc. can be defined.

You can allow or exclude isotopes (apart from D and T) and set or delete maximum free sites after selecting the atom(s) within the menu Query

2.7 Structure Query Options (global attributes)

Options which will be taken into account for the whole structure query can be set

• in the Structure Editor from the menu Query or
• in the Commander by opening the dialog box with the Options...-button (hereby you can use those options for drawings imported from other structure editors such as ISIS)

These options define if stereochemistry is taken into account and if tautomers etc. are allowed.

2.8 Creating User-defined Generic Groups

1. Choose from the atom box : Generics... , and select a number
2. Place the G_n-atom symbol in the structure you are drawing
3. Draw the desired fragments for the generic group and select those fragments
4. Press the -button and choose the number of the generic group

For fragments containing more than one atom you have to set attachment points:

1. Click at that atom of the fragment by which it is to be attached to the parent structure (edit mode)
2. Press the Attachments...-button in the atom dialog box
3. Click the appropriate number(s)
4. While defining a generic group the attachment points in the parent structure are displayed; otherwise they are not visible

To define a frequency click at the [Gn]:-symbol marking the generic group (edit mode) (see manual for details)

2.9 Creating User-defined Atom Groups

1. Choose from the atom menu : Generics... and select a number
2. Place the A_n-atom symbol in the structure you are drawing
3. Press the -button and select the number of the atom group
4. Choose the desired atoms from the periodic table appearing on the screen

2.10 Generics: Tips & Tricks

You can always edit and delete structures within a Gn-group or add further structures

To see the definitions of the pre-defined generic groups listed in the table use the help button and select "pre-defined generic groups" to view the hierarchical order

The pre-defined generic groups except G and G* can only have one bond to the parent structure whereas user-defined generic groups and atom lists can have more than one bond

2.11 Reaction Attributes

First draw the molecules in the structure edit mode, then switch to reaction edit mode by using the -button or choose from the menu Editmode: Reaction.

The function bar changes to allow reaction role setting and the select mode is activated.

Select a molecule and press the /-buttons to define its role as reactant or product

• You can define one or more reactants and one or more products
• You can also define only reactant(s) or product(s), so-called "half-reactions"

2.12 Further Reaction Attributes (optional)

Mapping: links corresponding atoms in the reactant(s) and product(s) respectively by drawing a dashed line between them in the same way a chemical bond usually is drawn

Reaction centre: defines that a reaction must take place (or must not take place) at a particular atom

Bond change: defines if and how a particular bond is altered during the reaction

Those reaction attributes are set in the edit mode by clicking at the atom or bond (reaction mode)

Use the -button to delete product and reactant definitions

Use the -button to delete all the mappings

Change the structure of the molecules taking part in the reaction by switching to the structure edit mode with the -button or selecting Editmode: Structure from the menu.

2.13 Special Hot Keys (Structure Editor)

	Shift + Click (edit mode): replaces an exsisting atom or bond by the one currently active
	Shift + Drag (select mode): copies the selected structure

3 Fact Editor

3.1 Field Name

Fill in the code of the field you want to search for:

• Type the codes directly into the field or
• Pick them from the data structure, which can be opened by the -button or F2-key. Select the appropriate field code by double click.
• You can search for a special field name by using the Find-button and typing the name of the desired property or attribute in the "Expand Field Names" dialog box

3.2 Field Value

Fill in the search term(s) (e. g. values, keywords, phrases) you are looking for:

• You can fill in ranges or use "<" and ">"-operators when looking for numerical values
• You can use truncation when you look for text ("*" for any number of letters, "?" for exactly one letter); you can truncate at the beginning, middle or end of the word
• You can see a list of field values (index of all entries in this field) by the -button or F2-key

3.3 Operators

Use the logical operators proximity, and , not, or to combine fact queries:

• Proximity means that the search terms have to appear in the same field (see manual for details)
• Hierarchical order of the operators: proximity > and, not > or
• If you want to combine fact queries in another order use parentheses
• The parentheses appear as a "+" in front of the operator in the fact editor table (but within the fact editor window in the commander they are shown as parentheses).

