| iPhoneAppsPlus->Education->Molecules 
Molecules | | Last changed: Sep 08, 2009 |
 | Category: Education | | Rating:  (24282) | Version: 1.3.2 | Size: 0.3 MB | Price: Free  |

Description:
Molecules is an application for viewing three-dimensional renderings of molecules and manipulating them using your fingers. You can rotate the molecules by moving your finger across the display, zoom in or out by using two-finger pinch gestures, or pan the molecule by moving two fingers across the screen at once. Double-tapping on the display lets you switch visualization modes. New molecules can be downloaded from the RCSB Protein Data Bank (http://www.rcsb.org/pdb), an international repository of biological molecules and their 3-D structures. Molecules can be downloaded directly to your iPhone or iPod touch and stored there for later viewing. Custom molecular structures can also be downloaded to the device from any publicly available web server. The location of these structures can either be manually specified in the application or custom URLs can be clicked on within Safari or Mail on the device. For more details, please visit our website. Molecules is a BSD-licensed open source project.


Reviews:
Your tax dollars at work!  By: Dphurst - Apr 16, 2009 Version: 1.3.1 Red=oxygen
Blue=nitrogen
Yellow=sulfur
White=hydrogen
Gray=carbon
Green=chlorine
Those are the typical colors used in molecular modeling software. The Protein data bank is service for researchers that contains "pdb" files of the coordinates of proteins whose structures were solved by xray crystallography or NMR experiments. It is nice to have this resource available on an iTouch! Many free viewers are available for Linux, Windows and Mac OSes.
Love this!  By: bubblybabs - Feb 4, 2009 Version: 1.3.1 Wow! I'm amazed at the molecules you can d/l into your iphone! I love looking at them and trying to picture them. These people did a lot of work on this app and on the molecules you can download. Look up trypsin, thrombin, fibrin, insulin - cool stuff... 5 stars for it being a free app, free downloads, and the work that went into it... My only wish would be for some type of tutorial for us non-chem majors to understand what each color means, etc. - I have to keep looking that up...
Fascinating and Functional  By: CheatEate - Jan 4, 2009 Version: 1.3 The range of viewing options for each molecule is breathtaking and I find myself looking at and analyIing these structures more often than I thought I would be when I downloaded this app. Other users are having difficulty downloading new molecules must be doing something wrong because it is most certainly possible to download new structures as I have done it for weeks. Fantastic app- a must for any enthusiast.
How to zoom in  By: Piano_man_2009 - Sep 3, 2008 Version: 1.1 I think that this is a great app. Although the rabies virus crashed my phone, I'm guessing that's because it's such a big molecule. I think it's really useful and I like it!
I discovered this completely by accident, but in order to zoom in, place two fingers on the screen fairly close together and move them further apart. So in order to zoom out, place two fingers on the screen and move them together.
To whoever Chris J. is, you spelled waste wrong. A waist is the waist on your body as part of your anatomy. So if this app. is a waist then we've got serious problems. LOL
Sweet!  By: Bradgib - Sep 3, 2008 Version: 1.1 This is *so* cool! What a neat idea.
It'd be cool to integrate some learning tools into this - allow sciece teachers to create repos of simple molecules one might encounter in textbooks, for example, and associate textual descriptions & diagrams about them, for example.
Also, knowing nothing about 3d rendering of molecules, I'd personally like to see some documentation explaining how to read this stuff - what atom each color represents, etc.
Excellent start  By: Dr MC - 4-Aug-2008 Version: 1.0.1 This is a great application that allows one to view molecular structures. The app made it very simple to download structures from the pdb, and then have them rendered and displayed on screen. This said, it would be great if more flexibility in 3-D model display were included in updates of the app. The current version displays molecular models in only "ball and stick" mode. Additional renderings, such as ribbons, space filling, etc., would be a nice improvement in future versions. This said, this is an excellent start for an app that will likely be a favourite of molecular modellers everywhere.
Polished app - but no simple molecules  By: AdamJTP - 18-Oct-2008 Version: 1.2 A well executed app. In particular, the user interface has a polished feel - there's real attention to detail (e.g. progress bar instead of spinner where possible). However, the molecules in the database are too complex for me. I was hoping for simple molecules to help my children with basic chemistry. In fairness, the app summary does say that it accesses a protein database - so what did I expect?
A good start!  By: Chris Huang - 03-Oct-2008 Version: 1.2 This app shows just what the iPhone/iPod touch can be used for apart from games, and has a lot of potential. I look forward to its development in the future. Suggestions for the developer:
1) Althernative views from ball and stick (spacefilles etc.) would be good, as a previous reviewer has said.
2) A better graphics engine - the app slows down a lot with large, complex molecules.
3) When searching for molecules, the search term should stay in the search box as it does in all other iPhone programs I have seen, so that more than one of the search results can be dowloaded without having to search for the same term again.
4) The program crashes sometimes when rendering molecules, usually large, comple ones.
A great start  By: A university teacher - 19-Aug-2008 Version: 1.0.1 I was really impressed with the ease of use and the ease of download of data files. I have tried quite a range of protein files and only a few present well and in an interpretable way with the present limited display. a good one is 1gu5 - a promoter/leucine zipper complex. The problem with most is that the display of all atoms makes the picture too complex. It would be great to have the option to remove side chains, or as another review said, to use cartoons. Great potential here for teaching protein structure. I can hardly believe the foolish, ignorant comments that it is 'pointless'
Nice idea  By: AnActualScientist - 18-Jul-2008 Version: 1.0 It does exactly what it claims to do. Unfortunately its functionality is currently very limited and therefore it is unlikely to be of use to anyone who works with molecular structures. It is also unlikely to appeal to most people, as finding and comprehending protein structues is not straightforward. I've given it four stars though, becacuse there's certainly room for improvement, and I like the idea of answering the question "So, what do you work on?" with a flourish and a simple "This".

