file format help
Tue, 05/24/2011 - 10:14
I am a physicist and not familiar with the dozens of molecular structure file types. I work with carbon nanotubes and would like to use your program to visualize nanotubes with different geometries. I can use Mathematica to generate lists of vertices and then export those lists as .sdf files. My question is twofold:
1) What are the required fields for Molecules to properly work? How much metadata needs to be included? Are vertices and element types enough?
2) In iPod OS4 there is (apparently) the ability to add files to the app in iTunes. I can add files to the list (and retrieve them from the list) in iTunes, but they don't show up in the app. I saw some other forum posts in which you stated that you could NOT transfer files in iTunes, but I was assuming that those were out of date since I clearly can see the files being transferred in iTunes....they just don't work when I open Molecules!
In a related question, is there a way to provide a key in the 3D model to quickly reference which colors refer to which elements or groups? Many of the molecules and proteins I've found have chemical names but not chemical formulae, so unless I bone up on my chemistry there's no way for me to tell definitively which atoms are where! Of course, I realize the app is designed more for chemists, but I would love to use it as a self-teaching tool in some cases. For example, I am reading a paper and they mention a particular surfactant - I'd love to go to Molecules, look up the name, view the structure, and be able to come to some basic understanding of what it's doing by seeing where the atoms are. ( a recent example was lauryl sulfate - what's that yellow thing on one end? that's obviously related to they hydrophobic end somehow....)
Please excuse my ignorance, and thanks for a great product!
Tue, 05/24/2011 - 12:31
#2
Magic!
Mathematica also knows about pdb files and I was able to get it to work the first time. Molecules even shows the structure name as the file name, so I don't even have to include any "Title" metadata if I don't want to. Got it to display my nanotubes on the first try. Thanks for the prompt response! Now to memorize atom colors....
Tue, 05/24/2011 - 13:38
#3
Thanks again for a great product. I'm looking forward to future versions.
For the SDF file format, I only look at atoms and bonds when parsing the file. I just added the bare minimum required to interpret the SDF files used by PubChem. I also didn't think far enough ahead to enable the reading of custom SDF files through the iTunes file sharing, so I'll need to add that in the next version.
If you want to do a custom molecular structure, you might be better off to create it as a PDB format file. These I do load if you upload them to the application via iTunes file sharing. I do parse a bunch of the metadata for these files, but you don't need that information to create a structure, just the atom and bond specifications.
For an example of a simple PDB file, you could grab the caffeine.pdb.gz file from within the application through the iTunes file sharing and uncompress it to get the caffeine.pdb file. I believe this file simply contains the atoms and bonds for that small molecule, and it should be easy to see how to generate something similar. The PDB and SDF file formats aren't all that different in the way that they specify atom and bond locations. In fact, I know that I've seen nanotubes in various chiralities as PDB files somewhere out there. Our machinery has been used to deposit and grow nanotubes, so I was looking for models to show off to potential customers myself.
The color scheme I use is the standard CPK scheme, as used by applications like Rasmol. I don't currently include a color key in the application because I didn't want to clutter up the interface and couldn't find a good way of displaying this information. Enough people seem to be having difficulties with this that I'll see if I can work a legend into the application somewhere.