Using ISIS/Base and ISIS/Draw

Data is initially entered into MACiE using ISIS/Base, a chemical database program by MDL. Eventually, we will obsolete using ISIS/Base, and (quite probably) enter the data directly into the SQL database, but we do not yet have the tools to do this. Thus, the first step in creating an entry in MACiE is to enter it into ISIS. Following are details on this process.

Opening and closing a database in ISIS/Base

To open the database, either use: File > Open Database or Ctrl + O

Figure 1: Opening a database in ISIS/Base

this will take you into a standard file browser, and then you simply need to find the location of your database. As can be seen in Figure 1, recent databases opened are remembered. So instead of browsing the file locations, one can simply select one of the recent databases.

Once the database is open, the data is still not available for editing. To retrieve all the data make sure the Query tab is selected and then select Search > Retrieve All.

Figure 2: Retrieving data in ISIS/Base

Once any changes have been made to the database, press Ctrl + U to update the database and then simply close the program.

Note: ISIS/Base will automatically save itself when changes are made and the user goes onto the next field/entry. It is better to update manually before exiting though, just in case...

The Tabs in ISIS/Base

There are four views of the database in ISIS/Base, and these are accessed through the tabs.

Figure 3: The Tabs in ISIS/Base

Forms - This is the tab in which the database is designed, it displays the various fields available in the database, along with their names. This view should only be used for information, and never altered.

Query - This is query interface. It is also the view that ISIS/Base opens a database with. From here one can either retrieve all the database entries, or perform a search.

Browse - This is interface from which ISIS/Base should most frequently be used. In this tab it is not possible to edit an entry, merely view it.

Update - This is interface from which entries are added and updated. It is important to note that the undo functionality only work before an entry has been updated, and that changing fields automatically updates an entry!

Editing Entries in MACiE

Make sure you are in the Update tab.

To create a new entry, check that the top level ID field is selected and then press Ctrl + k. Entries can also be added by using the Edit pull down menu and the add record option.

Figure 4: Creating a New Entry

To add a new reaction step, make sure you are in the reaction step list, and on the step you wish to add the new step after and then repeat the procedure above. e.g. if you want to add a step between current steps 2 and 3 make sure that step 2 is selected, then press Ctrl + k.

To edit a chemical reaction diagram, simply double click on the diagram already there, or the empty space where a new one is to be. This will open up ISIS/Draw.

Using ISIS/Draw

ISIS/Draw is a sister program to ISIS/Base and the two are very closely linked.

Figure 5: Using ISIS/Draw

There are fifteen buttons down the left hand side of the drawing interface. In all cases, holding the left button of the mouse down whilst hovering over the button will produce more options and more detailed instructions on the use of the tool. The Tools most commonly used are:

	Select tool. This is the selection option, and holding down the left mouse button over this button will produce three options, the lasso select tool, which is a freehand selection option, the normal select tool, which selects everything within a square or rectangular frame, and finally, the molecule select tool
	2D rotate tool. This rotates the selected molecules, or drawing frame, in 2-dimensions.
	Eraser tool
	Atom tool. This is the tool used to change an atom from the default (carbon) to another type. Some care should be used with this tool, any text typed in the options box will be considered an atom!
	Bond tool. This defaults to the Singe Bond, other options are the double bond and triple bond. The default atom types for this bond are carbon.
	Stereochemical bond tool. The default is the Down bond, other options include the up wedge, down wedge, either up or down bond, up bond and down bond. Again, the default atom types for this bond are carbon.
	Plus tool. This is only used in MACiE for the overall reaction, and only very rarely in the reaction steps. It helps the software recognise a chemical reaction.
	Arrow tool. This is the tool that produces reaction arrows. Care must be taken when choosing a reaction arrow, as not all are valid for creating a reaction. The default arrow is valid and this arrow should be used for entering reactions into MACiE.
	Atom-Atom map tool. This is used to map atoms between either side of a reaction arrow. The other option is the de-map tool. To map, select the atom you wish to start at, then select the atom to which it maps. If a mistake is made, hold the atom-atom mapping tool down and select the button which looks like a number 1 with a diagonal line through it. This is the de-mapping tool, then drag the cursor over the atoms for which you wish to undo the mapping.

