Want to build a tiny crystal of salt from just sodium and chlorine atoms, try this app on for size.
Download the version we have right now for Windows 8/9/10 (32-bit) written in VB.NET.
https://www.mediafire.com/file/wq0mw053l5s5qbg/MolDefAlphaBuild4.zip
Addendum: hang onto this installer because its very difficult to do this since we've introduced "classical radii" and other stuff. This build is fun to play with, the latest build isn't so...fun (more like work).
Uses the Microsoft stock installer so it should come off okay. Its not signed because... hey I'm a maker, so I can't afford the signing fees. Just blow past the warnings that its not signed... I know its not signed.
OK, remember that this version doesn't save and only has support for one molecule. We're working on coding but there is more than enough in here to build and visualize various nanostructures (we did a super cool boron nitride matrix with this exact version...the trick is to use hexagons and realize that the nitrogens and the borons are alternating). So if you construct let's say a histone (I'm TOTALLY kidding lol....they are way to complicated to model this way) just remember you can't save it with this demo version.
Molecular "Transcription"A very powerful technique that we've come up with with Moldef is something called "transcription", or a standardized process to take two 3D shots of a molecule from somewhere like molview.org and quickly copy it to Moldef. We anticipate people building their own molecular libraries this way (I modeled a methane and an isopropyl alcohol molecule like this and its fun as hell) basically taking screen shots from actual academic sources and having a version of their very own on their computer.
What you do is you align the 3D molecule model on your screen such that its major plane (every molecule has a major plane that it would sit on a table stably, an analogy) is "flat" looking down on it. So you take a screen shot of it and save it like this "filename_xy.png" and this is your XY (or top view) pic. Then you take your mouse and "roll" the molecule exactly 90 degrees to produce the corresponding XZ pic, saving it as "filename_xz.png".
Then you bring them into moldef by entering the filenames of the two on the first screen. You then "place" them using the Place 2D/XY/XZ buttons on the second window. You then just select the appropriate atoms and click over the poached images. You can toggle the background image with the same buttons.
Primarily by using the Top View (XY) and the Front View (XZ) you can move stuff around in such a way that when you hit the RENDER button that you can get very close to the original professional molecule. To do this requires a good command of the "Use FB" checkbox though. See if you can figure out how it works.
Can't do real nano designs this way?
Here is a Boron Nitride lattice I was working on to debug the new quickbond feature. Its similar to carbon nano tube.
Comparison of moldef vs professional renderings:
Comments