Further work on PDB hetdict

Previously... After using setFormalCharge instead of setCharge, some of the null atom types disappeared. Specifically, the quaternary (SP3?) nitrogens, that have to have a +1 formal charge.

What is left? Mostly FeS clusters, and other metals. Turns out that the height-1 signature is clearer for 'clustering' the atoms into types. This is because a signature of this height records only the immediate neighbours of the atom.

One fairly frequent example is "[Co]([N][N][N][N])", but fortunately there is a patch for this based on a bug report. The atom is found in cobalamine and other cobalt-haemes.

Still, there are quite a few 'odd' ligands - either due to unusual elements, like Iridium; or unusual coordinations, like this iron with 6 oxygen neighbours. Hmmm, PDBeChem's image (at the bottom of the page) doesn't show all six bonds. It's clearer in Jmol from PDBSum, where the C3 symmetry of the iron ligands makes it seem (to me) that it is 6-coordinate.

Wow, that's a lot of links.

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chalky

I wanted to show something that hints at the things that the new architecture can afford us: This is using a Java2D graphics Paint object to make it look like chalk...kindof. It's a very simplistic way of doing it by making a small image with a random number of white, gray, lightgray, and black pixels. edit: it doesn't look so good at small scales some tweaking of stroke widths and so on is essential.

The Gale-Ryser Theorem

This is a small aside. While reading a paper by Grüner, Laue, and Meringer on generation by homomorphism they mentioned the Gale-Ryser (GR) theorem. As it turns out, this is a nice small theorem closely related to the better known Erdős-Gallai (EG). So, GR says that given two partitions of an integer ( p and q) there exists a (0, 1) matrix A iff p* dominates q such that the row sum vector r(A) = p and the column sum vector c(A) = q . As with most mathematics, that's quite terse and full of terminology like 'dominates' : but it's relatively simple. Here is an example: The partitions p and q are at the top left, they both sum to 10. Next, p is transposed to get p* = [5, 4, 1] and this is compared to q at the bottom left. Since the sum at each point in the sequence is greater (or equal) for p* than q , the former dominates. One possible matrix is at the top left with the row sum vector to the right, and th...

1,2-dichlorocyclopropane and a spiran

As I am reading a book called "Symmetry in Chemistry" (H. H. Jaffé and M. Orchin) I thought I would try out a couple of examples that they use. One is 1,2-dichlorocylopropane : which is, apparently, dissymmetric because it has a symmetry element (a C2 axis) but is optically active. Incidentally, wedges can look horrible in small structures - this is why: The box around the hydrogen is shaded in grey, to show the effect of overlap. A possible fix might be to shorten the wedge, but sadly this would require working out the bounds of the text when calculating the wedge, which has to be done at render time. Oh well. Another interesting example is this 'spiran', which I can't find on ChEBI or ChemSpider: Image again courtesy of JChempaint . I guess the problem marker (the red line) on the N suggests that it is not a real compound? In any case, some simple code to determine potential chiral centres (using signatures) finds 2 in the cyclopropane structure, and 4 in the ...

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