Saturday, August 11, 2007

messing around with Damian's deposition mechanism (DDM)

I planned on using the same basic approach to recreate this one as I have with others, one piece at a time, and small pieces at that. I decided to start with the outer ring, so I needed to isolate it. The entire part was sent as a protein databank file, so it is all one chunk. I need to delete everything not part of the ring:

Here I am removing everything else. Next I try to find a symmetry or some basic pattern I can start with:

Orientating the ring this way it appears that maybe there are two similar rings joined together. The middle seems to resemble a type of seam to me. I figure I can cut the ring in half, reverse-engineer one half and join two together to recreate this part. I deleted all the atoms left of the seam, leaving the red oxygens:

Here is one half of the ring with the oxygens displayed in CPK view. If you look closely you'll see there is not a perfect pattern for the locations of the oxygen atoms. Damian said this was built before NE1 and its extrude function. This means I cannot piece-out a single moiety and extrude it to get this exact ring. Unfortunately I don't have the patience (and probably skill!) to build a ring like this without using the extrude function. <- That's sort of the way I do these: piece out the moiety and extrude it, just like with carbon nanotube bearing. I am going to have to deviate from the original design, hopefully the changes will be immaterial.

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