It can be downloaded from here (24MB), this version requires Mac OS X 10.6 or higher and OpenBabel 2.3
Much will seem familiar to previous users of iBabel and the screenshots of the old version give a good overview of the capabilities, whilst the images below highlight a few of the new features.
The “Add title and index” option appends a title (default is Mol, but you can edit this in the adjacent text box) and an index number to multi-molecular files, e.g. Mol 1, Mol 2, Mol 3 etc. This is essential if you want to search files displayed in the “Viewer” since you need a unique identifier for each structure. In many cases the molecules will already have a molecule id.
Another new feature with OpenBabel 2.3 is the ability to generate 2D and 3D coordinates.
Perhaps the biggest changes have come with the “Viewer”, by storing the table data in an array we can use some of the cool ObjC functions such as the continuously updating selection count and the live searching of the “Name” text field. To import records identify the input file using the input button and then click the “Import” button.
The buttons highlighted in green allow the user to delete the highlighted row, delete all the “Selected” rows or clear all records completely. The selection can be modified using the buttons highlighted in pale blue.
For the other viewers, JMOL/JChemPaint are in the application bundle. ChemBioDraw needs to be in the Application folder but only works on some machines (something to do with only supporting 32-bit which I think we will have to wait for CambridgeSoft to address). Because of Java security issues Marvin has to be in the same file structure as the htm page, I think you only need to put an alias to Marvin in the Macintosh HD:Public folder or User:Public folder. the 2D and 3D radio buttons allow you to choose an appropriate display.
It also support JME as the editor but you need to get a copy from Peter Ertl directly and put it in the Public folder.
The PChem button pulls structures from PubChem, this can either be a single structure of a list (here is an example caslist.txt you can download to try).
As you can see the list contains a mixture of systematic names, trivial names, drug names and CAS numbers but the smart people at PubChem sort all that out nicely.
The result is two files on your output.smi which contains the successful searches and NoStructure.txt which contains cases where no structure was found. You can then import the file to view the structures.
I’d be delighted to hear of any bugs (honest) any suggestions for how iBabel might be improved.
There are a number Safari Extensions described on this site that access similar services and with the help of Matt I'm happy to anounce a new addition.
The Safari Extension for Opsin (download) allows the user to highlight a chemical name in a web page and then control click affords a dropdown menu, click on "Display ... using Opsin" and a small window will open displaying the chemical structure. What is particularly nice is that in addition to providing the structure in png format the same web service also provides the chemical structure in SMILES, InChi and CML format. If you click one of the buttons and the bottom of the structure window the structure will be downloaded in the appropriate format. You can read more about this extension here.
There is a full listing of the Safari Extensions here.
However I’ve just been sent an email from Amazon suggesting they will be having four days of sales starting from Nov 22, so now we have a Amazon Black Friday Week I guess that is inflation for you.
According to the email there will be up to 60% off Nintendo Wii Consoles it might be worth having a browse around next week.
iResearch was created to allow the user to read American Institute of Physics article content offline and store articles locally. The application caches all content that it receives, and does require a wireless or wifi connection to obtain the content initially and to subsequently update that content.
FieldView provides a richer more informative view of how molecules are likely to behave in biological systems.
FieldView enables you to load your structures from SDF and MOL2 files as well as showing results from all Cresset applications. You can import and compare up to 10,000 compounds at once or copy and paste them into FieldView from your favourite drawing package.
Using FieldView you will be able to:
- Create and modify structures using the in-built molecular editor
- Automatically convert structures from 2D to a minimized 3D conformation
- Clone and compare molecules side by side or overlaid using Cresset's unique Field technology
- Understand how a compound’s activity, ADME and toxicity properties vary with their molecular Fields
- View virtual screening results, such as those from FieldScreen, comparing 2D structures with a 3D overlay showing all the Fields of every ligand
- Filter molecules based on the exact mix of properties you need
It is excellent we now have FieldView available on the Mac platform, I’d urge all chemists or biologists to download it and give it a trial.
The structure is displayed in a larger window as shown below. Clicking the “Save” button downloads the structure in .mol format.
Back to list of extensions
A selection of extensions that should be useful for chemists.
Chemspider :- Displays structure of highlighted chemical/drug and links to ChemSpider page.
PubChem :- Search PubChem for the highlighted compound
eMolecules :- Search eMolecules for the highlighted compound
Chemicalize :- Submit the current URL to chemicalize.org
DrugBank :- Search DrugBank for the highlighted compound
Unfortunately I don’t have ChemBiodraw 11 (or earlier versions) so I can’t explore the problem but perhaps it might be possible to offer a work around using Applescript. Read More...