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How to save a collection

Compound collections are named lists of molecules that you can use to identify libraries, or to perform complex queries around sets of molecules. This article goes over building collections from search results, import validation report, and one molecule at a time.


There are several ways to add molecules to collections. The most common way is to start with search results.

From search results

After you run a search either based on one parameter or multi-parameter from search engine, a table of search results is displayed at the bottom. Notice the green check-boxes running down the left side of the structures in the results table. The check-boxes are checked by default which includes all of the displayed molecules in your view. Unselecting a check-box predictably excludes the molecule from the selection. This selection mechanism is used by all of the tools in the result table tool-bar: in the below screen-shot, a total of 2 results was returned by the search, and the first molecule was unselected, leaving 1 molecule in the selection to be plotted, exported or added to a collection.

You can append molecules to an existing collection, or start a new collection.



Append to an existing collection:

If you are adding new molecules to an established collection, for example adding newly synthesized analogs to a particular series of compounds, choose the "existing collection" option, and select it from the drop-down list. Since only new molecules are added to a collection, any duplicates will be excluded. You need “Full Access” role or higher to add new molecules to a collection created by another user. Molecules are never subtracted or removed when this option is used, but keep reading about new collections to learn how to subtract molecules.


Start a new collection:

Enter a name for your new collection, and select which project it will be associated with - this collection will be accessible to all project members. Project association for collections is mandatory, just like for all other data in the CDD Vault, unless you choose to make the collection private. Once you've saved a collection to a project, you will see an option to share it with your colleagues: when you click on the link in the green status bar above the results table, you will be able to create a message and e-mail notifications with a hyperlink to the new collection.


If you enter a name of a collection that already exists, you will be asked whether or not you are trying to overwrite an existing collection. If you choose to overwrite, the list of molecules will be replaced rather than appended, or you may choose another name for your new collection. This is the main mechanism to remove molecules from an existing collection.

From the validation report after import

After each file is imported, the validation report offers a short-cut to "Explore imported data".


The same shortcut is available from the list of previously imported files on the Import tab.


Both of these handy links will load all results from the file on the search page, including any protocol data and a temporary collection of all molecules in the file. If all of them belong to the same collection, this is the quickest way to save a permanent copy.

One molecule at a time

If you wish to associate (or remove) a single molecule to a collection, you may do so directly from the molecule details page. There is a shortcut underneath the structure, and a "Collections" tab where you may manage this molecule's membership in all collections. When you click on the "remove" link, you are not deleting a collection, or a molecule, you are simply removing the name of that molecule from the collection list.


From Visualization

You can create a collection from the selected molecules in visualization.  Once you have the molecules you want, simply click the plus (+) sign above toolbar.  This will bring up a dialog box where you can either create a new collection or add the molecules to an existing collection.  If you want to create a new collection to share with project members, enter the name you what for the collection and select the project.  To create a new collection for yourself, enter the name you what for the collection and check the box next to Save as a private collection.  To add molecules to an existing collection, select the appropriate collection from the pick list.