Wonderful APP, but needs 2 things...  By: Xrandomxnamex - Nov 15, 2008 Version: 1.3 As much as I freaking love this app, I WOULD use it every single day if it had a broader choice of molecules other than just proteins. I'd like to look at simpler compounds and even basic stuff like H2O. Perhaps u could update this so that we could go to a wikipedia article and use their molecular models with this app?
Also, I'd like to see ribbon models!
If those 2 things are added I would gladly give this app 5 stars.
Nice Program but Caution with Big Files  By: Dr Dan the Man - Jul 27, 2008 Version: 1.0.1 This is great little program for showing the 3 dimensional structure of proteins (caffeine is not a protein, by the way). You can look up proteins in the Protein Databank web page, but if you don't have chemistry/biology background, it may be difficult. I made the mistake of downloading a high resolution alcohol dehydrogenase file. When I tried to look at the image it kept rendering and rendering with no way to cancel. After about 10 minutes it finished, but then when I pushed the info icon in the lower right it would shut the application, rather than allow me to look at other molecules. I ended up having to remove the application then reinstall. A good hemoglobin molecule is 1o1k.
This app is amazing  By: yreal - Jul 13, 2008 Version: 1.0 This is the most useful and amazing app I have seen so far
Help, I Need caffeine  By: RNMartin - Jul 11, 2008 Version: 1.0 no seriously, how could they not include one of the most fundamental molecules in human experience. Anyone know the PDB code for Caffeine?
Amazing!  By: Whiteknight521 - Jul 11, 2008 Version: 1.0 This is revolutionary at the very least. This PDB viewer is more responsive and intuitive than the majority of native apps like swissprot. This app should become standard in biomolecular chemistry. All it is missing is a search function, but this can be done in safari.
Thank you  By: Geovanni JimenezGarcia - Jul 10, 2008 Version: 1.0 For being free, it is actually a rather interesting and useful app. Thanks!
Great! And free!  By: timtamchen - 08-Aug-2008 Version: 1.0.1 Initial version had issues with new molecule downloading but is now all fixed! Good software and very interesting!!
cool  By: Qqwerrty - 27-Aug-2009 Version: 1.3.1 This is a really nifty app. wish I could open ".pdb" files and not just ".pdb.gz" files. that would be awesome.
Love it  By: Mobioguy - Jan 6, 2010 Version: 1.3.2 The shizzle. Of course selecting amino acid and ribbon would be nice but hey it's a free iPhone app. Cool stuff for sure
Nice app  By: gfbxsgd - 28-Jul-2008 Version: 1.0.1 This app is cool.

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