Monday, July 30, 2007

water saved me

So everything is bonded together at the hub. It went much faster during this session, thanks a lot to the water function. Turning on this view places a semi-transparent filter across the part. The depth of the water (its position relative to the viewer) is adjustable, and only atoms above the surface are "pickable". When I first started I was rather overwhelmed with all the open carbon atoms. Atoms that looked next to each other would actually be across the hub.

First I tried hiding tubes not in the immediate area I was working on, but I really need the whole picture all the time. Then I tried displaying different tubes in CPK view (This is the solid view that the previous two pictures use. Now I believe it stands for Corey, Pauling and Koltun and not California Pizza Kitchen. Trust me; you don't want to make that mistake at a cocktail party with a bunch of chemists <- and NEVER leave your cocktail unattended*), but this view still obscured too much. Finally I switched to water, and all was clear.

Now I will focus on clean up. I find it is easier to "rough in" the lattice. By this I mean I try to close as many rings as possible with either hexagons or pentagons, but at this point I don't sweat larger rings, and there are a couple doozies in there. But it is pretty easy to focus on one of these at a time and break them up into smaller, more regular, rings.

Also this part is still unadjusted. By that I mean I have not yet had NE1 adjust the atoms and bonds to a geometry fitting with the molecular mechanics module. I would adjust a few atoms here and there as I was working, but not the whole hub. Don't worry. I am in no way expecting this to distort all my hard work; it has been my experience that this will only tighten things up more.


* my apologies to any chemists that may take offense to that advice.

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