Molecules 1.3 submitted for review

Molecules icon

Earlier today, I submitted version 1.3 of Molecules for review in the iTunes App Store. The major new feature that this version adds is the ability to download custom molecular structures. For those of you who can't wait, the source code has been updated .

I apologize for the delay in providing a new version. I'm working on a new iPhone application that I hope to unveil within the next couple weeks and it is taking most of my available time.

One of the features that I get constant requests for in Molecules is the ability to download custom molecular structures, or at least ones not in the database at the Protein Data Bank. This version adds two ways of getting those structures onto your iPhone / iPod: clicking on a specially-formatted link in Mail or Safari, or navigating to the file using an embedded web browser.


The custom URL method requires the least typing on the iPhone, because you don't have to manually enter in an address. First, you'll need to place your custom molecule on a web server that your iPhone or iPod can access. Second, you'll need to create a specially formatted URL like the following: molecules:// This URL is the same address you would use to download your molecule file normally, only the http:// portion has been replaced by molecules://. Finally, you'll need to either place this URL on a web page or email it to yourself (when emailing, you'll need to enclose the URL in brackets). If you've installed Molecules on your device, either go to the page in Safari and click on the link (you can try this on the link above) or click on the link in the message in Mail. Molecules will automatically open, download, and render your custom molecule structure.

You can also direct Molecules to download this custom file from within the application. When you go to "Download new molecules", you now can choose to either search the Protein Data Bank or download from a custom location. If you select the custom location, a blank view will appear with a text bar at the top. Either manually enter the address of the file or type in a web page from which the file is accessible. The view on this screen is a web browser, and any molecule file that you click on in this view will be automatically downloaded to the device.

A great place to try this out is by visiting the site of the Institute for Molecular Manufacturing at The Institute has funded work into proper nanotechnology (before that term became a buzzword and was slapped onto everything) and has many models of simple molecular machines, designed from the atoms up. The model I link to above (also with the spacefilling rendering to the right) is for a pump that only allows neon atoms to flow through the center channel, designed by Dr. K. Eric Drexler. More models can be found in their research section. Seriously, take some time to read up on the work they've done. It's awesome. I have a copy of Nanosystems near my desk right now.

Currently, only PDB formatted text structure files (and Gzipped PDB files) are supported. I plan on adding support for more formats soon.

This is still not as easy a process as I would like, so I plan on releasing a desktop version of Molecules that will be able to sync structures to the portable client. I just wanted to make sure that I got a version with some custom structure support in time for the American Geophysical Union meeting that some users will be attending.

I'd like to thank Olivier Kaluzny for going through the code, adding localization hooks, and providing a complete French localization for Molecules. Unfortunately, I added a few words here and there, so 1.3 isn't completely French-localized. I realized this after I submitted the application, so I'll try to fix it for a later version.

Again, I'm sorry that work on this has been slow lately and may continue to be slow for the next month. As I indicated earlier, I'm working on a significant new iPhone application that I hope to release by early December and that's taking up most of my time.


I really like Molecules and I have lots of feature requests that would make it much, much more useful for my students.

I listed them here:

And, if it helps, I know Cn3D is open source. Cn3D is available here:

thanks for making such a fun program!

I just posted a comment on the AppStore today.
What impresses me most is that, when I graduated (20 years ago ...), the top level Silicon Graphics was not able to display proteins like the iPhone can now with this tiny beautiful peace of software..
Of course I have many requests, but I will limit my comments at Congratulations !
Nice job

Very best regards


Of course I have many requests, but I will limit my comments at Congratulations !
Nice job.

Can I suggest adding the ability to down/upload cif files. I tend to need smaller molecules than proteins

Syndicate content