How can I customize metabolic pathways (to look similar to Ariadne metabolic pathways)?

Figure 1 - Ariadne Metabolic Pathway Example

Figure 2: Automatic Layout

Figure 3: Manual Layout with Inflection Points

Figure 4: Changing an Enzyme’s Shape

Figure 5: Changing an Enzyme’s Shape

Figure 6: Applying Styles

Figure 7: Applying Styles

Figure 8: Applying Styles

Figure 9: Changing style of small molecules

Figure 10: Changing style of small molecules

Figure 11: Applying Transparent Appearance

Figure 12: Adjusting Label Sizes

Figure 13 - Finished Chemical Pathway Layout

You can customize the layout of these pathways (Figure 1 - Ariadne Metabolic Pathway Example) you have built by performing the following steps:

Step 1 – Prepare a Chemical Pathway

Use the “Add->Entities” menu to add molecules and enzymes (functional classes) to the network.

You can connect chemical entities as follows:

1.) Select the two entities you want to connect.
2.) Open the “Add” tool. 
3.) Pick Advanced settings
4.) Select “Direct Interactions”
5.) On the Filter Page, select only “Chemical Reactions.”

If additional relationships are added that you don’t want, simply delete them.
See results in Figure 2:  Automatic Layout without Manual Formatting
 

Step 2 – Manual Layout with Default Style Sheets

You can customize the layout of the networks.  For example, click on a line and add or remove an inflection point.  [To add an inflection point, right-click on relation, select Style > Advanced and select Link Shape > line.  Then click and drag relation to create an inflection point.]
You should save your pathway during this process.  In this layout we put the enzymes on top and products on the bottom.  The layout is your choice.
See Figure 3:  Manual Layout with Inflection Points
 
 
Step 3 – Customizing the layout to be similar to Ariadne’s Metabolic Pathways.
You can make the layout similar to Ariadne’s metabolic pathways or choose your own style.  To repeat Ariadne’s style:

Change the Shape of an Enzyme
1.) Right click on an enzyme (which are called functional classes.)
2.) Select style
3.) Pick the rectangle shape.
See Figure 4 and 5:  Changing an Enzyme’s Shape

Apply Style to the other Enzymes
1.) Select the square enzyme.
2.) Click “Style” from the toolbar.

Figure 6 and 7 and 8:  Applying Styles

3.) Now, click on style again,
4.) Then click “Save style to active style sheet”
5.) Then, click “Copy style to all objects of the same type in this pathway.”

Now all the enzymes will be changed.
 
Now, to change the small molecules so that they display names only (no border or colors):

1.) Select a small molecule
2.) Right click and select style.
3.) Click and select “Advanced.”

Figure 9 and 10: Changing style of small molecules

4.) Click the “Border Color”, change it to white.  Do the same with Center Color.   (Border color displayed as Blue in following image.)
 
5.) Repeat the process of copying the style and applying it to the other similar entities.
Figure 11:  Applying Transparent Appearance to Small Molecules

6.) There are many tools to adjust the label size.  Advance scaling of the text is one.

Figure 12:  Adjusting Label Sizes

Conclusion:
In the end, it is easy to layout a chemical pathway using Pathway Studio. 
 
Figure 13 - Finished Chemical Pathway Layout

Next steps:

If you would like to map individual proteins to the functional classes (so you can use the pathways in Gene Set Enrichment Analysis and “Find Pathways/Groups Enriched with Selected Entities”) please review the FAQ:  “How can I add proteins to a functional class?”