I looked at some enzymes and DNA fragments using Rasmol. OK, now I see.
Miguel wrote:
I have made an initial implementation of:
colo(u)r hbonds type
The RasMol manual says:
-----
HBond Type Colours
The RasMol 'type' colour scheme applies only to hydrogen bonds, hence is used in the command 'colour hbonds type'. This scheme colour codes each hydrogen bond according to the distance along a protein chain between hydrogen bond donor and acceptor. This schematic representation was introduced by Belhadj-Mostefa and Milner-White. This representation gives a good insight into protein secondary structure (hbonds forming alpha helices appear red, those forming sheets appear yellow and those forming turns appear magenta).
Offset Colour Triple +2 white [255,255,255] +3 magenta [255,0,255] +4 red [255,0,0] +5 orange [255,165,0] -3 cyan [0,255,255] -4 green [0,255,0] default yellow [255,255,0]
-----
I have a few questions ...
Q: Is there a literature reference I should read on this? If so, send it.
What would you like to understand that you don't now?
Q: Under what circumstances do you get bonding with residue -3 or -4? Can
you give me an example pdb file so that I can see this?
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"
Q: These are for proteins. Shouldn't there be another color (or set ofChime delivers these as yellow, which is appropriate, because they are BETWEEN chains, thus have no significant "offset."
colors) for nucleotide chains? What color should nucleotide hbonds be?
Q: I always feel the need to play with colors ... Are these rgb values good?
I think so.
Miguel
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