mineral structures

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mickell
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This is such an impressive application and a very nice use of OpenGl. I am going to the American Geophysical Union meeting in SF in December. Of all the geoscientist professional meetings this one is the nerdiest and the largest with about 15,000 projected to attend this year (www.agu.org). It would be fantastic if some of us could show off mineral specimens in Molecules and push these people and their students and colleagues at this app from our little community. Every earth scientist I have met loves these kinds of visualizations, and there is a strong Viz influence in this crowd. You could see a lot of external work come your way for other OpenGl apps.

Perhaps an interface element like the one used in the app "PangeaVR" and others might be used to select vetted web sites. Certainly I would like to be able to load pdb mineral files like those that appear on this site:

http://pages.pomona.edu/~wsteinmetz/Chem6/kaolinite.pdb

which is typical of mineral pdb collections.

Thanks and great work!

Mike

Brad Larson
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Is the PDB format the primary one used for mineral structures, or are there others (XYZ, mmCIF, etc.) that are more common? I ask because I'm starting to draw up the plans for the desktop client of Molecules, which will let you load in any files you have on your computer and sync them with the iPhone client, and I'll be adding support for a couple more file formats. If I know which ones are most important, I can focus my efforts on those.

Unless my other work calls me away for an extended period, I should have that desktop version ready by the end of October at the latest. That should give you plenty of time to load structures on your device for use at the AGU.

As far as other data sources go, I've been contacted by a couple of people associated with databases of inorganic structures. With the addition of the keyword searching of the Protein Data Bank in the latest version, I should have a workable template to use for interfacing with the web services of other databases. I'm just working on performance improvements and new visualization modes now, and it may be a little bit before I can spare the time to add these other data sources. I'm hoping that manual loading of custom structures via the desktop will be satisfactory stopgap measure.

mickell
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Hey Brad,
Mineralogists have used .amd and .cif formats, and some have recognized that .pdb is the most supported by viewers because of the number of molecular biologists pushing from that direction. The preferred format I believe is .cif which is defined here:
http://journals.iucr.org/iucr-top/index.html

I think these guys have the largest online database for minerals:
http://rruff.geo.arizona.edu/AMS/amcsd.php

(this link gave me a few problems today but eventually worked)

The plans for a desktop client that can sync with the iPhone will be most welcome. Good luck and I would be glad to beta test it on Mac or Win.

Mike

simon
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Hello Brad,

Firstly, I'd like to thank you, extremely impressed by Molecules.

Really looking forward to support for inorganic structures.

cif support would be amazing and possibly a link up with the ICSD?

Regards

Simon

Brad Larson
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1.3 is now under review (source code is available right now), and it adds the ability to load custom structures. Unfortunately, I haven't had the time to add CIF support yet and might not be able to in time for your conference. I hope that this will be good enough for your needs.

maccam
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I am also interested in mineral structures on the iPad. Crystalmaker Software can read numerous formats including CIF and it can export structures to PDB. I have tried this without success. PDB file will download from my MobleMe public Folder, but does not display in Molecules. Crystalmaker support have checked their binary format against the PDB file and claim all is in order.

Saw on a Mar 30 comments somewhere that direct transfer was not possible. This is probably resolved or known already, but applications like GoodReader can load USB files via iTunes.

Brad Larson
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There have been other reports of PDB files hosted on MobileMe not working correctly, but I'm still tracking down what could cause that.

I'm preparing an update for the application that I hopefully will be able to submit this weekend which will add the ability to drag files into the application via iTunes on the iPad. Once that's submitted, you should be able to try your structures directly on the device to see if it's a parser error on my end.

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