The implication here is simply that you have a
O (n) -- N(n-4) (offset -4; green)
An example is 1qnf.pdb, DNA lyase, where O(asn 144) is hydrogen bonded to NH(ser 140) You won't find many of these, but "the circumstances" are just "because that's what it does"
OK ... so it is not related to any special type of structure.
right. You just take the difference in the two group numbers as a pointer into the list of colors. It's important to identify which is the donor and which is the acceptor to get the sign right. That's probably the tricky part unless the PDB format specifies it.
Q: These are for proteins. Shouldn't there be another color (or set of colors) for nucleotide chains? What color should nucleotide hbonds be?
Chime delivers these as yellow, which is appropriate, because they are BETWEEN chains, thus have no significant "offset."
It doesn't seem right to me that hbonds between chains are the same color as hbonds within a chain (like beta-sheets).
OK, but that's the standard. Maybe there's another way to number, as, perhaps:
colour hbonds secondary
which could mean "color the hbonds based on the type of secondary structure identified" but that would be completely different.
It also seems to me that sidechain hbonds should be different from mainchain hbonds.
Alas,...
Q: I always feel the need to play with colors ... Are these rgb values good?
I think so.
OK
Miguel
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Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr
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