The Alloy Tab provides an interface to modify the Alloy definition of your project. If no definition is loaded then this page will be blank, but a new definition can be created from scratch. If a definition is loaded then you should see something like the image below.
Here you can manage your elements, molecules, molecule constituents and mass windows. To select one of the small cards you can right click on it. A white border will be drawn around the currently selected cards.
To create new definitions or delete existing ones you can use the buttons on the left side.
Add Definition opens up the periodic table and allows you to select an element and add it to the list of elements by clicking the add button. Clicking on an element will display the information of the element on the left side of the screen.
Modifying a Card
If you double click a card then a larger card will be shown where you can modify the information as follows:
The large Button contains the symbol of the element. Clicking it allows you to change the element and choose new one from the periodic table. Clicking on the color will allow you to modify the color of that element. The name of an element can be modified as a text Density and radius are 2 more parameters for the element that you can modify. Density should never be 0. To save the changes click OK.
Works in the same way as the Element definitions.
The only difference is that when you click the symbol button you have to manually input the symbol of that molecule
The constituent definition is very simple. The Symbol of the element specifies what element it is. The shift coordinates specify the position of that constituent with regards to the center of the molecule
Mass Window definition
The mass window definition allows to change the element or molecule of that window. Zou can change that by clicking the symbol of the element/molecule. There you can select a new element/molecule from the list of the already defined ones.
The color is the same color of the element/molecule and cannot be changed from here but rather it is changed by modifying the element/molecule. The charge of the mass window can also be changed. The range at the bottom is the minimum and maximum mass that fall into it. Clicking Ok saves the changes.
The last 2 buttons in the left side are Save and Apply.
Save will update the alloy file(.aly) to contain the changes made to the definition so that you can load it at a later project.
The apply button will assign to every event an element based on which mass window their mass falls in. After applying the Composition chart will update to display the concentration of every element. Event that don’t belong to any mass window are considered as noise.
The composition chart also displays what percentage of the non-noise data belongs to every element.