	If you use the "expand"-function by clicking the -button or F2-key, make sure the cursor is placed in the field you want to expand
	The F3-key opens a window where you can type in the query

3.4 Special Hot Keys (Fact Editor)

Ctrl + X	Cut Query	cuts the whole fact query
Ctrl + C	Copy Query	copies the whole fact query
Shift + Del	Cut Selection	cuts the field selected previously
Ctrl + Ins	Copy Selection	copies the field selected previously
Ctrl + V	Paste	caution: pasting a whole query will delete the lines written previously
Ctrl + D	Delete All	deletes the whole fact query
Ctrl + L or	Delete Line	deletes the single fact query line the cursor is placed in

4 Display Hits

After performing a search open the Display Hits-Window by the -button

4.1 Customising the Display of the Hits with the View-Menu

Short/Full-Display (-button): changes between full and short display

Full display: each hit in its own window

Short display: within one window up to sixteen hits are shown (see Options-menu 4.2)

Customization of the Hit Display applies to printing

Field Availability (-button): opens an additional window which shows the names and codes of all available fields including the number of occurences of each field for the current hit; you can browse the list and select a field by double click for immediate positioning in the main document.

Highlight Hit: highlights the data or (sub)structures that have been searched for

Include structure (-button): shows structures of the reactant(s) and product(s) for each displayed reaction as thumbnail sketches

Include Field Availability: displays a table of all available fields after the IDE-data for each hit

Preparation: Displays only those reactions in which the title compound is product of the reaction (applies only to graphical reactions)

Structure (-button): shows or hides an additional window with the molecular structure for each hit

4.2 Change Settings with the Options-Menu

Select Short Rows and Columns: changes the number of hits within the short display; up to four rows and columns can be selected independently (this has no effect on the Short Display in citation context)

Define User View: Sets a user-defined filter for the display of the hits; the fields can be selected and combined freely from the data structure displayed in the user view window

"Define User View" does not automatically activate it (see View-menu)

4.3 Browsing the Hitset (Short Cuts)

Menu Edit: Go to hit	Button	Hot Keys
First Hit		Ctrl + Home
Previous Hit		Ctrl + PgUp
Next Hit		Ctrl + PgDown
Last Hit		Ctrl + End
Select Hit Number		Alt + S

You can select and copy both structure and facts from the Display Hits and paste it into the Structure or Fact Editor where you can change and modify it to submit a new query. You can also paste it into any other application.

5 Special Features

5.1 The File Menu (Loading, Saving, Printing...)

The menu File always refers to the task which is currently active

If you choose Print within the Commander, the current query will be printed; within the Structure Editor the molecule(s) drawn there will be printed and within the Display Hits window you will get a printout of the data displayed.

The same applies to the Save-command; saving within the Structure Editor saves a copy of the structure currently drawn, within the Commander the query (both structure and fact) will be saved and in the Display Hit window the current hitset is saved.

	A hitset cannot be saved locally on the disk, it is always saved on the server. It is only valid for a current update of the database.
	Queries are best saved from the Commander rather than from the Fact or Structure Editor

The current session is captured automatically as long as you are logged in. You can view former queries and hitsets by using the Hitset- or History-command:

History...: opens a window that contains all submitted queries, where you can browse and pick queries you want to use again.

Hitset...: opens a similar window with all retrieved hitsets

• From the Structure or Fact Editor you can use History... to browse and pick a formerly submitted query.
• Within Display Hits you can use Open Hitset... to browse all hitsets of the current session and load a hitset again by double click.
• From the Commander you can view either Hitset... or History... but you can only load the queries into the Commander and not the corresponding hitsets.

	The command New should never be used within the Structure or Fact Editor!
	The command New within the Fact or Structure Editor opens a new window of the same application, but it is not connected to the Commander; the information stored there will not be transferred to the Commander.

5.2 The Options Menu

The Menu Options also refers only to the currently active task (e. g. Commander, Structure or Fact Editor, Display Hits) and you can define different settings for each:

Molecule View...: the display mode of structures can be set for each application

Save Settings on Exit: can be enabled or disabled for each application independently

Connections...(only in Commander): shows the address of and the connections to the CrossFire server; these should be checked if problems with the login-procedure occur