There are further buttons across the top of the drawing window. Again, holding the left button of the mouse down whilst hovering over the button will produce more options and more detailed instructions on the use of the tool. The tools most commonly used are:

	ISIS/Base Transfer. Transfers the current contents of the drawing window to ISIS/Base.
	Run Chem Inspector. Runs ISIS/Draw's chemical inspector, which checks for chemical sense in the reaction entered.
	Open Last Template. Opens the last template used in ISIS/Draw.
Common Templates

Finally, there is a pull down menu at the top of the drawing window.

Figure 6: ISIS/Draw transfer menu

This menu selects the destination of the transfer button, and there are three basic options, the query interface, the browse interface and the update interface. In MACiE, only the query and update options are used.

Creating a reaction diagram with ISIS/Draw

There are two types of reaction in MACiE, the overall and the step reaction, and both are drawn in ISIS slightly differently, following are the protocols for drawing both of these reactions in MACiE.

The Overall Reaction

The overall reaction is a simple chemical representation of the overall chemical transformation, it does not include any of the apparatus brought to the reaction by the enzyme, and should be the same as the chemical reaction described by the Enzyme Commission.

Figure 7: Example of a MACiE overall reaction in ISIS/Draw

In this reaction type, the Plus Tool is used to separate the different molecules on the reactant and product side of the reaction arrow (added using the reaction arrow tool).

The Reaction Step

There are two differences with editing a reaction step compared to an overall reaction, firstly, the reaction step contains amino acid residues and cofactors as well as the overall reactants and products.

Amino acid residues are treated differently from normal atoms. When we include an amino acid residue in the chemical diagram only the functional portion is included. A single atom is then designated to hold the label identifying the amino acid (this should be an R group, unless the residue contains multiple locations, which which case the atom should be the alpha-carbon). Then from the Chemistry pull down menu go to Residue, and then Create. This will open a dialogue box to name the residue, which is named by the three letter code and residue number.

Figure 8: Creating an amino acid residue

It should be noted that if the residue comes from a different chain to the rest of the amino acid residues this is denoted in the name by the chain identifier. Cofactors are treated in the same manner. A cofactor should, wherever possible, be names from the HET group code found in the PDB file.

The second main difference between the overall reaction and the reaction steps is that the reaction step does not contain distinct molecules. So once you have drawn the chemical reaction, in order for the reaction to be correctly transferred from ISIS/Draw to ISIS/base the following must be done:

1. Group all the reactant molecules together. To do this, select the lasso tool, select all the reactant molecule, then press Ctrl + G or select Object > Group.

   
   
   
   Figure 9: Grouping the reactant molecules

2. Repeat the first process for all the product molecules together
3. Click on the transfer button in the top left hand corner (next to the pull down box under the File, Edit, etc. menus) to upload the changes to ISIS/Base.

Querying Entries in MACiE

Make sure you are in the Query tab.

There are two basic types of query, the chemical query, and the text query. With the chemical query, simply double click upon a field that allows for a chemical structure. This will take you into ISIS/Draw, draw your query molecule and then transfer back to ISIS/Base. Once the query is entered into ISIS/Base, from the Search pull down menu, select the By Form option.

Figure 10: Querying MACiE

The text field query is run in the same way, but instead of a chemical formula, a text string is entered. Partial string matches should be entered as like %text string% (see Figure 10 above) otherwise no results will be returned. Exact string matches, e.g. PDB codes, can be entered without the like and percent signs.

Exporting From ISIS

Make sure you are in the Browse tab.

Once you have finished entering data into ISIS/Base, the database must be exported. There are two file types that are exported, the RDFile (all the text fields in the database) and the RXN file (the chemical reactions in the database). The export process should always be done from the Browse tab in ISIS.

To export the RDFile:

1. Select File > Export > RDFile... This will pull up a dialogue box.

   
   
   Figure 11: Opening the RDFile export dialogue box

2. Select the ROOT level of the tree to then click on ADD to add all the data fields in the database

   
   
   Figure 12: The RDFile export dialogue box

3. Click on OK and then save the file.

To export the RXN files:

1. Select the reaction you want to export
2. > Select File > Export > REACCS RxnFile

   
   
   Figure 13: Exporting an RXN file

3. Make sure you name the RXN File correctly using either the unique identifier for the overall reaction, or the step id for the reaction step.
4. Save the file