Macs in Chemistry

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Updated

The latest version of iBabel can be found here

This is an old page please use the link above.

iBabel Update

This is an updated version of iBabel, the key new feature is the ability to get the structures corresponding to CAS Numbers from PubChem. It uses the Entrez Programming Utilities (eUtils). If it proves useful I can look at adding further search facilities using PubChem.

On the viewer tab there is a new button "CAS" click this and....

a dialog box opens, to look at a single structure type in the CAS Number and click on the button "Get CAS”.

You can also choose a file containing CAS Numbers but please look at the PubChem guidelines before you do so. In particular

”Do not overload NCBI's systems. Users intending to send numerous queries and/or retrieve large numbers of records from Entrez should comply with the following: Run retrieval scripts on weekends or between 9 pm and 5 am Eastern Time weekdays for any series of more than 100 requests."

After about 10 seconds (depending on network speeds and server load) the SMILES string for the structure will be downloaded to your desktop and the "Input file" text box will be filled. Click on the "Import" button.

And the structure will be imported into the table, now click on the entry in the table and the structure will be displayed.

A few important notes, to display the structure you will need either the Marvin java applet from ChemAxon or ChemDraw from Cambridgesoft.

Due to Java security restrictions the Marvin folder must be in the same folder hierarchy as the folder containing the structures to be displayed as shown below (or a similar relative location in your user folder).

Look at the iBabel3 page for the latest news.